diff --git a/README.md b/README.md index 6be1fd1..f3b4447 100644 --- a/README.md +++ b/README.md @@ -1,48 +1,3 @@ -# [Hugo Research Group Theme](https://github.com/wowchemy/starter-hugo-research-group) +# seaflow.netflity.com -[![Screenshot](preview.png)](https://hugoblox.com/hugo-themes/) - -The **Research Group Template** empowers your research group to easily create a beautiful website with a stunning homepage, news, academic publications, events, team profiles, and a contact form. - -️**Trusted by 250,000+ researchers, educators, and students.** Highly customizable via the integrated **no-code, widget-based Wowchemy page builder**, making every site truly personalized ⭐⭐⭐⭐⭐ - -[![Get Started](https://img.shields.io/badge/-Get%20started-ff4655?style=for-the-badge)](https://hugoblox.com/hugo-themes/) -[![Discord](https://img.shields.io/discord/722225264733716590?style=for-the-badge)](https://discord.com/channels/722225264733716590/742892432458252370/742895548159492138) -[![Twitter Follow](https://img.shields.io/twitter/follow/GetResearchDev?label=Follow%20on%20Twitter)](https://twitter.com/wowchemy) - -Easily write technical content with plain text Markdown, LaTeX math, diagrams, RMarkdown, or Jupyter, and import publications from BibTeX. - -[Check out the latest demo](https://research-group.netlify.app/) of what you'll get in less than 60 seconds, or [view the showcase](https://hugoblox.com/creators/). - -The integrated [**Wowchemy**](https://hugoblox.com) website builder and CMS makes it easy to create a beautiful website for free. Edit your site in the CMS (or your favorite editor), generate it with [Hugo](https://github.com/gohugoio/hugo), and deploy with GitHub or Netlify. Customize anything on your site with widgets, light/dark themes, and language packs. - -- 👉 [**Get Started**](https://hugoblox.com/hugo-themes/) -- 📚 [View the **documentation**](https://docs.hugoblox.com/) -- 💬 [Chat with the **Wowchemy research community**](https://discord.gg/z8wNYzb) or [**Hugo community**](https://discourse.gohugo.io) -- ⬇️ **Automatically import citations from BibTeX** with the [Hugo Academic CLI](https://github.com/GetRD/academic-file-converter) -- 🐦 Share your new site with the community: [@wowchemy](https://twitter.com/wowchemy) [@GeorgeCushen](https://twitter.com/GeorgeCushen) [#MadeWithWowchemy](https://twitter.com/search?q=%23MadeWithWowchemy&src=typed_query) -- 🗳 [Take the survey and help us improve #OpenSource](https://forms.gle/NioD9VhUg7PNmdCAA) -- 🚀 [Contribute improvements](https://github.com/HugoBlox/hugo-blox-builder/blob/main/CONTRIBUTING.md) or [suggest improvements](https://github.com/HugoBlox/hugo-blox-builder/issues) -- ⬆️ **Updating?** View the [Update Guide](https://docs.hugoblox.com/hugo-tutorials/update/) and [Release Notes](https://github.com/HugoBlox/hugo-blox-builder/releases) - -## We ask you, humbly, to support this open source movement - -Today we ask you to defend the open source independence of the Wowchemy website builder and themes 🐧 - -We're an open source movement that depends on your support to stay online and thriving, but 99.9% of our creators don't give; they simply look the other way. - -### [❤️ Click here to become a GitHub Sponsor, unlocking awesome perks such as _exclusive academic templates and widgets_](https://github.com/sponsors/gcushen) - -## Demo credits - -Please replace the demo images with your own. - -- [Female scientist](https://unsplash.com/photos/uVnRa6mOLOM) -- [2 Coders](https://unsplash.com/photos/kwzWjTnDPLk) -- [Cafe](https://unsplash.com/photos/RnDGGnMEOao) -- Blog posts - - https://unsplash.com/photos/AndE50aaHn4 - - https://unsplash.com/photos/OYzbqk2y26c -- Avatars - - https://unsplash.com/photos/5yENNRbbat4 - - https://unsplash.com/photos/WNoLnJo7tS8 +This repository holds [Netlify](https://netlify.com) site source for the [SeaFlow website](https://seaflow.netflity.com). It uses the [Academic](https://sourcethemes.com/academic) theme. \ No newline at end of file diff --git a/assets/media/Avatar.png b/assets/media/Avatar.png new file mode 100644 index 0000000..d0b8ad6 Binary files /dev/null and b/assets/media/Avatar.png differ diff --git a/assets/media/cell-laser.jpg b/assets/media/cell-laser.jpg new file mode 100644 index 0000000..64281ab Binary files /dev/null and b/assets/media/cell-laser.jpg differ diff --git a/assets/media/coders.jpg b/assets/media/coders.jpg deleted file mode 100644 index e77faf9..0000000 Binary files a/assets/media/coders.jpg and /dev/null differ diff --git a/assets/media/contact.jpg b/assets/media/contact.jpg deleted file mode 100644 index a7720ec..0000000 Binary files a/assets/media/contact.jpg and /dev/null differ diff --git a/assets/media/cruise-track.png b/assets/media/cruise-track.png new file mode 100644 index 0000000..30a48d4 Binary files /dev/null and b/assets/media/cruise-track.png differ diff --git a/assets/media/cruisetracks.jpg b/assets/media/cruisetracks.jpg new file mode 100644 index 0000000..f76f2de Binary files /dev/null and b/assets/media/cruisetracks.jpg differ diff --git a/assets/media/diagram_labeled.png b/assets/media/diagram_labeled.png new file mode 100644 index 0000000..992add1 Binary files /dev/null and b/assets/media/diagram_labeled.png differ diff --git a/assets/media/green_stream.jpg b/assets/media/green_stream.jpg new file mode 100644 index 0000000..90efde3 Binary files /dev/null and b/assets/media/green_stream.jpg differ diff --git a/assets/media/icon.png b/assets/media/icon.png index 1699fee..bf6fe39 100644 Binary files a/assets/media/icon.png and b/assets/media/icon.png differ diff --git a/assets/media/icons/icon.png b/assets/media/icons/icon.png new file mode 100644 index 0000000..bf6fe39 Binary files /dev/null and b/assets/media/icons/icon.png differ diff --git a/assets/media/mpm.png b/assets/media/mpm.png new file mode 100644 index 0000000..b244e0a Binary files /dev/null and b/assets/media/mpm.png differ diff --git a/assets/media/ocean.jpg b/assets/media/ocean.jpg new file mode 100644 index 0000000..a349582 Binary files /dev/null and b/assets/media/ocean.jpg differ diff --git a/assets/media/seaflow-instrument.jpg b/assets/media/seaflow-instrument.jpg new file mode 100644 index 0000000..1aeb906 Binary files /dev/null and b/assets/media/seaflow-instrument.jpg differ diff --git a/assets/media/seaflow-logo.png b/assets/media/seaflow-logo.png new file mode 100644 index 0000000..c6d27d6 Binary files /dev/null and b/assets/media/seaflow-logo.png differ diff --git a/assets/media/sunrise.jpg b/assets/media/sunrise.jpg new file mode 100644 index 0000000..9300d16 Binary files /dev/null and b/assets/media/sunrise.jpg differ diff --git a/assets/media/transitionzone.png b/assets/media/transitionzone.png new file mode 100644 index 0000000..6904572 Binary files /dev/null and b/assets/media/transitionzone.png differ diff --git a/assets/media/welcome.jpg b/assets/media/welcome.jpg deleted file mode 100644 index 667a310..0000000 Binary files a/assets/media/welcome.jpg and /dev/null differ diff --git a/config/_default/hugo.yaml b/config/_default/hugo.yaml index dc92120..2cce460 100644 --- a/config/_default/hugo.yaml +++ b/config/_default/hugo.yaml @@ -3,7 +3,7 @@ # Hugo Documentation: https://gohugo.io/getting-started/configuration/#all-configuration-settings # This file is formatted using YAML syntax - learn more at https://learnxinyminutes.com/docs/yaml/ -title: Wowchemy Research Group # Website name +title: SeaFlow Research Group # Website name baseURL: 'https://example.com/' # Website URL ############################ diff --git a/config/_default/menus.yaml b/config/_default/menus.yaml index 7936b5f..0d09b2d 100644 --- a/config/_default/menus.yaml +++ b/config/_default/menus.yaml @@ -4,20 +4,20 @@ # The weight parameter defines the order that the links will appear in. main: - - name: Tour - url: tour + - name: Research + url: research weight: 10 - - name: News - url: post - weight: 20 - name: People url: people - weight: 30 - - name: Events - url: event - weight: 40 + weight: 20 - name: Publications url: publication + weight: 30 + - name: SeaFlow + url: instrument + weight: 40 + - name: Software + url: software weight: 50 - name: Contact url: contact diff --git a/config/_default/params.yaml b/config/_default/params.yaml index 239ec05..9d15908 100644 --- a/config/_default/params.yaml +++ b/config/_default/params.yaml @@ -45,7 +45,7 @@ header: footer: copyright: - notice: '© {year} Me. This work is licensed under {license}' + notice: '© {year} François Ribalet. This work is licensed under {license}' license: enable: true allow_derivatives: false diff --git a/content/_index.md b/content/_index.md index 3954acd..ab4c657 100644 --- a/content/_index.md +++ b/content/_index.md @@ -5,76 +5,109 @@ date: 2022-10-24 type: landing sections: - - block: hero + - block: markdown content: - title: | - Wowchemy - Research Group - image: - filename: welcome.jpg - text: | -
- - The **Wowchemy Research Group** has been a center of excellence for Artificial Intelligence research, teaching, and practice since its founding in 2016. - - - block: collection + title: Welcome to the SeaFlow Research Group + text: The SeaFlow Research Group is an interdisciplinary team of scientists dedicated to understanding the role of phytoplankton in a changing planet. phytoplankton are the invisible engines of our oceans, driving the biological carbon pump that helps regulate Earth's climate. As our planet faces unprecedented climate change, understanding how these microscopic photosynthetic organisms respond to and influence environmental shifts has become increasingly critical. Our research focuses on developing innovative observational technologies and advanced computational approaches to transform our understanding of how phytoplankton drive and respond to environmental changes. We are committed to open science and reproducible research, and we welcome collaboration with other researchers and organizations. + + - block: slider content: - title: Latest News - subtitle: - text: - count: 5 - filters: - author: '' - category: '' - exclude_featured: false - publication_type: '' - tag: '' - offset: 0 - order: desc - page_type: post + slides: + - title: High-Resolution Ocean Observations + content: '800 billion cell measurements of phytoplankton collected across a distance equivalent to six global circumnavigations.' + align: left + background: + image: + filename: cruisetracks.jpg + filters: + brightness: 0.7 + position: center + color: '#555' + link: + icon: database + icon_pack: fas + text: Download Data + url: https://doi.org/10.5281/zenodo.2678021 + + - title: Observational Technology and Computational Tools + content: 'Continuous Flow-Cytometer, Matrix Population Models' + align: left + background: + image: + filename: cell-laser.jpg + filters: + brightness: 0.7 + position: center + color: '#555' + link: + icon: graduation-cap + icon_pack: fas + text: Open-source Software + url: ../software/ + + # - title: Interdisciplinary Team + # content: 'Biological Oceanography, Statistics, Computer Science, Engineering' + # align: right + # background: + # image: + # filename: coders.jpg + # filters: + # brightness: 0.5 + # position: center + # color: '#333' + # link: + # icon: graduation-cap + # icon_pack: fas + # text: Meet the Team + # url: ../people/ design: - view: card - columns: '1' - + # Slide height is automatic unless you force a specific height (e.g. '400px') + slide_height: '' + is_fullscreen: true + # Automatically transition through slides? + loop: true + # Duration of transition between slides (in ms) + interval: 6000 + - block: markdown content: - title: - subtitle: '' - text: - design: - columns: '1' - background: - image: - filename: coders.jpg - filters: - brightness: 1 - parallax: false - position: center - size: cover - text_color_light: true - spacing: - padding: ['20px', '0', '20px', '0'] - css_class: fullscreen + title: Latest News + subtitle: + text: Transform your phytoplankton research with SeaFlow, our innovative flow cytometer that operates continuously underway. Own a SeaFlow or rent it for your upcoming research expeditions - [contact us](mailto:ribalet@uw.edu) to discuss your research needs and become a part of the SeaFlow community. + {{% cta cta_link="./instrument/" cta_text="Meet the Instrument →" %}} + - block: collection content: - title: Latest Preprints + title: Latest Articles text: "" - count: 5 + count: 3 filters: folders: - publication - publication_type: 'article' design: - view: citation + view: compact columns: '1' - - block: markdown - content: - title: - subtitle: - text: | - {{% cta cta_link="./people/" cta_text="Meet the team →" %}} - design: - columns: '1' + +# - block: markdown +# content: +# title: +# subtitle: '' +# text: +# design: +# columns: '1' +# background: +# image: +# filename: coders.jpg +# filters: +# brightness: 1 +# parallax: false +# position: center +# size: cover +# text_color_light: true +# spacing: +# padding: ['20px', '0', '20px', '0'] +# css_class: fullscreen + --- diff --git a/content/authors/Aakriti Vijay/_index.md b/content/authors/Aakriti Vijay/_index.md new file mode 100644 index 0000000..47dd79f --- /dev/null +++ b/content/authors/Aakriti Vijay/_index.md @@ -0,0 +1,48 @@ +--- +# Display name +title: Aakriti Vijay + +# Is this the primary user of the site? +superuser: false + +# Role/position +role: Undergraduate student + +# Organizations/Affiliations +organizations: +- name: University of Washington + url: "https://www.washington.edu" + +# Short bio (displayed in user profile at end of posts) + +#interest: + +# Social/Academic Networking +# For available icons, see: https://sourcethemes.com/academic/docs/page-builder/#icons +# For an email link, use "fas" icon pack, "envelope" icon, and a link in the +# form "mailto:your-email@example.com" or "#contact" for contact widget. +social: +- icon: envelope + icon_pack: fas + link: 'mailto:aakritiv@uw.edu' # For a direct email link, use "mailto:test@example.org". +- icon: github + icon_pack: fab + link: https://github.com/aakriti-vijay + + + +# Link to a PDF of your resume/CV from the About widget. +# To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below. +# - icon: cv +# icon_pack: ai +# link: files/cv.pdf + +# Enter email to display Gravatar (if Gravatar enabled in Config) +email: "aakritiv@uw.edu" + +# Organizational groups that you belong to (for People widget) +# Set this to `[]` or comment out if you are not using People widget. +user_groups: +- Researchers +# - Visitors +--- diff --git a/content/authors/Aakriti Vijay/avatar.png b/content/authors/Aakriti Vijay/avatar.png new file mode 100644 index 0000000..e94832a Binary files /dev/null and b/content/authors/Aakriti Vijay/avatar.png differ diff --git a/content/authors/Annette Hynes/_index.md b/content/authors/Annette Hynes/_index.md new file mode 100644 index 0000000..af499b2 --- /dev/null +++ b/content/authors/Annette Hynes/_index.md @@ -0,0 +1,73 @@ +--- +# Display name +title: Annette Hynes + +# Username (this should match the folder name) +authors: +- annette + +# Is this the primary user of the site? +superuser: false + +# Role/position +role: Research Scientist + +# Organizations/Affiliations +organizations: +- name: University of Washington + url: "https://www.washington.edu" + +# Short bio (displayed in user profile at end of posts) +bio: I investigate picophytoplankton distribution and diversity across physical gradients using the SeaFlow underway flow cytometer. + +interests: +- Phytoplankton +- Ecology +- Diversity +- Mathematical Modeling + +education: + courses: + - course: PhD in Biological Oceanography + institution: Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, Cambridge, MA + year: 2009 + - course: BSc in Biological Sciences and Mathematics + institution: University of Nebraska-Lincoln, Lincoln, NE + year: 2001 + +# Social/Academic Networking +# For available icons, see: https://sourcethemes.com/academic/docs/page-builder/#icons +# For an email link, use "fas" icon pack, "envelope" icon, and a link in the +# form "mailto:your-email@example.com" or "#contact" for contact widget. +social: +- icon: envelope + icon_pack: fas + link: 'mailto:ahynes@uw.edu' # For a direct email link, use "mailto:test@example.org". +- icon: google-scholar + icon_pack: ai + link: https://scholar.google.com/citations?user=x3wGrNcAAAAJ&hl=en&oi=ao +- icon: orcid + icon_pack: fab + link: https://orcid.org/0000-0001-9610-5883 +# - icon: mendeley +# icon_pack: fab +# link: https://www.mendeley.com/profiles/francois-ribalet/ +- icon: github + icon_pack: fab + link: https://github.com/ANetTow + +# Link to a PDF of your resume/CV from the About widget. +# To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below. +# - icon: cv +# icon_pack: ai +# link: files/cv.pdf + +# Enter email to display Gravatar (if Gravatar enabled in Config) +email: "ahynes@uw.edu" + +# Organizational groups that you belong to (for People widget) +# Set this to `[]` or comment out if you are not using People widget. +user_groups: +- Alumni +# - Visitors +--- diff --git a/content/authors/Annette Hynes/avatar.jpg b/content/authors/Annette Hynes/avatar.jpg new file mode 100644 index 0000000..d27b27c Binary files /dev/null and b/content/authors/Annette Hynes/avatar.jpg differ diff --git a/content/authors/Baker van Buren/_index.md b/content/authors/Baker van Buren/_index.md new file mode 100644 index 0000000..20d0309 --- /dev/null +++ b/content/authors/Baker van Buren/_index.md @@ -0,0 +1,56 @@ +--- +# Display name +title: Baker van Buren + +# Is this the primary user of the site? +superuser: false + +# Role/position +role: Undergraduate student + +# Organizations/Affiliations +organizations: +- name: University of Washington + url: "https://www.washington.edu" + +# Short bio (displayed in user profile at end of posts) + +#interest: + +# Social/Academic Networking +# For available icons, see: https://sourcethemes.com/academic/docs/page-builder/#icons +# For an email link, use "fas" icon pack, "envelope" icon, and a link in the +# form "mailto:your-email@example.com" or "#contact" for contact widget. +social: +- icon: envelope + icon_pack: fas + link: 'mailto:bakervanb@gmail.com' # For a direct email link, use "mailto:test@example.org". +- icon: linkedin + icon_pack: fab + link: https://www.linkedin.com/in/baker-van-buren-811014259 +# - icon: orcid +# icon_pack: fab +# link: https://orcid.org/0000-0001-8567-3340 +# - icon: mendeley +# icon_pack: fab +# link: https://www.mendeley.com/profiles/francois-ribalet/ +- icon: github + icon_pack: fab + link: https://github.com/bakervb + + +# Link to a PDF of your resume/CV from the About widget. +# To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below. +# - icon: cv +# icon_pack: ai +# link: files/cv.pdf + +# Enter email to display Gravatar (if Gravatar enabled in Config) +email: "bakervanb@gmail.com" + +# Organizational groups that you belong to (for People widget) +# Set this to `[]` or comment out if you are not using People widget. +user_groups: +- Researchers +# - Visitors +--- diff --git a/content/authors/Baker van Buren/avatar.png b/content/authors/Baker van Buren/avatar.png new file mode 100644 index 0000000..d1c260a Binary files /dev/null and b/content/authors/Baker van Buren/avatar.png differ diff --git a/content/authors/Chris Berthiaume/_index.md b/content/authors/Chris Berthiaume/_index.md new file mode 100644 index 0000000..5b6070b --- /dev/null +++ b/content/authors/Chris Berthiaume/_index.md @@ -0,0 +1,68 @@ +--- +# Display name +title: Chris Berthiaume + +# Is this the primary user of the site? +superuser: false + +# Role/position +role: Software Developer + +# Organizations/Affiliations +organizations: +- name: University of Washington + url: "https://www.washington.edu" + +# Short bio (displayed in user profile at end of posts) +bio: I do computer things in the lab, mostly in Python, sometimes in Javascript or R. + +interests: +- Compute Infrastructure +- Software Analysis Tools +- Reproducible Research + +# education: +# courses: +# - course: +# year: +# - course: +# institution: +# year: + +# Social/Academic Networking +# For available icons, see: https://sourcethemes.com/academic/docs/page-builder/#icons +# For an email link, use "fas" icon pack, "envelope" icon, and a link in the +# form "mailto:your-email@example.com" or "#contact" for contact widget. +social: +- icon: envelope + icon_pack: fas + link: 'mailto:chrisbee@uw.edu' # For a direct email link, use "mailto:test@example.org". +# - icon: google-scholar +# icon_pack: ai +# link: hhttps://scholar.google.com/citations?user=x3wGrNcAAAAJ&hl=en&oi=ao +# - icon: orcid +# icon_pack: fab +# link: https://orcid.org/0000-0001-9610-5883 +# - icon: mendeley +# icon_pack: fab +# link: https://www.mendeley.com/profiles/francois-ribalet/ +- icon: github + icon_pack: fab + link: https://github.com/ctberthiaume + +# Link to a PDF of your resume/CV from the About widget. +# To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below. +# - icon: cv +# icon_pack: ai +# link: files/cv.pdf + +# Enter email to display Gravatar (if Gravatar enabled in Config) +email: "chrisbee@uw.edu" + +# Organizational groups that you belong to (for People widget) +# Set this to `[]` or comment out if you are not using People widget. +user_groups: +- Researchers +# - Visitors +--- +I do computer things in the lab, mostly in Python, sometimes in Javascript or R. diff --git a/content/authors/Chris Berthiaume/avatar.jpg b/content/authors/Chris Berthiaume/avatar.jpg new file mode 100644 index 0000000..ac7922a Binary files /dev/null and b/content/authors/Chris Berthiaume/avatar.jpg differ diff --git a/content/authors/Corinne Jones/_index.md b/content/authors/Corinne Jones/_index.md new file mode 100644 index 0000000..cb6a8e3 --- /dev/null +++ b/content/authors/Corinne Jones/_index.md @@ -0,0 +1,56 @@ +--- +# Display name +title: Corinne Jones + +# Is this the primary user of the site? +superuser: false + +# Role/position +role: PhD Candidate in Statistics + +# Organizations/Affiliations +organizations: +- name: University of Washington + url: "https://www.washington.edu" + +# Short bio (displayed in user profile at end of posts) + +interest: Change point detection + +# Social/Academic Networking +# For available icons, see: https://sourcethemes.com/academic/docs/page-builder/#icons +# For an email link, use "fas" icon pack, "envelope" icon, and a link in the +# form "mailto:your-email@example.com" or "#contact" for contact widget. +social: +# - icon: envelope +# icon_pack: fas +# link: 'mailto:kcain97@uw.edu' # For a direct email link, use "mailto:test@example.org". +# - icon: linkedin +# icon_pack: fab +# link: https://www.linkedin.com/in/kelsy-cain-529908112 +# - icon: orcid +# icon_pack: fab +# link: https://orcid.org/0000-0001-8567-3340 +# - icon: mendeley +# icon_pack: fab +# link: https://www.mendeley.com/profiles/francois-ribalet/ +- icon: github + icon_pack: fab + link: https://github.com/cjones6 + +# Link to a PDF of your resume/CV from the About widget. +# To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below. +# - icon: cv +# icon_pack: ai +# link: files/cv.pdf + +# Enter email to display Gravatar (if Gravatar enabled in Config) +# email: "kcain97@uw.edu" + +# Organizational groups that you belong to (for People widget) +# Set this to `[]` or comment out if you are not using People widget. +user_groups: +- Alumni +# - Visitors +--- +Corinne joined the SDSC as a senior data scientist in December 2020. She graduated with a PhD in Statistics from the University of Washington in 2020. Her doctoral research focused on representation learning for partitioning problems. Prior to her PhD, she obtained bachelor's degrees in Math, Statistics, and Economics, along with a master's degree in Economics, from Penn State University. Her research interests include deep learning and kernel-based methods, with applications in fields ranging from computer vision to oceanography. diff --git a/content/authors/Corinne Jones/avatar.png b/content/authors/Corinne Jones/avatar.png new file mode 100644 index 0000000..13f9647 Binary files /dev/null and b/content/authors/Corinne Jones/avatar.png differ diff --git a/content/authors/Cristian Swift/_index.md b/content/authors/Cristian Swift/_index.md new file mode 100644 index 0000000..89d8d0a --- /dev/null +++ b/content/authors/Cristian Swift/_index.md @@ -0,0 +1,57 @@ +--- +# Display name +title: Cristian Swift + +# Is this the primary user of the site? +superuser: false + +# Role/position +role: Undergraduate student + +# Organizations/Affiliations +organizations: +- name: University of Washington + url: "https://www.washington.edu" + +# Short bio (displayed in user profile at end of posts) + +#interest: + +# Social/Academic Networking +# For available icons, see: https://sourcethemes.com/academic/docs/page-builder/#icons +# For an email link, use "fas" icon pack, "envelope" icon, and a link in the +# form "mailto:your-email@example.com" or "#contact" for contact widget. +social: +- icon: envelope + icon_pack: fas + link: 'mailto:crisjay01@gmail.com' # For a direct email link, use "mailto:test@example.org". +- icon: linkedin + icon_pack: fab + link: https://www.linkedin.com/in/cristianswift +# - icon: orcid +# icon_pack: fab +# link: https://orcid.org/0000-0001-8567-3340 +# - icon: mendeley +# icon_pack: fab +# link: https://www.mendeley.com/profiles/francois-ribalet/ +- icon: github + icon_pack: fab + link: https://github.com/CristianSwift + + + +# Link to a PDF of your resume/CV from the About widget. +# To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below. +# - icon: cv +# icon_pack: ai +# link: files/cv.pdf + +# Enter email to display Gravatar (if Gravatar enabled in Config) +email: "crisjay01@gmail.com" + +# Organizational groups that you belong to (for People widget) +# Set this to `[]` or comment out if you are not using People widget. +user_groups: +- Alumni +# - Visitors +--- diff --git a/content/authors/Cristian Swift/avatar.png b/content/authors/Cristian Swift/avatar.png new file mode 100644 index 0000000..9c223ce Binary files /dev/null and b/content/authors/Cristian Swift/avatar.png differ diff --git a/content/authors/Denise Devlyn/_index.md b/content/authors/Denise Devlyn/_index.md new file mode 100644 index 0000000..c9707de --- /dev/null +++ b/content/authors/Denise Devlyn/_index.md @@ -0,0 +1,63 @@ +--- +# Display name +title: Denise Devlyn + +# Is this the primary user of the site? +superuser: false + +# Role/position +role: Undergraduate student + +# Organizations/Affiliations +organizations: +- name: University of Washington + url: "https://www.washington.edu" + +# Short bio (displayed in user profile at end of posts) +bio: + +# education: +# courses: +# - course: +# year: +# - course: +# institution: +# year: + +# Social/Academic Networking +# For available icons, see: https://sourcethemes.com/academic/docs/page-builder/#icons +# For an email link, use "fas" icon pack, "envelope" icon, and a link in the +# form "mailto:your-email@example.com" or "#contact" for contact widget. +social: +- icon: envelope + icon_pack: fas + link: 'mailto:ddevlyn@uw.edu' # For a direct email link, use "mailto:test@example.org". +- icon: linkedin + icon_pack: fab + link: https://www.linkedin.com/in/denise-devlyn +# - icon: orcid +# icon_pack: fab +# link: https://orcid.org/0000-0001-9610-5883 +# - icon: mendeley +# icon_pack: fab +# link: https://www.mendeley.com/profiles/francois-ribalet/ +# - icon: github +# icon_pack: fab +# link: https://github.com/ctberthiaume + +# Link to a PDF of your resume/CV from the About widget. +# To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below. +# - icon: cv +# icon_pack: ai +# link: files/cv.pdf + +# Enter email to display Gravatar (if Gravatar enabled in Config) +email: "ddevlyn@uw.edu" + +# Organizational groups that you belong to (for People widget) +# Set this to `[]` or comment out if you are not using People widget. +user_groups: +- Alumni +# - Visitors +--- +Denise is a sophomore at the University of Washington majoring in Oceanography and is expected to graduate in May of 2022. She also rows on the University of Washington's Division I women's crew team. Denise is currently seeking an internship involving water quality, environmental policy, ocean research or environmental health. diff --git a/content/authors/Denise Devlyn/avatar.png b/content/authors/Denise Devlyn/avatar.png new file mode 100644 index 0000000..7bea925 Binary files /dev/null and b/content/authors/Denise Devlyn/avatar.png differ diff --git a/content/authors/Franklin Thai/_index.md b/content/authors/Franklin Thai/_index.md new file mode 100644 index 0000000..07e7ec5 --- /dev/null +++ b/content/authors/Franklin Thai/_index.md @@ -0,0 +1,51 @@ +--- +# Display name +title: Franklin Thai + +# Is this the primary user of the site? +superuser: false + +# Role/position +role: Undergraduate student + +# Organizations/Affiliations +organizations: +- name: University of Washington + url: "https://www.washington.edu" + +# Short bio (displayed in user profile at end of posts) + +#interest: + +# Social/Academic Networking +# For available icons, see: https://sourcethemes.com/academic/docs/page-builder/#icons +# For an email link, use "fas" icon pack, "envelope" icon, and a link in the +# form "mailto:your-email@example.com" or "#contact" for contact widget. +social: +- icon: envelope + icon_pack: fas + link: 'mailto:fthai@cs.washington.edu' # For a direct email link, use "mailto:test@example.org". +- icon: linkedin + icon_pack: fab + link: https://www.linkedin.com/in/franklinthai +# - icon: github +# icon_pack: fab +# link: https://github.com/CristianSwift + + + +# Link to a PDF of your resume/CV from the About widget. +# To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below. +# - icon: cv +# icon_pack: ai +# link: files/cv.pdf + +# Enter email to display Gravatar (if Gravatar enabled in Config) +email: "fthai@cs.washington.edu" + +# Organizational groups that you belong to (for People widget) +# Set this to `[]` or comment out if you are not using People widget. +user_groups: +- Researchers +# - Visitors +--- diff --git a/content/authors/Franklin Thai/avatar.png b/content/authors/Franklin Thai/avatar.png new file mode 100644 index 0000000..deeaff7 Binary files /dev/null and b/content/authors/Franklin Thai/avatar.png differ diff --git a/content/authors/Jordan Winter/_index.md b/content/authors/Jordan Winter/_index.md new file mode 100644 index 0000000..1545803 --- /dev/null +++ b/content/authors/Jordan Winter/_index.md @@ -0,0 +1,71 @@ +--- +# Display name +title: Jordan Winter + +# Is this the primary user of the site? +superuser: false + +# Role/position +role: Undergraduate student + +# Organizations/Affiliations +organizations: +- name: University of Washington + url: "https://www.washington.edu" + +# Short bio (displayed in user profile at end of posts) +bio: + +# education: +# courses: +# - course: +# year: +# - course: +# institution: +# year: + +# Social/Academic Networking +# For available icons, see: https://sourcethemes.com/academic/docs/page-builder/#icons +# For an email link, use "fas" icon pack, "envelope" icon, and a link in the +# form "mailto:your-email@example.com" or "#contact" for contact widget. +social: +- icon: envelope + icon_pack: fas + link: 'mailto:jwinter2@uw.edu' # For a direct email link, use "mailto:test@example.org". +- icon: linkedin + icon_pack: fab + link: https://www.linkedin.com/in/jordan-winter-32013b19a +# - icon: orcid +# icon_pack: fab +# link: https://orcid.org/0000-0001-9610-5883 +# - icon: mendeley +# icon_pack: fab +# link: https://www.mendeley.com/profiles/francois-ribalet/ +# - icon: github +# icon_pack: fab +# link: https://github.com/ctberthiaume + +# Link to a PDF of your resume/CV from the About widget. +# To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below. +# - icon: cv +# icon_pack: ai +# link: files/cv.pdf + +# Enter email to display Gravatar (if Gravatar enabled in Config) +email: "jwinter2@uw.edu" + +# Organizational groups that you belong to (for People widget) +# Set this to `[]` or comment out if you are not using People widget. +user_groups: +- Alumni +# - Visitors +--- +Whenever people ask about my work in the Armbrust lab, I tell them I shoot lasers at phytoplankton. And while that may sound much more intense than the reality of prepping samples and making sure the flow cytometer (the laser) is running properly, I am still excited every time I see the thousands of phytoplankton dots appear on a graph. There’s something about seeing how small yet important these animals are that will always fascinate me. + +My love for the ocean started at a young age, when I practically devoured a Hawaiian Reef Fishes book. Ever since, I’ve found every opportunity to work near or in the ocean, from participating in beach cleanups to becoming Scuba certified at the age of 12. + +However, when the time came around to decide on a college, I decided to be an engineer like countless others in my school. For my freshman year, I attended Johns Hopkins University for Mechanical Engineering and quickly realized that was not the major or school for me. I made the big decision to transfer in order to study oceanography and am now happily immersed in the School of Oceanography at the University of Washington. I immediately got to work, taking classes during Summer Quarter and finding two part-time jobs that suit my interests. + +My job as a research assistant has shown me that what I have been curious about since the age of 5 is important and viable as a career. My work as an intern at COASST has taught me the power of citizen science and data collection. I am excited to continue learning about our oceans and the wonderful creatures in it. + +Relevant coursework: Fluid Mechanics and Waves, Integrative Oceans, Introduction to Field Oceanography, Coastal Oceanography, Introduction to Ocean Sensors diff --git a/content/authors/Jordan Winter/avatar.png b/content/authors/Jordan Winter/avatar.png new file mode 100644 index 0000000..4df9be4 Binary files /dev/null and b/content/authors/Jordan Winter/avatar.png differ diff --git a/content/authors/Kelsy Cain/_index.md b/content/authors/Kelsy Cain/_index.md new file mode 100644 index 0000000..5209b5f --- /dev/null +++ b/content/authors/Kelsy Cain/_index.md @@ -0,0 +1,67 @@ +--- +# Display name +title: Kelsy Cain + +# Is this the primary user of the site? +superuser: false + +# Role/position +role: Research Assistant + +# Organizations/Affiliations +organizations: +- name: University of Washington + url: "https://www.washington.edu" + +# Short bio (displayed in user profile at end of posts) +bio: I operate a BD Influx Cell Sorter and SeaFlow to generate and analyze flow cytometry data of phytoplankton and bacterial communities in the field and lab. + +interests: +- Flow Cytometry +- Bacteria +- Phytoplankton +- Field Research + +education: + courses: + - course: BSc in Oceanography, Magna Cum Laude + institution: University of Washington, Seattle WA + year: 2019 + +# Social/Academic Networking +# For available icons, see: https://sourcethemes.com/academic/docs/page-builder/#icons +# For an email link, use "fas" icon pack, "envelope" icon, and a link in the +# form "mailto:your-email@example.com" or "#contact" for contact widget. +social: +- icon: envelope + icon_pack: fas + link: 'mailto:kcain97@uw.edu' # For a direct email link, use "mailto:test@example.org". +- icon: linkedin + icon_pack: fab + link: https://www.linkedin.com/in/kelsy-cain-529908112 +- icon: orcid + icon_pack: fab + link: https://orcid.org/0000-0001-8567-3340 +# - icon: mendeley +# icon_pack: fab +# link: https://www.mendeley.com/profiles/francois-ribalet/ +- icon: github + icon_pack: fab + link: https://github.com/kelsycain + +# Link to a PDF of your resume/CV from the About widget. +# To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below. +# - icon: cv +# icon_pack: ai +# link: files/cv.pdf + +# Enter email to display Gravatar (if Gravatar enabled in Config) +email: "kcain97@uw.edu" + +# Organizational groups that you belong to (for People widget) +# Set this to `[]` or comment out if you are not using People widget. +user_groups: +- Alumni +# - Visitors +--- + I operate a BD Influx Cell Sorter and [SeaFlow](https://seaflow.netlify.com/) to generate and analyze flow cytometry data of phytoplankton and bacterial communities in the field and lab.
diff --git a/content/authors/Kelsy Cain/avatar.jpg b/content/authors/Kelsy Cain/avatar.jpg new file mode 100644 index 0000000..3edbc80 Binary files /dev/null and b/content/authors/Kelsy Cain/avatar.jpg differ diff --git a/content/authors/Kristof Glauninger/_index.md b/content/authors/Kristof Glauninger/_index.md new file mode 100644 index 0000000..16a37d2 --- /dev/null +++ b/content/authors/Kristof Glauninger/_index.md @@ -0,0 +1,60 @@ +--- +# Display name +title: Kristof Glauninger + +# Is this the primary user of the site? +superuser: false + +# Role/position +role: PhD Candidate in Statistics + +# Organizations/Affiliations +organizations: +- name: University of Washington + url: "https://www.washington.edu" + +# Short bio (displayed in user profile at end of posts) +bio: + +interests: +- Error Estimation +- Causal Inference + +education: + courses: + - course: PhD candidate + institution: University of Washington, Seattle, WA + - course: BSc in Mathematical Statistics & ACS Chemistry + institution: Purdue University, West Lafayette, IN + year: 2017 + +# Social/Academic Networking +# For available icons, see: https://sourcethemes.com/academic/docs/page-builder/#icons +# For an email link, use "fas" icon pack, "envelope" icon, and a link in the +# form "mailto:your-email@example.com" or "#contact" for contact widget. +social: +- icon: envelope + icon_pack: fas + link: 'mailto:kristofg@uw.edu' # For a direct email link, use "mailto:test@example.org". +# - icon: mendeley +# icon_pack: fab +# link: https://www.mendeley.com/profiles/francois-ribalet/ +- icon: github + icon_pack: fab + link: https://github.com/kglauninger + +# Link to a PDF of your resume/CV from the About widget. +# To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below. +# - icon: cv +# icon_pack: ai +# link: files/cv.pdf + +# Enter email to display Gravatar (if Gravatar enabled in Config) +email: "kristofg@uw.edu" + +# Organizational groups that you belong to (for People widget) +# Set this to `[]` or comment out if you are not using People widget. +user_groups: +- Alumni +# - Visitors +--- diff --git a/content/authors/Kristof Glauninger/avatar.jpg b/content/authors/Kristof Glauninger/avatar.jpg new file mode 100644 index 0000000..65db39e Binary files /dev/null and b/content/authors/Kristof Glauninger/avatar.jpg differ diff --git a/content/authors/Mattias Cape/_index.md b/content/authors/Mattias Cape/_index.md new file mode 100644 index 0000000..a4f4ffc --- /dev/null +++ b/content/authors/Mattias Cape/_index.md @@ -0,0 +1,74 @@ +--- +# Display name +title: Mattias Cape + +# Is this the primary user of the site? +superuser: false + +# Role/position +role: Postdoctoral Research Associate + +# Organizations/Affiliations +organizations: +- name: University of Washington + url: "https://www.washington.edu" + +# Short bio (displayed in user profile at end of posts) +bio: I am a biological oceanographer interested in the way interactions between atmosphere, cryosphere, and ocean impact the biomass, growth, and community composition of phytoplankton. I examine these processes using a combination of ship-based field work, satellite remote-sensing, and lab experiments, taking advantage of new technologies such as the Imaging FlowCytobot and SeaFlow flow cytometers to gain insight into the structure of phytoplankton communities. While I have a particular interest in polar regions, I am currently exploring these research themes in the North Pacific using the wealth of information collected by SeaFlow. I am also interested in science education and experiential learning, taking advantage of opportunities to teach oceanography and field methods with the Sea Education Association. + +interests: +- Phytoplankton Ecology +- Polar Oceanography +- Ice-Ocean Interactions +- Ocean Optics +- Experiential Education + +education: + courses: + - course: PhD in Oceanography + institution: Scripps Institution of Oceanography and University of California, San Diego, La Jolla, CA. + year: 2014 + - course: MSc in Oceanography + institution: Scripps Institution of Oceanography, UCSD, La Jolla, CA + year: 2009 + - course: BSc in Biology, Ecology, Behavior, Evolution + institution: University of California, San Diego, La Jolla, CA + year: 2002 + +# Social/Academic Networking +# For available icons, see: https://sourcethemes.com/academic/docs/page-builder/#icons +# For an email link, use "fas" icon pack, "envelope" icon, and a link in the +# form "mailto:your-email@example.com" or "#contact" for contact widget. +social: +- icon: envelope + icon_pack: fas + link: 'mailto:mcape@uw.edu' # For a direct email link, use "mailto:test@example.org". +- icon: google-scholar + icon_pack: ai + link: https://scholar.google.com/citations?user=CpzX9mEAAAAJ&hl=en&oi=ao +- icon: orcid + icon_pack: fab + link: https://orcid.org/0000-0002-5621-1128 +# - icon: mendeley +# icon_pack: fab +# link: https://www.mendeley.com/profiles/francois-ribalet/ +- icon: github + icon_pack: fab + link: https://github.com/mrcape + +# Link to a PDF of your resume/CV from the About widget. +# To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below. +# - icon: cv +# icon_pack: ai +# link: files/cv.pdf + +# Enter email to display Gravatar (if Gravatar enabled in Config) +email: "mcape@uw.edu" + +# Organizational groups that you belong to (for People widget) +# Set this to `[]` or comment out if you are not using People widget. +user_groups: +- Alumni +# - Visitors +--- +I am a biological oceanographer interested in the way interactions between atmosphere, cryosphere, and ocean impact the biomass, growth, and community composition of phytoplankton. I examine these processes using a combination of ship-based field work, satellite remote-sensing, and lab experiments, taking advantage of new technologies such as the Imaging FlowCytobot and SeaFlow flow cytometers to gain insight into the structure of phytoplankton communities. While I have a particular interest in polar regions, I am currently exploring these research themes in the North Pacific using the wealth of information collected by SeaFlow. I am also interested in science education and experiential learning, taking advantage of opportunities to teach oceanography and field methods with the Sea Education Association.
diff --git a/content/authors/Mattias Cape/avatar.jpg b/content/authors/Mattias Cape/avatar.jpg new file mode 100644 index 0000000..fabbbbe Binary files /dev/null and b/content/authors/Mattias Cape/avatar.jpg differ diff --git a/content/authors/Mia Wang/_index.md b/content/authors/Mia Wang/_index.md new file mode 100644 index 0000000..8dc17a6 --- /dev/null +++ b/content/authors/Mia Wang/_index.md @@ -0,0 +1,50 @@ +--- +# Display name +title: Mia Wang + +# Is this the primary user of the site? +superuser: false + +# Role/position +role: Undergraduate student + +# Organizations/Affiliations +organizations: +- name: University of Washington + url: "https://www.washington.edu" + +# Short bio (displayed in user profile at end of posts) + +#interest: + +# Social/Academic Networking +# For available icons, see: https://sourcethemes.com/academic/docs/page-builder/#icons +# For an email link, use "fas" icon pack, "envelope" icon, and a link in the +# form "mailto:your-email@example.com" or "#contact" for contact widget. +social: +- icon: envelope + icon_pack: fas + link: 'mailto:yingyw2@uw.edu' # For a direct email link, use "mailto:test@example.org". +# - icon: github +# icon_pack: fab +# link: https://github.com/CristianSwift +- icon: linkedin + icon_pack: fab + link: https://www.linkedin.com/in/yingying-wang-350350295/en + + +# Link to a PDF of your resume/CV from the About widget. +# To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below. +# - icon: cv +# icon_pack: ai +# link: files/cv.pdf + +# Enter email to display Gravatar (if Gravatar enabled in Config) +email: "yingyw2@uw.edu" + +# Organizational groups that you belong to (for People widget) +# Set this to `[]` or comment out if you are not using People widget. +user_groups: +- Researchers +# - Visitors +--- diff --git a/content/authors/Mia Wang/avatar.png b/content/authors/Mia Wang/avatar.png new file mode 100644 index 0000000..782e2f3 Binary files /dev/null and b/content/authors/Mia Wang/avatar.png differ diff --git a/content/authors/admin/_index.md b/content/authors/admin/_index.md index b804d6b..0cc7231 100644 --- a/content/authors/admin/_index.md +++ b/content/authors/admin/_index.md @@ -1,59 +1,65 @@ --- # Display name -title: Nelson Bighetti +title: Francois Ribalet # Full Name (for SEO) -first_name: Nelson -last_name: Bighetti +first_name: François +last_name: Ribalet # Is this the primary user of the site? superuser: true # Role/position -role: Professor of Artificial Intelligence +role: Principal Research Scientist # Organizations/Affiliations organizations: - - name: Stanford University - url: '' + - name: University of Washington + url: "https://www.washington.edu" # Short bio (displayed in user profile at end of posts) -bio: My research interests include distributed robotics, mobile computing and programmable matter. +bio: My research interest include population modeling, microbial ecology, oceanography, and flow cytometry. interests: - - Artificial Intelligence - - Computational Linguistics - - Information Retrieval + - Population Modeling + - Microbial Ecology + - Oceanography + - Flow Cytometry education: courses: - - course: PhD in Artificial Intelligence - institution: Stanford University - year: 2012 - - course: MEng in Artificial Intelligence - institution: Massachusetts Institute of Technology - year: 2009 - - course: BSc in Artificial Intelligence - institution: Massachusetts Institute of Technology - year: 2008 + - course: PhD in Biological Sciences + institution: Open University, London UK + year: 2007 + - course: MSc in Biological Oceanology and Marine Environment + institution: Sorbonne University, Paris FR + year: 2003 + - course: BSc in Population Biology and Ecosystems + institution: Sorbonne University, Paris FR + year: 2001 + # Social/Academic Networking # For available icons, see: https://docs.hugoblox.com/getting-started/page-builder/#icons # For an email link, use "fas" icon pack, "envelope" icon, and a link in the # form "mailto:your-email@example.com" or "#contact" for contact widget. social: - - icon: envelope - icon_pack: fas - link: 'mailto:test@example.org' - - icon: twitter - icon_pack: fab - link: https://twitter.com/GeorgeCushen - - icon: google-scholar - icon_pack: ai - link: https://scholar.google.co.uk/citations?user=sIwtMXoAAAAJ - - icon: github - icon_pack: fab - link: https://github.com/gcushen +- icon: envelope + icon_pack: fas + link: 'mailto:ribalet@uw.edu' # For a direct email link, use "mailto:test@example.org". +- icon: google-scholar + icon_pack: ai + link: https://scholar.google.com/citations?user=oiCmdqIAAAAJ&hl=en +- icon: orcid + icon_pack: fab + link: https://orcid.org/0000-0002-7431-0234 +# - icon: mendeley +# icon_pack: fab +# link: https://www.mendeley.com/profiles/francois-ribalet/ +- icon: github + icon_pack: fab + link: https://github.com/seaflow-uw + # Link to a PDF of your resume/CV from the About widget. # To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below. # - icon: cv @@ -61,17 +67,16 @@ social: # link: files/cv.pdf # Enter email to display Gravatar (if Gravatar enabled in Config) -email: '' +email: 'ribalet@uw.edu' # Highlight the author in author lists? (true/false) -highlight_name: false +highlight_name: true # Organizational groups that you belong to (for People widget) # Set this to `[]` or comment out if you are not using People widget. user_groups: - - Researchers + - Principal Investigator --- -Nelson Bighetti is a professor of artificial intelligence at the Stanford AI Lab. His research interests include distributed robotics, mobile computing and programmable matter. He leads the Robotic Neurobiology group, which develops self-reconfiguring robots, systems of self-organizing robots, and mobile sensor networks. - -Lorem ipsum dolor sit amet, consectetur adipiscing elit. Sed neque elit, tristique placerat feugiat ac, facilisis vitae arcu. Proin eget egestas augue. Praesent ut sem nec arcu pellentesque aliquet. Duis dapibus diam vel metus tempus vulputate. +As a phytoplankton ecologist, I study the mechanisms that shape the distribution of photosynthetic microbes across scales, from the microscopic level to entire ocean basins. These organisms are responsible for half of the photosynthesis on Earth, playing a critical role in the global carbon cycle and climate regulation. +I use a quantitative and interdisciplinary approach, combining mathematical modeling and statistical analysis to understand these processes and predict how phytoplankton may respond to future ocean conditions, including climate-driven changes. To test these models, I conduct fieldwork and collect extensive data using our custom SeaFlow cytometer, which allows for high-frequency, in situ measurements of phytoplankton community composition. diff --git a/content/authors/admin/avatar.jpg b/content/authors/admin/avatar.jpg index 4739195..de054df 100644 Binary files a/content/authors/admin/avatar.jpg and b/content/authors/admin/avatar.jpg differ diff --git a/content/authors/jarred/_index.md b/content/authors/jarred/_index.md new file mode 100644 index 0000000..64d7fe1 --- /dev/null +++ b/content/authors/jarred/_index.md @@ -0,0 +1,66 @@ +--- +# Display name +name: Jarred Swalwell + +# Username (this should match the folder name) +authors: +- jarred + +# Is this the primary user of the site? +superuser: false + +# Role/position +role: Senior Research Engineer + +# Organizations/Affiliations +organizations: +- name: University of Washington + url: "https://www.washington.edu" + +interests: +- Instrumentation +- Flow cytometry + +education: + courses: + - course: Msc in Mechanical Engineering + institution: The University of Texas at Austin + year: 1999 + - course: BSc in Physics + institution: University of Washington + year: 1997 + + +# Short bio (displayed in user profile at end of posts) +bio: I develop new instrumentation to study the complex structure of microbial communities in the oceans. My work spans the fields of optical, mechanical, software and electrical/electronic engineering. Instruments such as the SeaFlow sheathless flow cytometer are designed and built from the ground up in my laboratory and machine shop. SeaFlow is currently being operated monthly on Hawaii Ocean Time-Series cruises and annual SCOPE funded cruises. I am currently working on a new flow cytometer for autonomous platforms. This cytometer, named PipeCyte, uses an immersion primary optic combined with sheathless detection optics to perform in situ single cell measurements in any fluid scaled to any size. The first target platform will be on board a CTD to perform continuous depth profiles of the phytoplankton community. + +# Social/Academic Networking +# For available icons, see: https://sourcethemes.com/academic/docs/page-builder/#icons +# For an email link, use "fas" icon pack, "envelope" icon, and a link in the +# form "mailto:your-email@example.com" or "#contact" for contact widget. +social: +- icon: envelope + icon_pack: fas + link: 'mailto:jarred@uw.edu' # For a direct email link, use "mailto:test@example.org". +- icon: linkedin + icon_pack: fab + link: https://www.linkedin.com/in/jarred-swalwell-88579763 + + + +# Link to a PDF of your resume/CV from the About widget. +# To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below. +# - icon: cv +# icon_pack: ai +# link: files/cv.pdf + +# Enter email to display Gravatar (if Gravatar enabled in Config) +email: "jarred@uw.edu" + +# Organizational groups that you belong to (for People widget) +# Set this to `[]` or comment out if you are not using People widget. +# user_groups: +# - "Principal Investigators" +# - Visitors +--- +I develop new instrumentation to study the complex structure of microbial communities in the oceans. My work spans the fields of optical, mechanical, software and electrical/electronic engineering. Instruments such as the SeaFlow sheathless flow cytometer are designed and built from the ground up in my laboratory and machine shop. SeaFlow is currently being operated monthly on Hawaii Ocean Time-Series cruises and annual SCOPE funded cruises. I am currently working on a new flow cytometer for autonomous platforms. This cytometer, named PipeCyte, uses an immersion primary optic combined with sheathless detection optics to perform in situ single cell measurements in any fluid scaled to any size. The first target platform will be on board a CTD to perform continuous depth profiles of the phytoplankton community. diff --git a/content/authors/jarred/avatar.jpg b/content/authors/jarred/avatar.jpg new file mode 100644 index 0000000..93f819d Binary files /dev/null and b/content/authors/jarred/avatar.jpg differ diff --git a/content/authors/kathy/_index.md b/content/authors/kathy/_index.md new file mode 100644 index 0000000..97e2f85 --- /dev/null +++ b/content/authors/kathy/_index.md @@ -0,0 +1,66 @@ +--- +# Display name +name: Katherine Qi + +# Username (this should match the folder name) +authors: +- kathy + +# Is this the primary user of the site? +superuser: false + +# Role/position +role: PhD Candidate in Oceanography + +# Organizations/Affiliations +organizations: +- name: University of Washington + url: "https://www.washington.edu" + +# Short bio (displayed in user profile at end of posts) + +#interest: + +education: + courses: + - course: BSc in Marine Biology and Biological Oceanography + institution: University of California San Diego + year: 2020 + +# Social/Academic Networking +# For available icons, see: https://sourcethemes.com/academic/docs/page-builder/#icons +# For an email link, use "fas" icon pack, "envelope" icon, and a link in the +# form "mailto:your-email@example.com" or "#contact" for contact widget. +social: +- icon: envelope + icon_pack: fas + link: 'mailto:klqi@uw.edu' # For a direct email link, use "mailto:test@example.org". +- icon: linkedin + icon_pack: fab + link: https://www.linkedin.com/in/klqi-ucsd +# - icon: orcid +# icon_pack: fab +# link: https://orcid.org/0000-0001-8567-3340 +# - icon: mendeley +# icon_pack: fab +# link: https://www.mendeley.com/profiles/francois-ribalet/ +- icon: github + icon_pack: fab + link: https://github.com/klqi + +# Link to a PDF of your resume/CV from the About widget. +# To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below. +# - icon: cv +# icon_pack: ai +# link: files/cv.pdf + +# Enter email to display Gravatar (if Gravatar enabled in Config) +email: "klqi@uw.edu" + +# Organizational groups that you belong to (for People widget) +# Set this to `[]` or comment out if you are not using People widget. +user_groups: +# - "Students" +# - Visitors +--- +Corinne joined the SDSC as a senior data scientist in December 2020. She graduated with a PhD in Statistics from the University of Washington in 2020. Her doctoral research focused on representation learning for partitioning problems. Prior to her PhD, she obtained bachelor's degrees in Math, Statistics, and Economics, along with a master's degree in Economics, from Penn State University. Her research interests include deep learning and kernel-based methods, with applications in fields ranging from computer vision to oceanography. diff --git a/content/authors/kathy/avatar.png b/content/authors/kathy/avatar.png new file mode 100644 index 0000000..503018d Binary files /dev/null and b/content/authors/kathy/avatar.png differ diff --git "a/content/authors/\345\220\263\346\201\251\351\201\224/_index.md" "b/content/authors/\345\220\263\346\201\251\351\201\224/_index.md" deleted file mode 100644 index 668c54e..0000000 --- "a/content/authors/\345\220\263\346\201\251\351\201\224/_index.md" +++ /dev/null @@ -1,79 +0,0 @@ ---- -# Display name -title: Alice Wu 吳恩達 - -# Full name (for SEO) -first_name: Alice -last_name: Wu - -# Username (this should match the folder name) -authors: - - 吳恩達 - -# Is this the primary user of the site? -superuser: false - -# Role/position -role: Professor of Artificial Intelligence - -# Organizations/Affiliations -organizations: - - name: Stanford University - url: '' - -# Short bio (displayed in user profile at end of posts) -bio: My research interests include distributed robotics, mobile computing and programmable matter. - -interests: - - Artificial Intelligence - - Computational Linguistics - - Information Retrieval - -education: - courses: - - course: PhD in Artificial Intelligence - institution: Stanford University - year: 2012 - - course: MEng in Artificial Intelligence - institution: Massachusetts Institute of Technology - year: 2009 - - course: BSc in Artificial Intelligence - institution: Massachusetts Institute of Technology - year: 2008 - -# Social/Academic Networking -# For available icons, see: https://docs.hugoblox.com/getting-started/page-builder/#icons -# For an email link, use "fas" icon pack, "envelope" icon, and a link in the -# form "mailto:your-email@example.com" or "#contact" for contact widget. -social: - - icon: envelope - icon_pack: fas - link: 'mailto:test@example.org' - - icon: twitter - icon_pack: fab - link: https://twitter.com/GeorgeCushen - - icon: google-scholar - icon_pack: ai - link: https://scholar.google.co.uk/citations?user=sIwtMXoAAAAJ - - icon: github - icon_pack: fab - link: https://github.com/gcushen -# Link to a PDF of your resume/CV from the About widget. -# To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below. -# - icon: cv -# icon_pack: ai -# link: files/cv.pdf - -# Enter email to display Gravatar (if Gravatar enabled in Config) -email: '' - -# Organizational groups that you belong to (for People widget) -# Set this to `[]` or comment out if you are not using People widget. -user_groups: - - Researchers - - Visitors ---- - -吳恩達 is a professor of artificial intelligence at the Stanford AI Lab. His research interests include distributed robotics, mobile computing and programmable matter. He leads the Robotic Neurobiology group, which develops self-reconfiguring robots, systems of self-organizing robots, and mobile sensor networks. - -Lorem ipsum dolor sit amet, consectetur adipiscing elit. Sed neque elit, tristique placerat feugiat ac, facilisis vitae arcu. Proin eget egestas augue. Praesent ut sem nec arcu pellentesque aliquet. Duis dapibus diam vel metus tempus vulputate. diff --git "a/content/authors/\345\220\263\346\201\251\351\201\224/avatar.jpg" "b/content/authors/\345\220\263\346\201\251\351\201\224/avatar.jpg" deleted file mode 100644 index 49337e4..0000000 Binary files "a/content/authors/\345\220\263\346\201\251\351\201\224/avatar.jpg" and /dev/null differ diff --git a/content/contact/index.md b/content/contact/index.md index d1e4f65..713b177 100644 --- a/content/contact/index.md +++ b/content/contact/index.md @@ -7,63 +7,43 @@ type: landing sections: - block: contact content: - title: Contact - text: |- - Lorem ipsum dolor sit amet, consectetur adipiscing elit. Integer tempus augue non tempor egestas. Proin nisl nunc, dignissim in accumsan dapibus, auctor ullamcorper neque. Quisque at elit felis. Vestibulum ante ipsum primis in faucibus orci luctus et ultrices posuere cubilia curae; Aenean eget elementum odio. Cras interdum eget risus sit amet aliquet. In volutpat, nisl ut fringilla dignissim, arcu nisl suscipit ante, at accumsan sapien nisl eu eros. - email: test@example.org - phone: 888 888 88 88 - address: - street: 450 Serra Mall - city: Stanford - region: CA - postcode: '94305' - country: United States - country_code: US + title: Contact Us + text: Dr. François Ribalet
+ School of Oceanography
+ University of Washington
+ Ocean Science Building
+ Seattle, WA 98105
+ email: ribalet@uw.edu coordinates: - latitude: '37.4275' - longitude: '-122.1697' - directions: Enter Building 1 and take the stairs to Office 200 on Floor 2 - office_hours: - - 'Monday 10:00 to 13:00' - - 'Wednesday 09:00 to 10:00' - appointment_url: 'https://calendly.com' + latitude: '47.65118' + longitude: '-122.31271' + appointment_url: 'https://calendar.google.com/calendar/u/0/appointments/schedules/AcZssZ1inKfrVv2hXXytYw2JaS8I_nFwd3QfV9yYZxl-n1SxtyN7xwQp-Ze7o45F475_5NAH_lqNO6Wo' #contact_links: # - icon: comments # icon_pack: fas - # name: Discuss on Forum # link: 'https://discourse.gohugo.io' - + # Automatically link email and phone or display as text? autolink: true - # Email form provider - form: - provider: netlify - formspree: - id: - netlify: - # Enable CAPTCHA challenge to reduce spam? - captcha: false - design: - columns: '1' - - block: markdown - content: - title: - subtitle: '' - text: - design: - columns: '1' - background: - image: - filename: contact.jpg - filters: - brightness: 1 - parallax: false - position: center - size: cover - text_color_light: true - spacing: - padding: ['20px', '0', '20px', '0'] - css_class: fullscreen + # - block: markdown + # content: + # title: + # subtitle: '' + # text: + # design: + # columns: '1' + # background: + # image: + # filename: seaflow-logo.png + # filters: + # brightness: 1 + # parallax: false + # position: center + # size: cover + # text_color_light: true + # spacing: + # padding: ['20px', '40', '20px', '40'] + # css_class: auto --- diff --git a/content/event/_index.md b/content/event/_index.md deleted file mode 100644 index 3925684..0000000 --- a/content/event/_index.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -title: Recent & Upcoming Events - -# Listing view -view: compact - -# Optional header image (relative to `assets/media/` folder). -banner: - caption: '' - image: '' ---- diff --git a/content/event/example/featured.jpg b/content/event/example/featured.jpg deleted file mode 100644 index 7b16c3c..0000000 Binary files a/content/event/example/featured.jpg and /dev/null differ diff --git a/content/event/example/index.md b/content/event/example/index.md deleted file mode 100644 index abdf008..0000000 --- a/content/event/example/index.md +++ /dev/null @@ -1,63 +0,0 @@ ---- -title: Example Event - -event: Wowchemy Conference -event_url: https://example.org - -location: Wowchemy HQ -address: - street: 450 Serra Mall - city: Stanford - region: CA - postcode: '94305' - country: United States - -summary: An example event. -abstract: 'Lorem ipsum dolor sit amet, consectetur adipiscing elit. Duis posuere tellusac convallis placerat. Proin tincidunt magna sed ex sollicitudin condimentum. Sed ac faucibus dolor, scelerisque sollicitudin nisi. Cras purus urna, suscipit quis sapien eu, pulvinar tempor diam.' - -# Talk start and end times. -# End time can optionally be hidden by prefixing the line with `#`. -date: '2030-06-01T13:00:00Z' -date_end: '2030-06-01T15:00:00Z' -all_day: false - -# Schedule page publish date (NOT talk date). -publishDate: '2017-01-01T00:00:00Z' - -authors: [] -tags: [] - -# Is this a featured talk? (true/false) -featured: false - -image: - caption: 'Image credit: [**Unsplash**](https://unsplash.com/photos/bzdhc5b3Bxs)' - focal_point: Right - -url_code: '' -url_pdf: '' -url_slides: '' -url_video: '' - -# Markdown Slides (optional). -# Associate this talk with Markdown slides. -# Simply enter your slide deck's filename without extension. -# E.g. `slides = "example-slides"` references `content/slides/example-slides.md`. -# Otherwise, set `slides = ""`. -slides: - -# Projects (optional). -# Associate this post with one or more of your projects. -# Simply enter your project's folder or file name without extension. -# E.g. `projects = ["internal-project"]` references `content/project/deep-learning/index.md`. -# Otherwise, set `projects = []`. -projects: ---- - -Slides can be added in a few ways: - -- **Create** slides using Wowchemy's [_Slides_](https://docs.hugoblox.com/managing-content/#create-slides) feature and link using `slides` parameter in the front matter of the talk file -- **Upload** an existing slide deck to `static/` and link using `url_slides` parameter in the front matter of the talk file -- **Embed** your slides (e.g. Google Slides) or presentation video on this page using [shortcodes](https://docs.hugoblox.com/writing-markdown-latex/). - -Further event details, including page elements such as image galleries, can be added to the body of this page. diff --git a/content/instrument/_index.md b/content/instrument/_index.md new file mode 100644 index 0000000..ca854e1 --- /dev/null +++ b/content/instrument/_index.md @@ -0,0 +1,20 @@ +--- +title: High-Resolution Ocean Observations + +# Listing view +view: compact + +# Optional banner image (relative to `assets/media/` folder). +banner: + caption: '' + image: 'green_stream.jpg' + +--- + +To address the challenges of studying marine phytoplankton in their natural environment, we developed the SeaFlow cytometer, an automated instrument that provides new ways to study phytoplankton population dynamics. Unlike traditional flow cytometers, SeaFlow enables continuous, high-frequency sampling of surface waters, capturing unprecedented spatial and temporal resolutions. This allows for a deeper exploration of phytoplankton interactions with their environment, from microscopic to ocean-basin-scales. + +Since 2010, SeaFlow has been deployed on nearly 100 research cruises to collect per cell fluorescence and light scatter data for approximately 800 billion phytoplankton cells less than 5 micron in size. We converted the light scatter data to cell diameter to map out high resolutions distributions of phytoplankton cell size and carbon quotas across 200,000 km of surface ocean and 80 degrees of latitude. An example dataset from 64 cruise is freely available at [Zenodo](https://doi.org/10.5281/zenodo.2678021.). + +**NEW! Own a SeaFlow or rent it for your upcoming research expeditions** - [Contact Us](mailto:ribalet@uw.edu) to discuss your research needs and become a part of the SeaFlow community. + +
\ No newline at end of file diff --git a/content/instrument/inventory/featured.png b/content/instrument/inventory/featured.png new file mode 100644 index 0000000..30a48d4 Binary files /dev/null and b/content/instrument/inventory/featured.png differ diff --git a/content/instrument/inventory/index.md b/content/instrument/inventory/index.md new file mode 100644 index 0000000..6119162 --- /dev/null +++ b/content/instrument/inventory/index.md @@ -0,0 +1,30 @@ +--- +title: Other Information +lastmod: "2024-01-15" +--- +The ship’s real-time feed of position, time, temperature, salinity is broadcast either over the ship’s network and recorded by the SeaFlow computer. + +Additional data streams from the SeaFlow instrument, such as sample stream pressure and event rate are also recorded. The format of the underway data differs among ships, so we use custom scrips to convert/curate the ship data into a format recognized by our analysis software. + +[Click here to access the original data](https://github.com/seaflow-uw/seaflow-sfl) + +Each SFL file contains the following information: + +* FILE: SeaFlow filename +* DATE: data and time in GMT +* FILE DURATION: acquisition time (sec) +* LAT: latitude (deg N) +* LON: longitude (deg W) +* CONDUCTIVITY: seawater conductivity (s/m) +* SALINITY: seawater salinity (psu) +* OCEAN TEMP: seawater temperature (deg C) +* PAR: Photosynthetic Active Radiations above surface water (µmol/m2/s) +* BULK RED: bulk red fluorescence measured by SeaFlow (unitless) +* STREAM PRESSURE: pressure of the sample line (psi), usually set at 12, which can then be converted to sample flow rate (mL min-1) +* EVENT RATE: number of events (i.e., particles) recorded per second (should be below 18,000 for quality data) by SeaFlow + +Any other data not broadcasted during the cruise can be retrieved later from the [Rolling Deck to Repository](https://www.rvdata.us/) (R2R). + +List of datasets and associated cruise and geolocation metadata. + + diff --git a/content/instrument/seaflow/_index.md b/content/instrument/seaflow/_index.md new file mode 100644 index 0000000..7113783 --- /dev/null +++ b/content/instrument/seaflow/_index.md @@ -0,0 +1,11 @@ +--- +title: Meet the Instrument +lastmod: "2024-06-01" +--- + +The SeaFlow instrument is a shipboard underway flow cytometer that provides continuous multi-parameter single particle measurements without the need for clean water. Detailed information can be found in [Swalwell et al. (2011)](https://doi.org/10.4319/lom.2011.9.466). + +The instrument eliminates the traditional need for a sheath fluid by employing a unique optical system that relies on three photodetectors to create a virtual core in the sample stream within which the properties of particles are accurately measured. In this way, the instrument is able to collect the equivalent of 1 sample every 3 minutes or every 1 km (for a ship moving at 10 knots) from the ship’s flow-through seawater system. See [article](https://doi.org/10.4319/lom.2011.9.466) for more information. SeaFlow performs rapid quantification (up to 24,000 cells per second) of multidimensional characteristics of phytoplankton cells in the pico- to nanophytoplankton size range (0.5-20 µm) to analyze the equivalent of 480 traditional flow cytometry samples per day while on board a research vessel. Image analysis is used to automatically align the laser with the optical system and then monitor and correct for drift. Data analysis tools have been created to automatically cluster and count phytoplankton populations with geo-referenced data visualization. + +See our **Real-Time Analysis Dashboard** [here](https://gradientscruise.org/d/Ybbbrzqae/tn427-by-time?orgId=1). + diff --git a/content/instrument/seaflow/featured.png b/content/instrument/seaflow/featured.png new file mode 100644 index 0000000..d0b8ad6 Binary files /dev/null and b/content/instrument/seaflow/featured.png differ diff --git a/content/people/index.md b/content/people/index.md index c10a00e..11516f5 100644 --- a/content/people/index.md +++ b/content/people/index.md @@ -11,7 +11,7 @@ sections: # Choose which groups/teams of users to display. # Edit `user_groups` in each user's profile to add them to one or more of these groups. user_groups: - - Principal Investigators + - Principal Investigator - Researchers - Grad Students - Administration diff --git a/content/post/20-12-01-wowchemy-prize/featured.jpg b/content/post/20-12-01-wowchemy-prize/featured.jpg deleted file mode 100644 index 8916615..0000000 Binary files a/content/post/20-12-01-wowchemy-prize/featured.jpg and /dev/null differ diff --git a/content/post/20-12-01-wowchemy-prize/index.md b/content/post/20-12-01-wowchemy-prize/index.md deleted file mode 100644 index 402ecc5..0000000 --- a/content/post/20-12-01-wowchemy-prize/index.md +++ /dev/null @@ -1,14 +0,0 @@ ---- -title: Richard Hendricks Wins First Place in the Wowchemy Prize -date: 2020-12-01 ---- - -Congratulations to Richard Hendricks for winning first place in the Wowchemy Prize. - - - -Lorem ipsum dolor sit amet, consectetur adipiscing elit. Integer tempus augue non tempor egestas. Proin nisl nunc, dignissim in accumsan dapibus, auctor ullamcorper neque. Quisque at elit felis. Vestibulum ante ipsum primis in faucibus orci luctus et ultrices posuere cubilia curae; Aenean eget elementum odio. Cras interdum eget risus sit amet aliquet. In volutpat, nisl ut fringilla dignissim, arcu nisl suscipit ante, at accumsan sapien nisl eu eros. - -Sed eu dui nec ligula bibendum dapibus. Nullam imperdiet auctor tortor, vel cursus mauris malesuada non. Quisque ultrices euismod dapibus. Aenean sed gravida risus. Sed nisi tortor, vulputate nec quam non, placerat porta nisl. Nunc varius lobortis urna, condimentum facilisis ipsum molestie eu. Ut molestie eleifend ligula sed dignissim. Duis ut tellus turpis. Praesent tincidunt, nunc sed congue malesuada, mauris enim maximus massa, eget interdum turpis urna et ante. Morbi sem nisl, cursus quis mollis et, interdum luctus augue. Aliquam laoreet, leo et accumsan tincidunt, libero neque aliquet lectus, a ultricies lorem mi a orci. - -Mauris dapibus sem vel magna convallis laoreet. Donec in venenatis urna, vitae sodales odio. Praesent tortor diam, varius non luctus nec, bibendum vel est. Quisque id sem enim. Maecenas at est leo. Vestibulum tristique pellentesque ex, blandit placerat nunc eleifend sit amet. Fusce eget lectus bibendum, accumsan mi quis, luctus sem. Etiam vitae nulla scelerisque, eleifend odio in, euismod quam. Etiam porta ullamcorper massa, vitae gravida turpis euismod quis. Mauris sodales sem ac ultrices viverra. In placerat ultrices sapien. Suspendisse eu arcu hendrerit, luctus tortor cursus, maximus dolor. Proin et velit et quam gravida dapibus. Donec blandit justo ut consequat tristique. diff --git a/content/post/20-12-02-ICML-best-paper/featured.jpg b/content/post/20-12-02-ICML-best-paper/featured.jpg deleted file mode 100644 index a0f77a3..0000000 Binary files a/content/post/20-12-02-ICML-best-paper/featured.jpg and /dev/null differ diff --git a/content/post/20-12-02-ICML-best-paper/index.md b/content/post/20-12-02-ICML-best-paper/index.md deleted file mode 100644 index 3dca848..0000000 --- a/content/post/20-12-02-ICML-best-paper/index.md +++ /dev/null @@ -1,16 +0,0 @@ ---- -title: Jian Yang and Monica Hall Win the Best Paper Award at Wowchemy 2020 -date: 2020-12-02 -image: - focal_point: 'top' ---- - -Congratulations to Jian Yang and Monica Hall for winning the Best Paper Award at the 2020 Conference on Wowchemy for their paper “Learning Wowchemy”. - - - -Lorem ipsum dolor sit amet, consectetur adipiscing elit. Integer tempus augue non tempor egestas. Proin nisl nunc, dignissim in accumsan dapibus, auctor ullamcorper neque. Quisque at elit felis. Vestibulum ante ipsum primis in faucibus orci luctus et ultrices posuere cubilia curae; Aenean eget elementum odio. Cras interdum eget risus sit amet aliquet. In volutpat, nisl ut fringilla dignissim, arcu nisl suscipit ante, at accumsan sapien nisl eu eros. - -Sed eu dui nec ligula bibendum dapibus. Nullam imperdiet auctor tortor, vel cursus mauris malesuada non. Quisque ultrices euismod dapibus. Aenean sed gravida risus. Sed nisi tortor, vulputate nec quam non, placerat porta nisl. Nunc varius lobortis urna, condimentum facilisis ipsum molestie eu. Ut molestie eleifend ligula sed dignissim. Duis ut tellus turpis. Praesent tincidunt, nunc sed congue malesuada, mauris enim maximus massa, eget interdum turpis urna et ante. Morbi sem nisl, cursus quis mollis et, interdum luctus augue. 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Donec blandit justo ut consequat tristique. diff --git a/content/post/_index.md b/content/post/_index.md deleted file mode 100644 index 28fbf80..0000000 --- a/content/post/_index.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -title: Latest News - -# Listing view -view: compact - -# Optional banner image (relative to `assets/media/` folder). -banner: - caption: '' - image: '' ---- diff --git a/content/publication/_index.md b/content/publication/_index.md index 940aa39..cae2c79 100644 --- a/content/publication/_index.md +++ b/content/publication/_index.md @@ -2,10 +2,10 @@ title: Publications # Listing view -view: citation +view: compact # Optional banner image (relative to `assets/media/` folder). banner: caption: '' - image: '' + image: 'sunrise.jpg' --- diff --git a/content/publication/beckett-2024/cite.bib b/content/publication/beckett-2024/cite.bib new file mode 100644 index 0000000..2a07eea --- /dev/null +++ b/content/publication/beckett-2024/cite.bib @@ -0,0 +1,9 @@ +@article{beckett_disentangling_2024 + abstract = {Photosynthesis fuels primary production at the base of marine food webs. Yet, in many surface ocean ecosystems, diel-driven primary production is tightly coupled to daily loss. This tight coupling raises the question: which top-down drivers predominate in maintaining persistently stable picocyanobacterial populations over longer time scales? Motivated by high-frequency surface water measurements taken in the North Pacific Subtropical Gyre (NPSG), we developed multitrophic models to investigate bottom-up and top-down mechanisms underlying the balanced control of Prochlorococcus populations. We find that incorporating photosynthetic growth with viral- and predator-induced mortality is sufficient to recapitulate daily oscillations of Prochlorococcus abundances with baseline community abundances. In doing so, we infer that grazers in this environment function as the predominant top-down factor despite high standing viral particle densities. The model-data fits also reveal the ecological relevance of light-dependent viral traits and non-canonical factors to cellular loss. Finally, we leverage sensitivity analyses to demonstrate how variation in life history traits across distinct oceanic contexts, including variation in viral adsorption and grazer clearance rates, can transform the quantitative and even qualitative importance of top-down controls in shaping Prochlorococcus population dynamics.}, + author = {Beckett, Stephen J. and Demory, David and Coenen, Ashley R. and Casey, John R. and Dugenne, Mathilde and Follett, Christopher L. and Connell, Paige and Carlson, Michael C. G. and Hu, Sarah K. and Wilson, Samuel T. and Muratore, Daniel and Rodriguez-Gonzalez, Rogelio A. and Peng, Shengyun and Becker, Kevin W. and Mende, Daniel R. and Armbrust, E. Virginia and Caron, David A. and Lindell, Debbie and White, Angelicque E. and Ribalet, François and Weitz, Joshua S.}, + doi = {10.1038/s41467-024-46165-3}, + journal = {Nature Communications}, + number = {1}, + title = {Disentangling top-down drivers of mortality underlying diel population dynamics of Prochlorococcus in the North Pacific Subtropical Gyre}, + volume = {15} +} diff --git a/content/publication/beckett-2024/featured.png b/content/publication/beckett-2024/featured.png new file mode 100644 index 0000000..b32a65f Binary files /dev/null and b/content/publication/beckett-2024/featured.png differ diff --git a/content/publication/beckett-2024/index.md b/content/publication/beckett-2024/index.md new file mode 100644 index 0000000..712938c --- /dev/null +++ b/content/publication/beckett-2024/index.md @@ -0,0 +1,13 @@ +--- +title : "Disentangling top-down drivers of mortality underlying diel population dynamics of Prochlorococcus in the North Pacific Subtropical Gyre" +date : "2024-03-01" +authors : ["Stephen J. Beckett", "David Demory", "Ashley R. Coenen", "John R. Casey", "Mathilde Dugenne", "Christopher L. Follett", "Paige Connell", "Michael C. G. Carlson", "Sarah K. Hu", "Samuel T. Wilson", "Daniel Muratore", "Rogelio A. Rodriguez-Gonzalez", "Shengyun Peng", "Kevin W. Becker", "Daniel R. Mende", "E. Virginia Armbrust", "David A. Caron", "Debbie Lindell", "Angelicque E. White", "François Ribalet", "Joshua S. Weitz"] +publication_types : ["2"] +publication : "in *Nature Communications*" +abstract : "Photosynthesis fuels primary production at the base of marine food webs. Yet, in many surface ocean ecosystems, diel-driven primary production is tightly coupled to daily loss. This tight coupling raises the question: which top-down drivers predominate in maintaining persistently stable picocyanobacterial populations over longer time scales? Motivated by high-frequency surface water measurements taken in the North Pacific Subtropical Gyre (NPSG), we developed multitrophic models to investigate bottom-up and top-down mechanisms underlying the balanced control of Prochlorococcus populations. We find that incorporating photosynthetic growth with viral- and predator-induced mortality is sufficient to recapitulate daily oscillations of Prochlorococcus abundances with baseline community abundances. In doing so, we infer that grazers in this environment function as the predominant top-down factor despite high standing viral particle densities. The model-data fits also reveal the ecological relevance of light-dependent viral traits and non-canonical factors to cellular loss. Finally, we leverage sensitivity analyses to demonstrate how variation in life history traits across distinct oceanic contexts, including variation in viral adsorption and grazer clearance rates, can transform the quantitative and even qualitative importance of top-down controls in shaping Prochlorococcus population dynamics." +featured : true +projects : [] +tags : [] +doi : "10.1038/s41467-024-46165-3" +math : false +--- diff --git a/content/publication/boysen-2021/cite.bib b/content/publication/boysen-2021/cite.bib new file mode 100644 index 0000000..10e3700 --- /dev/null +++ b/content/publication/boysen-2021/cite.bib @@ -0,0 +1,11 @@ +@article{boysen_particulate_2021 + abstract = {Light fuels photosynthesis and organic matter production by primary producers in the sunlit ocean. The quantity and quality of the organic matter produced influence community function, yet in situ measurements of metabolites, the products of cellular metabolism, over the diel cycle are lacking. We evaluated community level biochemical consequences of oscillations of light in the North Pacific Subtropical Gyre by quantifying 79 metabolites in particulate organic matter from 15 m every 4 h over 8 days. Total particulate metabolite concentration peaked at dusk and represented up to 2\% of total particulate organic carbon (POC). The concentrations of 55/79 (70\%) individual metabolites exhibited significant 24-h periodicity, with daily fold changes from 1.6 to 12.8, often greater than those of POC and flow cytometry-resolvable biomass, which ranged from 1.2 to 2.8. Paired metatranscrip-tome analysis revealed the taxa involved in production and consumption of a subset of metabolites. Primary metabolites involved in anabolism and redox maintenance had significant 24-h periodicity and diverse organisms exhibited diel periodicity in transcript abundance associated with these metabolites. Compounds with osmotic properties displayed the largest oscillations in concentration, implying rapid turnover and supporting prior evidence of functions beyond cell turgor maintenance. The large daily oscillation of trehalose paired with metatranscriptome and culture data showed that tre-halose is produced by the nitrogen-fixing cyanobacterium Crocosphaera, likely to store energy for nighttime metabolism. Together, paired measurements of particulate metabo-lites and transcripts resolve strategies that microbes use to manage daily energy and re-dox oscillations and highlight dynamic metabolites with cryptic roles in marine microbial ecosystems. IMPORTANCE Fueled by light, phytoplankton produce the organic matter that supports ocean ecosystems and carbon sequestration. Ocean change impacts microbial metabolism with repercussions for biogeochemical cycling. As the small molecule products of cellular metabolism, metabolites often change rapidly in response to environmental conditions and form the basis of energy and nutrient management and storage within cells. By pairing measurements of metabolites and gene expression in the stratified surface ocean, we reveal strategies of microbial energy management over the day-night cycle and hypothesize that oscillating metabolites are important substrates for dark respiration by phytoplankton. These high-resolution diel measurements of in situ metabolite concentrations form the basis for future work into the specific roles these compounds play in marine microbial communities. Metabolites and transcripts in surface ocean plankton reveal strategies for energy management over the day-night cycle.}, + author = {Boysen, Angela K. and Carlson, Laura T. and Durham, Bryndan P. and Groussman, Ryan D. and Aylward, Frank O. and Ribalet, François and Heal, Katherine R. and White, Angelicque E. and Delong, Edward F. and Armbrust, E. Virginia and Ingalls, Anitra E.}, + doi = {10/grzmhn}, + journal = {mSystems}, + number = {3}, + pages = {e00896--20}, + title = {Particulate {Metabolites} and {Transcripts} {Reflect} {Diel} {Oscillations} of {Microbial} {Activity} in the {Surface} {Ocean}}, + volume = {6}, + year = {2021} +} diff --git a/content/publication/boysen-2021/featured.png b/content/publication/boysen-2021/featured.png new file mode 100644 index 0000000..c9c7fcf Binary files /dev/null and b/content/publication/boysen-2021/featured.png differ diff --git a/content/publication/boysen-2021/index.md b/content/publication/boysen-2021/index.md new file mode 100644 index 0000000..5e621b0 --- /dev/null +++ b/content/publication/boysen-2021/index.md @@ -0,0 +1,13 @@ +--- +title : "Particulate metabolites and transcripts reflect diel oscillations of microbial activity in the surface ocean" +date : "2021-12-01T00:00:00" +authors : ["Angela K. Boysen", "Laura T. Carlson", "Bryndan P. Durham", "Ryan D. Groussman", "Frank O. Aylward", "François Ribalet", "Katherine R. Heal", "Angelicque E. White", "Edward F. Delong", "E. Virginia Armbrust", "Anitra E. Ingalls"] +publication_types : ["2"] +publication : "in *mSystems*" +abstract : "Light fuels photosynthesis and organic matter production by primary producers in the sunlit ocean. The quantity and quality of the organic matter produced influence community function, yet in situ measurements of metabolites, the products of cellular metabolism, over the diel cycle are lacking. We evaluated community level biochemical consequences of oscillations of light in the North Pacific Subtropical Gyre by quantifying 79 metabolites in particulate organic matter from 15 m every 4 h over 8 days. Total particulate metabolite concentration peaked at dusk and represented up to 2% of total particulate organic carbon (POC). The concentrations of 55/79 (70%) individual metabolites exhibited significant 24-h periodicity, with daily fold changes from 1.6 to 12.8, often greater than those of POC and flow cytometry-resolvable biomass, which ranged from 1.2 to 2.8. Paired metatranscrip-tome analysis revealed the taxa involved in production and consumption of a subset of metabolites. Primary metabolites involved in anabolism and redox maintenance had significant 24-h periodicity and diverse organisms exhibited diel periodicity in transcript abundance associated with these metabolites. Compounds with osmotic properties displayed the largest oscillations in concentration, implying rapid turnover and supporting prior evidence of functions beyond cell turgor maintenance. The large daily oscillation of trehalose paired with metatranscriptome and culture data showed that tre-halose is produced by the nitrogen-fixing cyanobacterium Crocosphaera, likely to store energy for nighttime metabolism. Together, paired measurements of particulate metabo-lites and transcripts resolve strategies that microbes use to manage daily energy and re-dox oscillations and highlight dynamic metabolites with cryptic roles in marine microbial ecosystems." +featured : false +projects : [] +tags : [] +doi : "10/grzmhn" +math : false +--- diff --git a/content/publication/carlson-2022/cite.bib b/content/publication/carlson-2022/cite.bib new file mode 100644 index 0000000..9741ebc --- /dev/null +++ b/content/publication/carlson-2022/cite.bib @@ -0,0 +1,11 @@ +@article{Carlson2022 + abstract = {The photosynthetic picocyanobacteria Prochlorococcus and Synechococcus are models for dissecting how ecological niches are defined by environmental conditions, but how interactions with bacteriophages affect picocyanobacterial biogeography in open ocean biomes has rarely been assessed. We applied single-virus and single-cell infection approaches to quantify cyanophage abundance and infected picocyanobacteria in 87 surface water samples from five transects that traversed approximately 2,200 km in the North Pacific Ocean on three cruises, with a duration of 2–4 weeks, between 2015 and 2017. We detected a 550-km-wide hotspot of cyanophages and virus-infected picocyanobacteria in the transition zone between the North Pacific Subtropical and Subpolar gyres that was present in each transect. Notably, the hotspot occurred at a consistent temperature and displayed distinct cyanophage-lineage composition on all transects. On two of these transects, the levels of infection in the hotspot were estimated to be sufficient to substantially limit the geographical range of Prochlorococcus. Coincident with the detection of high levels of virally infected picocyanobacteria, we measured an increase of 10–100-fold in the Synechococcus populations in samples that are usually dominated by Prochlorococcus. We developed a multiple regression model of cyanophages, temperature and chlorophyll concentrations that inferred that the hotspot extended across the North Pacific Ocean, creating a biological boundary between gyres, with the potential to release organic matter comparable to that of the sevenfold-larger North Pacific Subtropical Gyre. Our results highlight the probable impact of viruses on large-scale phytoplankton biogeography and biogeochemistry in distinct regions of the oceans. High-resolution sampling across thousands of kilometres of open ocean reveals a hotspot of viruses at the boundary of major oceanic gyres that, at times, shaped the abundance and biogeography of marine picocyanobacteria.}, + author = {Carlson, Michael. C. G. and Ribalet, Fran{\c{c}ois and Maidanik, Ilia and Durham, Bryndan P. and Hulata, Yotam and Ferr{\'{o}n, Sara and Weissenbach, Julia and Shamir, Nitzan and Goldin, Svetlana and Baran, Nava and Cael, B. B. and Karl, David M. and White, Angelicque E. and Armbrust, E. Virginia and Lindell, Debbie}, + doi = {10.1038/s41564-022-01088-x}, + journal = {Nature Microbiology 2022 7:4}, + number = {4}, + pages = {570--580}, + title = {Viruses affect picocyanobacterial abundance and biogeography in the North Pacific Ocean}, + volume = {7}, + year = {2022} +} diff --git a/content/publication/carlson-2022/featured.png b/content/publication/carlson-2022/featured.png new file mode 100644 index 0000000..53341ab Binary files /dev/null and b/content/publication/carlson-2022/featured.png differ diff --git a/content/publication/carlson-2022/index.md b/content/publication/carlson-2022/index.md new file mode 100644 index 0000000..3181a74 --- /dev/null +++ b/content/publication/carlson-2022/index.md @@ -0,0 +1,15 @@ +--- +title : "Viruses affect picocyanobacterial abundance and biogeography in the North Pacific Ocean" +date : 2022-04-06 +publishDate : 2022-04-01T17:46:51.934135Z +authors : ["Michael. C. G. Carlson", "Francois Ribalet", "Ilia Maidanik", "Bryndan P. Durham", "Yotam Hulata", "Sara Ferron", "Julia Weissenbach", "Nitzan Shamir", "Svetlana Goldin", "Nava Baran", "B. B. Cael", "David M. Karl", "Angelicque E. White", "E. Virginia Armbrust", "Debbie Lindell"] +publication_types : ["2"] +publication : "*Nature Microbiology*" +abstract : "The photosynthetic picocyanobacteria Prochlorococcus and Synechococcus are models for dissecting how ecological niches are defined by environmental conditions, but how interactions with bacteriophages affect picocyanobacterial biogeography in open ocean biomes has rarely been assessed. We applied single-virus and single-cell infection approaches to quantify cyanophage abundance and infected picocyanobacteria in 87 surface water samples from five transects that traversed approximately 2,200 km in the North Pacific Ocean on three cruises, with a duration of 2–4 weeks, between 2015 and 2017. We detected a 550-km-wide hotspot of cyanophages and virus-infected picocyanobacteria in the transition zone between the North Pacific Subtropical and Subpolar gyres that was present in each transect. Notably, the hotspot occurred at a consistent temperature and displayed distinct cyanophage-lineage composition on all transects. On two of these transects, the levels of infection in the hotspot were estimated to be sufficient to substantially limit the geographical range of Prochlorococcus. Coincident with the detection of high levels of virally infected picocyanobacteria, we measured an increase of 10–100-fold in the Synechococcus populations in samples that are usually dominated by Prochlorococcus. We developed a multiple regression model of cyanophages, temperature and chlorophyll concentrations that inferred that the hotspot extended across the North Pacific Ocean, creating a biological boundary between gyres, with the potential to release organic matter comparable to that of the sevenfold-larger North Pacific Subtropical Gyre. Our results highlight the probable impact of viruses on large-scale phytoplankton biogeography and biogeochemistry in distinct regions of the oceans. High-resolution sampling across thousands of kilometres of open ocean reveals a hotspot of viruses at the boundary of major oceanic gyres that, at times, shaped the abundance and biogeography of marine picocyanobacteria." +featured : false +projects : [] +tags : [] +doi : "10.1038/s41564-022-01088-x" +math : false +--- + diff --git a/content/publication/coesel-2021/cite.bib b/content/publication/coesel-2021/cite.bib new file mode 100644 index 0000000..d5c768c --- /dev/null +++ b/content/publication/coesel-2021/cite.bib @@ -0,0 +1,16 @@ +@article{Coesel2021, +abstract = {The 24-h cycle of light and darkness governs daily rhythms of complex behaviors across all domains of life. Intracellular photoreceptors sense specific wavelengths of light that can reset the internal circadian clock and/or elicit distinct phenotypic responses. In the surface ocean, microbial communities additionally modulate nonrhythmic changes in light quality and quantity as they are mixed to different depths. Here, we show that eukaryotic plankton in the North Pacific Subtropical Gyre transcribe genes encoding light-sensitive proteins that may serve as light-activated transcription factors, elicit light-driven electrical/chemical cascades, or initiate secondary messenger-signaling cascades. Overall, the protistan community relies on blue light-sensitive photoreceptors of the cryptochrome/photolyase family, and proteins containing the Light-Oxygen-Voltage (LOV) domain. The greatest diversification occurred within Haptophyta and photosynthetic stramenopiles where the LOV domain was combined with different DNA-binding domains and secondary signal-transduction motifs. Flagellated protists utilize green-light sensory rhodopsins and blue-light helmchromes, potentially underlying phototactic/photophobic and other behaviors toward specific wavelengths of light. Photoreceptors such as phytochromes appear to play minor roles in the North Pacific Subtropical Gyre. Transcript abundance of environmental light-sensitive protein-encoding genes that display diel patterns are found to primarily peak at dawn. The exceptions are the LOV-domain transcription factors with peaks in transcript abundances at different times and putative phototaxis photoreceptors transcribed throughout the day. Together, these data illustrate the diversity of light-sensitive proteins that may allow disparate groups of protists to respond to light and potentially synchronize patterns of growth, division, and mortality within the dynamic ocean environment.}, +author = {Coesel, Sacha N. and Durham, Bryndan P. and Groussman, Ryan D. and Hu, Sarah K. and Caron, David A. and Morales, Rhonda L. and Ribalet, Fran{\c{c}}ois and Armbrust, E. Virginia}, +doi = {10.1073/pnas.2011038118}, +issn = {0027-8424}, +journal = {Proceedings of the National Academy of Sciences}, +month = {feb}, +number = {6}, +pages = {e2011038118}, +publisher = {National Academy of Sciences}, +title = {Diel transcriptional oscillations of light-sensitive regulatory elements in open-ocean eukaryotic plankton communities}, +url = {http://www.pnas.org/lookup/doi/10.1073/pnas.2011038118}, +volume = {118}, +year = {2021} +} + diff --git a/content/publication/coesel-2021/featured.png b/content/publication/coesel-2021/featured.png new file mode 100644 index 0000000..670dd69 Binary files /dev/null and b/content/publication/coesel-2021/featured.png differ diff --git a/content/publication/coesel-2021/index.md b/content/publication/coesel-2021/index.md new file mode 100644 index 0000000..f688d56 --- /dev/null +++ b/content/publication/coesel-2021/index.md @@ -0,0 +1,13 @@ +--- +title: "Diel transcriptional oscillations of light-sensitive regulatory elements in open-ocean eukaryotic plankton communities" +date: 2021-02-09 +publishDate: 2021-02-09T17:46:51.934135Z +authors: ["S.N. Coesel", "B. Durham", "R. Groussman", "S. Hu", "D. Caron", "R. Morales", "F. Ribalet", "E.V. Armbrust"] +publication_types: ["2"] +abstract: "The 24-h cycle of light and darkness governs daily rhythms of complex behaviors across all domains of life. Intracellular photoreceptors sense specific wavelengths of light that can reset the internal circadian clock and/or elicit distinct phenotypic responses. In the surface ocean, microbial communities additionally modulate nonrhythmic changes in light quality and quantity as they are mixed to different depths. Here, we show that eukaryotic plankton in the North Pacific Subtropical Gyre transcribe genes encoding light-sensitive proteins that may serve as light-activated transcription factors, elicit light-driven electrical/chemical cascades, or initiate secondary messenger-signaling cascades. Overall, the protistan community relies on blue light-sensitive photoreceptors of the cryptochrome/photolyase family, and proteins containing the Light-Oxygen-Voltage (LOV) domain. The greatest diversification occurred within Haptophyta and photosynthetic stramenopiles where the LOV domain was combined with different DNA-binding domains and secondary signal-transduction motifs. Flagellated protists utilize green-light sensory rhodopsins and blue-light helmchromes, potentially underlying phototactic/photophobic and other behaviors toward specific wavelengths of light. Photoreceptors such as phytochromes appear to play minor roles in the North Pacific Subtropical Gyre. Transcript abundance of environmental light-sensitive protein-encoding genes that display diel patterns are found to primarily peak at dawn. The exceptions are the LOV-domain transcription factors with peaks in transcript abundances at different times and putative phototaxis photoreceptors transcribed throughout the day. Together, these data illustrate the diversity of light-sensitive proteins that may allow disparate groups of protists to respond to light and potentially synchronize patterns of growth, division, and mortality within the dynamic ocean environment." +featured: false +publication: "*Proceedings of the National Academy of Sciences*" +url_pdf: "http://www.pnas.org/lookup/doi/10.1073/pnas.2011038118" +doi: "10.1073/pnas.2011038118" +--- + diff --git a/content/publication/conference-paper/cite.bib b/content/publication/conference-paper/cite.bib deleted file mode 100644 index 98c3748..0000000 --- a/content/publication/conference-paper/cite.bib +++ /dev/null @@ -1,8 +0,0 @@ -@inproceedings{example1, - title={An example conference paper}, - author={Bighetti, Nelson and Ford, Robert}, - booktitle={Source Themes Conference}, - pages={1--6}, - year={2013}, - organization={IEEE} -} diff --git a/content/publication/conference-paper/conference-paper.pdf b/content/publication/conference-paper/conference-paper.pdf deleted file mode 100644 index 747064e..0000000 Binary files a/content/publication/conference-paper/conference-paper.pdf and /dev/null differ diff --git a/content/publication/conference-paper/featured.jpg b/content/publication/conference-paper/featured.jpg deleted file mode 100644 index 2ebab27..0000000 Binary files a/content/publication/conference-paper/featured.jpg and /dev/null differ diff --git a/content/publication/conference-paper/index.md b/content/publication/conference-paper/index.md deleted file mode 100644 index 3f1178b..0000000 --- a/content/publication/conference-paper/index.md +++ /dev/null @@ -1,86 +0,0 @@ ---- -title: 'An example conference paper' - -# Authors -# If you created a profile for a user (e.g. the default `admin` user), write the username (folder name) here -# and it will be replaced with their full name and linked to their profile. -authors: - - admin - - Robert Ford - -# Author notes (optional) -author_notes: - - 'Equal contribution' - - 'Equal contribution' - -date: '2013-07-01T00:00:00Z' -doi: '' - -# Schedule page publish date (NOT publication's date). -publishDate: '2017-01-01T00:00:00Z' - -# Publication type. -# Accepts a single type but formatted as a YAML list (for Hugo requirements). -# Enter a publication type from the CSL standard. -publication_types: ['paper-conference'] - -# Publication name and optional abbreviated publication name. -publication: In *Wowchemy Conference* -publication_short: In *ICW* - -abstract: Lorem ipsum dolor sit amet, consectetur adipiscing elit. 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You can use rich formatting such as including [code, math, and images](https://docs.hugoblox.com/content/writing-markdown-latex/). diff --git a/content/publication/connell-2020/cite.bib b/content/publication/connell-2020/cite.bib new file mode 100644 index 0000000..67457cf --- /dev/null +++ b/content/publication/connell-2020/cite.bib @@ -0,0 +1,16 @@ +@article{Connell2020, +abstract = {Daily oscillations in photosynthetically active radiation strongly influence the timing of metabolic processes in picocyanobacteria, but it is less clear how the light-dark cycle affects the activities of their consumers. We investigated the relationship between marine picocyanobacteria and nanoplanktonic consumers throughout the diel cycle to determine whether heterotrophic and mixotrophic protists (algae with phagotrophic ability) display significant periodicity in grazing pressure. Carbon biomass of Prochlorococcus and Synechococcus was estimated continuously from abundances and cell size measurements made by flow cytometry. Picocyanobacterial dynamics were then compared to nanoplankton abundances and ingestion of fluorescently labeled bacteria measured every 4 h during a 4 d survey in the North Pacific Subtropical Gyre. Grazing of the labeled bacteria by heterotrophic nanoplankton was significantly greater at night than during the day. The grazing activity of mixotrophic nanoplankton showed no diel periodicity, suggesting that they may feed continuously, albeit at lower rates than heterotrophic nanoplankton, to alleviate nutrient limitation in this oligotrophic environment. Diel changes in Prochlorococcus biomass indicated that they could support substantial growth of nanoplankton if those grazers are the main source of picocyanobacterial mortality, and that grazers may contribute to temporally stable abundances of picocyanobacteria.}, +author = {Connell, PE and Ribalet, F and Armbrust, EV and White, A and Caron, DA}, +doi = {10.3354/ame01950}, +issn = {0948-3055}, +journal = {Aquatic Microbial Ecology}, +keywords = {Bacterivory,Diel cycles,Mixotrophy,Nanoplankton grazing,Picocyanobacteria}, +month = {dec}, +pages = {167--181}, +publisher = {Inter-Research}, +title = {{Diel oscillations in the feeding activity of heterotrophic and mixotrophic nanoplankton in the North Pacific Subtropical Gyre}}, +url = {https://www.int-res.com/abstracts/ame/v85/p167-181/}, +volume = {85}, +year = {2020} +} + diff --git a/content/publication/connell-2020/featured.png b/content/publication/connell-2020/featured.png new file mode 100644 index 0000000..c852a23 Binary files /dev/null and b/content/publication/connell-2020/featured.png differ diff --git a/content/publication/connell-2020/index.md b/content/publication/connell-2020/index.md new file mode 100644 index 0000000..01fd541 --- /dev/null +++ b/content/publication/connell-2020/index.md @@ -0,0 +1,13 @@ +--- +title: "Diel oscillations in the feeding activity of heterotrophic and mixotrophic nanoplankton in the North Pacific Subtropical Gyre" +date: 2020-12-09 +publishDate: 2020-12-09T17:46:51.934135Z +authors: ["P.E. Connell", "F. Ribalet", "E.V. Armbrust", "A. White", "D.A. Caron"] +publication_types: ["2"] +abstract: "Daily oscillations in photosynthetically active radiation strongly influence the timing of metabolic processes in picocyanobacteria, but it is less clear how the light-dark cycle affects the activities of their consumers. We investigated the relationship between marine picocyanobacteria and nanoplanktonic consumers throughout the diel cycle to determine whether heterotrophic and mixotrophic protists (algae with phagotrophic ability) display significant periodicity in grazing pressure. Carbon biomass of Prochlorococcus and Synechococcus was estimated continuously from abundances and cell size measurements made by flow cytometry. Picocyanobacterial dynamics were then compared to nanoplankton abundances and ingestion of fluorescently labeled bacteria measured every 4 h during a 4 d survey in the North Pacific Subtropical Gyre. Grazing of the labeled bacteria by heterotrophic nanoplankton was significantly greater at night than during the day. The grazing activity of mixotrophic nanoplankton showed no diel periodicity, suggesting that they may feed continuously, albeit at lower rates than heterotrophic nanoplankton, to alleviate nutrient limitation in this oligotrophic environment. Diel changes in Prochlorococcus biomass indicated that they could support substantial growth of nanoplankton if those grazers are the main source of picocyanobacterial mortality, and that grazers may contribute to temporally stable abundances of picocyanobacteria." +featured: false +publication: "*Aquatic Microbial Ecology*" +url_pdf: "https://www.int-res.com/abstracts/ame/v85/p167-181/" +doi: "10.3354/ame01950" +--- + diff --git a/content/publication/dugenne-2023/cite.bib b/content/publication/dugenne-2023/cite.bib new file mode 100644 index 0000000..12ec026 --- /dev/null +++ b/content/publication/dugenne-2023/cite.bib @@ -0,0 +1,11 @@ +@article{dugenne_nitrogen_2023 + abstract = {Mesoscale eddies have been shown to support elevated dinitrogen (N2) fixation rates (NFRs) and abundances of N2-fixing microorganisms (diazotrophs), but the mechanisms underlying these observations are not well understood. We sampled two pairs of mesoscale cyclones and anticyclones in the North Pacific Subtropical Gyre in 2017 and 2018 and compared our observations with seasonal patterns from the Hawaii Ocean Time-series (HOT) program. Consistent with previous reports, we found that NFRs were anomalously high for this region (up to 3.7-fold above previous monthly HOT observations) in the centers of both sampled anticyclones. In 2017, these elevated rates coincided with high concentrations of the diazotroph Crocosphaera. We then coupled our field-based observations, together with transcriptomic analyses of nutrient stress marker genes and ecological models, to evaluate the role of biological (via estimates of growth and grazing rates) and physical controls on populations of Crocosphaera, Trichodesmium, and diatom symbionts at the mesoscale. Our results suggest that increased Crocosphaera abundances in the 2017 anticyclone resulted from the alleviation of phosphate limitation, allowing cells to grow at rates exceeding grazing losses. In contrast, distributions of larger, buoyant taxa (Trichodesmium and diatom symbionts) appeared less affected by eddy-driven biological controls. Instead, they appeared driven by physical dynamics along frontal boundaries that separate cyclonic and anticyclonic eddies. No examined controls were able to explain our 2018 findings of higher NFRs in the anticyclone. A generalized explanation of elevated NFRs in mesoscale eddies remains challenging due to the interplay of eddy-driven bottom-up, top-down, and physical control mechanisms.}, + author = {Dugenne, Mathilde and Gradoville, Mary R. and Church, Matthew J. and Wilson, Samuel T. and Sheyn, Uri and Harke, Matthew J. and Björkman, Karin M. and Hawco, Nicholas J. and Hynes, Annette M. and Ribalet, François and Karl, David M. and DeLong, Edward F. and Dyhrman, Sonya T. and Armbrust, E. Virginia and John, Seth and Eppley, John M. and Harding, Katie and Stewart, Brittany and Cabello, Ana M. and Turk-Kubo, Kendra A. and Caffin, Mathieu and White, Angelicque E. and Zehr, Jonathan P.}, + doi = {10.1029/2022GB007386}, + journal = {Global Biogeochemical Cycles}, + number = {4}, + pages = {e2022GB007386}, + title = {Nitrogen fixation in mesoscale eddies of the North Pacific Subtropical Gyre: patterns and mechanisms}, + volume = {37}, + year = {2023} +} diff --git a/content/publication/dugenne-2023/featured.png b/content/publication/dugenne-2023/featured.png new file mode 100644 index 0000000..ec24a6f Binary files /dev/null and b/content/publication/dugenne-2023/featured.png differ diff --git a/content/publication/dugenne-2023/index.md b/content/publication/dugenne-2023/index.md new file mode 100644 index 0000000..17652db --- /dev/null +++ b/content/publication/dugenne-2023/index.md @@ -0,0 +1,13 @@ +--- +title : "Nitrogen fixation in mesoscale eddies of the North Pacific Subtropical Gyre: patterns and mechanisms" +date : "2023-12-01T00:00:00" +authors : ["Mathilde Dugenne", "Mary R. Gradoville", "Matthew J. Church", "Samuel T. Wilson", "Uri Sheyn", "Matthew J. Harke", "Karin M. Björkman", "Nicholas J. Hawco", "Annette M. Hynes", "François Ribalet", "David M. Karl", "Edward F. DeLong", "Sonya T. Dyhrman", "E. Virginia Armbrust", "Seth John", "John M. Eppley", "Katie Harding", "Brittany Stewart", "Ana M. Cabello", "Kendra A. Turk-Kubo", "Mathieu Caffin", "Angelicque E. White", "Jonathan P. Zehr"] +publication_types : ["2"] +publication : "in *Global Biogeochemical Cycles*" +abstract : "Mesoscale eddies have been shown to support elevated dinitrogen (N2) fixation rates (NFRs) and abundances of N2-fixing microorganisms (diazotrophs), but the mechanisms underlying these observations are not well understood. We sampled two pairs of mesoscale cyclones and anticyclones in the North Pacific Subtropical Gyre in 2017 and 2018 and compared our observations with seasonal patterns from the Hawaii Ocean Time-series (HOT) program. Consistent with previous reports, we found that NFRs were anomalously high for this region (up to 3.7-fold above previous monthly HOT observations) in the centers of both sampled anticyclones. In 2017, these elevated rates coincided with high concentrations of the diazotroph Crocosphaera. We then coupled our field-based observations, together with transcriptomic analyses of nutrient stress marker genes and ecological models, to evaluate the role of biological (via estimates of growth and grazing rates) and physical controls on populations of Crocosphaera, Trichodesmium, and diatom symbionts at the mesoscale. Our results suggest that increased Crocosphaera abundances in the 2017 anticyclone resulted from the alleviation of phosphate limitation, allowing cells to grow at rates exceeding grazing losses. In contrast, distributions of larger, buoyant taxa (Trichodesmium and diatom symbionts) appeared less affected by eddy-driven biological controls. Instead, they appeared driven by physical dynamics along frontal boundaries that separate cyclonic and anticyclonic eddies. No examined controls were able to explain our 2018 findings of higher NFRs in the anticyclone. A generalized explanation of elevated NFRs in mesoscale eddies remains challenging due to the interplay of eddy-driven bottom-up, top-down, and physical control mechanisms." +featured : false +projects : [] +tags : [] +doi : "10.1029/2022GB007386" +math : false +--- diff --git a/content/publication/dutkiewicz-2024/cite.bib b/content/publication/dutkiewicz-2024/cite.bib new file mode 100644 index 0000000..f2e7fbb --- /dev/null +++ b/content/publication/dutkiewicz-2024/cite.bib @@ -0,0 +1,11 @@ +@article{dutkiewicz_multiple_2024 + abstract = {The combination of taxa and size classes of phytoplankton that coexist at any location affects the structure of the marine food web and the magnitude of carbon fluxes to the deep ocean. But what controls the patterns of this community structure across environmental gradients remains unclear. Here, we focus on the North East Pacific Transition Zone, a 10° region of latitude straddling warm, nutrient-poor subtropical and cold, nutrient-rich subpolar gyres. Data from three cruises to the region revealed intricate patterns of phytoplankton community structure: poleward increases in the number of cell size classes; increasing biomass of picoeukaryotes and diatoms; decreases in diazotrophs and Prochlorococcus; and both increases and decreases in Synechococcus. These patterns can only be partially explained by existing theories. Using data, theory, and numerical simulations, we show that the patterns of plankton distributions across the transition zone are the result of gradients in nutrient supply rates, which control a range of complex biotic interactions. We examine how interactions such as size-specific grazing, multiple trophic strategies, shared grazing between several phytoplankton size classes and heterotrophic bacteria, and competition for multiple resources can individually explain aspects of the observed community structure. However, it is the combination of all these interactions together that is needed to explain the bulk compositional patterns in phytoplankton across the North East Pacific Transition Zone. The synthesis of multiple mechanisms is essential for us to begin to understand the shaping of community structure over large environmental gradients.}, + author = {Dutkiewicz, Stephanie and Follett, Christopher L. and Follows, Michael J. and Henderikx-Freitas, Fernanda and Ribalet, Francois and Gradoville, Mary R. and Coesel, Sacha N. and Farnelid, Hanna and Finkel, Zoe V. and Irwin, Andrew J. and Jahn, Oliver and Karl, David M. and Mattern, Jann Paul and White, Angelicque E. and Zehr, Jonathan P. and Armbrust, E. Virginia}, + doi = {10.1002/lno.12555}, + journal = {Limnology and Oceanography}, + number = {5}, + pages = {1086--1100}, + title = {Multiple biotic interactions establish phytoplankton community structure across environmental gradients}, + volume = {69}, + year = {2024} +} diff --git a/content/publication/dutkiewicz-2024/featured.png b/content/publication/dutkiewicz-2024/featured.png new file mode 100644 index 0000000..49644a2 Binary files /dev/null and b/content/publication/dutkiewicz-2024/featured.png differ diff --git a/content/publication/dutkiewicz-2024/index.md b/content/publication/dutkiewicz-2024/index.md new file mode 100644 index 0000000..bfc9a27 --- /dev/null +++ b/content/publication/dutkiewicz-2024/index.md @@ -0,0 +1,13 @@ +--- +title : "Multiple biotic interactions establish phytoplankton community structure across environmental gradients" +date : "2024-03-01" +authors : ["Stephanie Dutkiewicz", "Christopher L. Follett", "Michael J. Follows", "Fern Henderikx-Freitas", "a", "Francois Ribalet", "Mary R. Gradoville", "Sacha N. Coesel", "Hanna Farnelid", "Zoe V. Finkel", "Andrew J. Irwin", "Oliver Jahn", "David M. Karl", "Jann Paul Mattern", "Angelicque E. White", "Jonathan P. Zehr", "E. Virginia Armbrust"] +publication_types : ["2"] +publication : "in *Limnology and Oceanography*" +abstract : "The combination of taxa and size classes of phytoplankton that coexist at any location affects the structure of the marine food web and the magnitude of carbon fluxes to the deep ocean. But what controls the patterns of this community structure across environmental gradients remains unclear. Here, we focus on the North East Pacific Transition Zone, a 10° region of latitude straddling warm, nutrient-poor subtropical and cold, nutrient-rich subpolar gyres. Data from three cruises to the region revealed intricate patterns of phytoplankton community structure: poleward increases in the number of cell size classes; increasing biomass of picoeukaryotes and diatoms; decreases in diazotrophs and Prochlorococcus; and both increases and decreases in Synechococcus. These patterns can only be partially explained by existing theories. Using data, theory, and numerical simulations, we show that the patterns of plankton distributions across the transition zone are the result of gradients in nutrient supply rates, which control a range of complex biotic interactions. We examine how interactions such as size-specific grazing, multiple trophic strategies, shared grazing between several phytoplankton size classes and heterotrophic bacteria, and competition for multiple resources can individually explain aspects of the observed community structure. However, it is the combination of all these interactions together that is needed to explain the bulk compositional patterns in phytoplankton across the North East Pacific Transition Zone. The synthesis of multiple mechanisms is essential for us to begin to understand the shaping of community structure over large environmental gradients." +featured : false +projects : [] +tags : [] +doi : "10.1002/lno.12555" +math : false +--- diff --git a/content/publication/follett-2022/cite.bib b/content/publication/follett-2022/cite.bib new file mode 100644 index 0000000..d5c768c --- /dev/null +++ b/content/publication/follett-2022/cite.bib @@ -0,0 +1,16 @@ +@article{Coesel2021, +abstract = {The 24-h cycle of light and darkness governs daily rhythms of complex behaviors across all domains of life. Intracellular photoreceptors sense specific wavelengths of light that can reset the internal circadian clock and/or elicit distinct phenotypic responses. In the surface ocean, microbial communities additionally modulate nonrhythmic changes in light quality and quantity as they are mixed to different depths. Here, we show that eukaryotic plankton in the North Pacific Subtropical Gyre transcribe genes encoding light-sensitive proteins that may serve as light-activated transcription factors, elicit light-driven electrical/chemical cascades, or initiate secondary messenger-signaling cascades. Overall, the protistan community relies on blue light-sensitive photoreceptors of the cryptochrome/photolyase family, and proteins containing the Light-Oxygen-Voltage (LOV) domain. The greatest diversification occurred within Haptophyta and photosynthetic stramenopiles where the LOV domain was combined with different DNA-binding domains and secondary signal-transduction motifs. Flagellated protists utilize green-light sensory rhodopsins and blue-light helmchromes, potentially underlying phototactic/photophobic and other behaviors toward specific wavelengths of light. Photoreceptors such as phytochromes appear to play minor roles in the North Pacific Subtropical Gyre. Transcript abundance of environmental light-sensitive protein-encoding genes that display diel patterns are found to primarily peak at dawn. The exceptions are the LOV-domain transcription factors with peaks in transcript abundances at different times and putative phototaxis photoreceptors transcribed throughout the day. Together, these data illustrate the diversity of light-sensitive proteins that may allow disparate groups of protists to respond to light and potentially synchronize patterns of growth, division, and mortality within the dynamic ocean environment.}, +author = {Coesel, Sacha N. and Durham, Bryndan P. and Groussman, Ryan D. and Hu, Sarah K. and Caron, David A. and Morales, Rhonda L. and Ribalet, Fran{\c{c}}ois and Armbrust, E. Virginia}, +doi = {10.1073/pnas.2011038118}, +issn = {0027-8424}, +journal = {Proceedings of the National Academy of Sciences}, +month = {feb}, +number = {6}, +pages = {e2011038118}, +publisher = {National Academy of Sciences}, +title = {Diel transcriptional oscillations of light-sensitive regulatory elements in open-ocean eukaryotic plankton communities}, +url = {http://www.pnas.org/lookup/doi/10.1073/pnas.2011038118}, +volume = {118}, +year = {2021} +} + diff --git a/content/publication/follett-2022/featured.png b/content/publication/follett-2022/featured.png new file mode 100644 index 0000000..f1eaff8 Binary files /dev/null and b/content/publication/follett-2022/featured.png differ diff --git a/content/publication/follett-2022/index.md b/content/publication/follett-2022/index.md new file mode 100644 index 0000000..0a00c5c --- /dev/null +++ b/content/publication/follett-2022/index.md @@ -0,0 +1,13 @@ +--- +title: "Trophic interactions with heterotrophic bacteria limit the range of Prochlorococcus" +date: 2022-01-02 +publishDate: 2022-01-02T17:46:51.934135Z +authors: ["C. Follett", "S. Dutkiewitz", "F. Ribalet", "E. Zakem", "D. Caron", "E.V. Armbrust", "M.J. Follow"] +publication_types: ["2"] +abstract: "Prochlorococcus is the smallest and most abundant photosynthetic organism on Earth and is thought to be confined to low-latitude regions by its requirement for warm waters. Latitudinal transects in the North Pacific, however, demonstrate that the poleward decrease of this species occurs across a wide range of temperatures. An additional mechanism is likely required. We use theory, computational models, and additional observational data to suggest that the poleward decrease is caused by an ecological interaction: a shared predator which consumes both Prochlorococcus and similar-sized heterotrophic bacteria. Understanding the fate of this organism requires a knowledge of the interconnected ecosystem of other organisms, where both direct and indirect interactions control community structure." +featured: false +publication: "*Proceedings of the National Academy of Sciences*" +url_pdf: "https://www.pnas.org/content/119/2/e2110993118" +doi: "10.1073/PNAS.2110993118" +--- + diff --git a/content/publication/gradoville-2020/cite.bib b/content/publication/gradoville-2020/cite.bib new file mode 100644 index 0000000..b65ad8d --- /dev/null +++ b/content/publication/gradoville-2020/cite.bib @@ -0,0 +1,12 @@ +@article{Gradoville2020, +abstract = {The number of marine environments known to harbor dinitrogen (N2)-fixing (diazotrophic) microorganisms is increasing, prompting a reassessment of the biogeography of marine diazotrophs and N2 fixation rates (NFRs). Here, we investigate the diversity, abundance, and activity of diazotrophic microorganisms in the North Pacific Subtropical Gyre (NPSG), a diazotrophic habitat, and the North Pacific Transition Zone (NPTZ), a region characterized by strong physical, chemical, and biological gradients. Samples were collected on two springtime meridional cruises during 2016 and 2017, spanning from 23.5°N to 41.4°N along 158°W. We observed an abrupt decrease in diazotrophic abundances near the southern edge of the NPTZ, which coincided with a salinity front and with a ∼10-fold increase in Synechococcus abundance, but without a concomitant change in phosphate or nitrate concentrations. In NPSG waters south of this diazotrophic boundary, nifH genes and NFRs were consistently detected and diazotrophic communities were dominated by UCYN-A, an uncultivated, symbiotic cyanobacterium (2.8 × 103 to 1.0 × 106 nifH gene copies L−1). There was a significant positive relationship between quantitative polymerase chain reaction-derived UCYN-A nifH gene abundances and community NFRs in the NPSG, suggesting a large contribution of UCYN-A to community NFRs. In the NPTZ waters to the north, NFRs were low or undetected and nifH genes were rare, with the few detected sequences represented by UCYN-A and noncyanobacterial diazotrophs. The patterns we observed in UCYN-A abundance in the context of local biogeochemistry suggest that the environmental controls of this organism may differ from those of cultivated marine cyanobacterial diazotrophs.}, +author = {Gradoville, Mary R. and Farnelid, Hanna and White, Angelicque E. and Turk-Kubo, Kendra A. and Stewart, Brittany and Ribalet, Fran{\c{c}}ois and Ferr{\'{o}}n, Sara and Pinedo-Gonzalez, Paulina and Armbrust, E. Virginia and Karl, David M. and John, Seth and Zehr, Jonathan P.}, +doi = {10.1002/lno.11423}, +file = {:home/francois/Downloads/lno.11423.pdf:pdf}, +issn = {19395590}, +journal = {Limnology and Oceanography}, +publisher = {Wiley Blackwell}, +title = {{Latitudinal constraints on the abundance and activity of the cyanobacterium UCYN-A and other marine diazotrophs in the North Pacific}}, +year = {2020} +} + diff --git a/content/publication/gradoville-2020/featured.png b/content/publication/gradoville-2020/featured.png new file mode 100644 index 0000000..7b3d534 Binary files /dev/null and b/content/publication/gradoville-2020/featured.png differ diff --git a/content/publication/gradoville-2020/index.md b/content/publication/gradoville-2020/index.md new file mode 100644 index 0000000..046622f --- /dev/null +++ b/content/publication/gradoville-2020/index.md @@ -0,0 +1,13 @@ +--- +title: "Latitudinal constraints on the abundance and activity of the cyanobacterium UCYN-A and other marine diazotrophs in the North Pacific" +date: 2020-03-05 +publishDate: 2020-03-05T17:46:51.934135Z +authors: ["R. Gradoville", "H. Farnelid", "A. White", "K. Turk-Kubo", "B. Steward", "F. Ribalet", "S. Ferron", "P. Pinedo-Gonzalez", "E.V. Armbrust", "D.M. Karl","S. John", "J. Zehr"] +publication_types: ["2"] +abstract: "The number of marine environments known to harbor dinitrogen (N2)-fixing (diazotrophic) microorganisms is increasing, prompting a reassessment of the biogeography of marine diazotrophs and N2 fixation rates (NFRs). Here, we investigate the diversity, abundance, and activity of diazotrophic microorganisms in the North Pacific Subtropical Gyre (NPSG), a diazotrophic habitat, and the North Pacific Transition Zone (NPTZ), a region characterized by strong physical, chemical, and biological gradients. Samples were collected on two springtime meridional cruises during 2016 and 2017, spanning from 23.5°N to 41.4°N along 158°W. We observed an abrupt decrease in diazotrophic abundances near the southern edge of the NPTZ, which coincided with a salinity front and with a ∼10-fold increase in Synechococcus abundance, but without a concomitant change in phosphate or nitrate concentrations. In NPSG waters south of this diazotrophic boundary, nifH genes and NFRs were consistently detected and diazotrophic communities were dominated by UCYN-A, an uncultivated, symbiotic cyanobacterium (2.8 × 103 to 1.0 × 106 nifH gene copies L−1). There was a significant positive relationship between quantitative polymerase chain reaction-derived UCYN-A nifH gene abundances and community NFRs in the NPSG, suggesting a large contribution of UCYN-A to community NFRs. In the NPTZ waters to the north, NFRs were low or undetected and nifH genes were rare, with the few detected sequences represented by UCYN-A and noncyanobacterial diazotrophs. The patterns we observed in UCYN-A abundance in the context of local biogeochemistry suggest that the environmental controls of this organism may differ from those of cultivated marine cyanobacterial diazotrophs." +featured: false +publication: "*Limnology and Oceanography*" +url_pdf: "https://aslopubs.onlinelibrary.wiley.com/doi/full/10.1002/lno.11423" +doi: "10.1002/lno.11423" +--- + diff --git a/content/publication/halperin-2013/cite.bib b/content/publication/halperin-2013/cite.bib new file mode 100644 index 0000000..5273fb9 --- /dev/null +++ b/content/publication/halperin-2013/cite.bib @@ -0,0 +1,12 @@ +@inproceedings{Halperin2013, + abstract = {We consider a case study using SQL-as-a-Service to support "instant analysis" of weakly structured relational data at a multi-investigator science retreat. Here, "weakly structured" means tabular, rows-and-columns datasets that share some common context, but that have limited a priori agreement on file formats, relationships, types, schemas, metadata, or semantics. In this case study, the data were acquired from hundreds of distinct locations during a multi-day oceanographic cruise using a variety of physical, biological, and chemical sensors and assays. Months after the cruise when preliminary data processing was complete, 40+ researchers from a variety of disciplines participated in a two-day "data synthesis workshop." At this workshop, two computer scientists used a web-based query-as-a-service platform called SQLShare to perform"SQL stenography": capturing the scientific discussion in real time to integrate data, test hypotheses, and populate visualizations to then inform and enhance further discussion. In this "field test" of our technology and approach, we found that it was not only feasible to support interactive science Q & A with essentially pure SQL, but that we significantly increased the value of the "face time" at the meeting: researchers from different fields were able to validate assumptions and resolve ambiguity about each others' fields. As a result, new science emerged from a meeting that was originally just a planning meeting. In this paper, we describe the details of this experiment, discuss our major findings, and lay out a new research agenda for collaborative science database services.}, + author = {Halperin, D. and Weitz, K. and Howe, B. and Ribalet, F. and Saito, M.A. and Virginia Armbrust, E.}, + booktitle = {ACM International Conference Proceeding Series}, + doi = {10.1145/2484838.2484880}, + file = {:Users/ribalet/Library/Application Support/Mendeley Desktop/Downloaded/Halperin et al. - 2013 - Real-time collaborative analysis with (almost) pure SQL A case study in biogeochemical oceanography.pdf:pdf}, + isbn = {9781450319218}, + keywords = {Design,Experimentation,Human factors,Management}, + title = {Real-time collaborative analysis with (almost) pure SQL: A case study in biogeochemical oceanography}, + year = {2013} +} + diff --git a/content/publication/halperin-2013/featured.png b/content/publication/halperin-2013/featured.png new file mode 100644 index 0000000..70039cc Binary files /dev/null and b/content/publication/halperin-2013/featured.png differ diff --git a/content/publication/halperin-2013/index.md b/content/publication/halperin-2013/index.md new file mode 100644 index 0000000..8bdc60a --- /dev/null +++ b/content/publication/halperin-2013/index.md @@ -0,0 +1,13 @@ +--- +title: "Real-time collaborative analysis with (almost) pure SQL: A case study in biogeochemical oceanography" +date: 2013-01-01 +publishDate: 2020-03-09T17:46:51.934135Z +authors: ["D. Halperin", "K. Weitz", "B. Howe", "F. Ribalet", "M.A. Saito", "E. Virginia Armbrust"] +publication_types: ["1"] +abstract: "We consider a case study using SQL-as-a-Service to support \"instant analysis\" of weakly structured relational data at a multi-investigator science retreat. Here, \"weakly structured\" means tabular, rows-and-columns datasets that share some common context, but that have limited a priori agreement on file formats, relationships, types, schemas, metadata, or semantics. In this case study, the data were acquired from hundreds of distinct locations during a multi-day oceanographic cruise using a variety of physical, biological, and chemical sensors and assays. Months after the cruise when preliminary data processing was complete, 40+ researchers from a variety of disciplines participated in a two-day \"data synthesis workshop.\" At this workshop, two computer scientists used a web-based query-as-a-service platform called SQLShare to perform\"SQL stenography\": capturing the scientific discussion in real time to integrate data, test hypotheses, and populate visualizations to then inform and enhance further discussion. In this \"field test\" of our technology and approach, we found that it was not only feasible to support interactive science Q & A with essentially pure SQL, but that we significantly increased the value of the \"face time\" at the meeting: researchers from different fields were able to validate assumptions and resolve ambiguity about each others' fields. As a result, new science emerged from a meeting that was originally just a planning meeting. In this paper, we describe the details of this experiment, discuss our major findings, and lay out a new research agenda for collaborative science database services." +featured: false +publication: "*ACM International Conference Proceeding Series*" +tags: ["Design", "Experimentation", "Human factors", "Management"] +doi: "10.1145/2484838.2484880" +--- + diff --git a/content/publication/hamilton-2017/cite.bib b/content/publication/hamilton-2017/cite.bib new file mode 100644 index 0000000..3ed301b --- /dev/null +++ b/content/publication/hamilton-2017/cite.bib @@ -0,0 +1,14 @@ +@article{Hamilton2017, + abstract = {The mixotrophic ciliate, Mesodinium rubrum, is a globally distributed ciliate that relies on the acquisition and use of chloroplasts derived from its cryptophyte prey. The ecology and physiology of the cryptophytes is not well known, nor is it clear how their growth influences M. rubrum blooms. A 4-week survey was conducted in the Columbia River estuary in 2013 during the decline of the annual M. rubrum bloom to better understand how environmental factors influence the dynamics of the cryptophyte prey, Teleaulax amphioxeia. Abundances and division rates of free-living Teleaulax-like cryptophytes were continuously monitored using flow cytometry. Cryptophyte division rates, estimated in situ for the first time using a size-structured division rate model, ranged from 0.2 to 1.5 d-1, with the highest rates observed in accordance with high abundances. These division rates were positively correlated with concentrations of dissolved inorganic nitrogen and phosphorus, suggesting nutrient availability limited the growth of Teleaulax-like cryptophytes at that time. Assuming a minimum ingestion rate of ∼1 cryptophyte ciliate d-1, the growth of M. rubrum may have been limited by the low abundance of Teleaulax-like cryptophytes during the M. rubrum bloom decline. Our results highlight the importance of prey availability for understanding the dynamics of red water blooms.}, + author = {Hamilton, M. and Hennon, G.M.M. and Morales, R. and Needoba, J. and Peterson, T.D. and Schatz, M. and Swalwell, J. and Armbrust, E.V. and Ribalet, F.}, + doi = {10.1093/plankt/fbx029}, + file = {:Users/ribalet/Library/Application Support/Mendeley Desktop/Downloaded/Hamilton et al. - 2017 - Dynamics of Teleaulax -like cryptophytes during the decline of a red water bloom in the Columbia River Estuary.pdf:pdf}, + issn = {14643774}, + journal = {Journal of Plankton Research}, + keywords = {Mesodinium rubrum,SeaFlow,Teleaulax,cryptophytes,division rates}, + number = {4}, + title = {Dynamics of Teleaulax -like cryptophytes during the decline of a red water bloom in the Columbia River Estuary}, + volume = {39}, + year = {2017} +} + diff --git a/content/publication/hamilton-2017/featured.png b/content/publication/hamilton-2017/featured.png new file mode 100644 index 0000000..eb40eb4 Binary files /dev/null and b/content/publication/hamilton-2017/featured.png differ diff --git a/content/publication/hamilton-2017/index.md b/content/publication/hamilton-2017/index.md new file mode 100644 index 0000000..8d77b26 --- /dev/null +++ b/content/publication/hamilton-2017/index.md @@ -0,0 +1,13 @@ +--- +title: "Dynamics of Teleaulax -like cryptophytes during the decline of a red water bloom in the Columbia River Estuary" +date: 2017-01-01 +publishDate: 2020-03-09T17:46:51.929393Z +authors: ["M. Hamilton", "G.M.M. Hennon", "R. Morales", "J. Needoba", "T.D. Peterson", "M. Schatz", "J. Swalwell", "E.V. Armbrust", "F. Ribalet"] +publication_types: ["2"] +abstract: "The mixotrophic ciliate, Mesodinium rubrum, is a globally distributed ciliate that relies on the acquisition and use of chloroplasts derived from its cryptophyte prey. The ecology and physiology of the cryptophytes is not well known, nor is it clear how their growth influences M. rubrum blooms. A 4-week survey was conducted in the Columbia River estuary in 2013 during the decline of the annual M. rubrum bloom to better understand how environmental factors influence the dynamics of the cryptophyte prey, Teleaulax amphioxeia. Abundances and division rates of free-living Teleaulax-like cryptophytes were continuously monitored using flow cytometry. Cryptophyte division rates, estimated in situ for the first time using a size-structured division rate model, ranged from 0.2 to 1.5 d-1, with the highest rates observed in accordance with high abundances. These division rates were positively correlated with concentrations of dissolved inorganic nitrogen and phosphorus, suggesting nutrient availability limited the growth of Teleaulax-like cryptophytes at that time. Assuming a minimum ingestion rate of ∼1 cryptophyte ciliate d-1, the growth of M. rubrum may have been limited by the low abundance of Teleaulax-like cryptophytes during the M. rubrum bloom decline. Our results highlight the importance of prey availability for understanding the dynamics of red water blooms." +featured: false +publication: "*Journal of Plankton Research*" +tags: ["Mesodinium rubrum", "SeaFlow", "Teleaulax", "cryptophytes", "division rates"] +doi: "10.1093/plankt/fbx029" +--- + diff --git a/content/publication/heal-2017/cite.bib b/content/publication/heal-2017/cite.bib new file mode 100644 index 0000000..08126a2 --- /dev/null +++ b/content/publication/heal-2017/cite.bib @@ -0,0 +1,14 @@ +@article{Heal2017, + abstract = {Organisms within all domains of life require the cofactor cobalamin (vitamin B 12), which is produced only by a subset of bacteria and archaea. On the basis of genomic analyses, cobalamin biosynthesis in marine systems has been inferred in three main groups: select heterotrophic Proteobacteria, chemoautotrophic Thaumarchaeota, and photoautotrophic Cyanobacteria. Culture work demonstrates that many Cyanobacteria do not synthesize cobalamin but rather produce pseudocobalamin, challenging the connection between the occurrence of cobalamin biosynthesis genes and production of the compound in marine ecosystems. Here we show that cobalamin and pseudocobalamin coexist in the surface ocean, have distinct microbial sources, and support different enzymatic demands. Even in the presence of cobalamin, Cyanobacteria synthesize pseudocobalamin likely reflecting their retention of an oxygen-independent pathway to produce pseudocobalamin, which is used as a cofactor in their specialized methionine synthase (MetH). This contrasts a model diatom, Thalassiosira pseudonana, which transported pseudocobalamin into the cell but was unable to use pseudocobalamin in its homolog of MetH. Our genomic and culture analyses showed that marine Thaumarchaeota and select heterotrophic bacteria produce cobalamin. This indicates that cobalamin in the surface ocean is a result of de novo synthesis by heterotrophic bacteria or via modification of closely related compounds like cyanobacterially produced pseudocobalamin. Deeper in the water column, our study implicates Thaumarchaeota as major producers of cobalamin based on genomic potential, cobalamin cell quotas, and abundance. Together, these findings establish the distinctive roles played by abundant prokaryotes in cobalamin-based microbial interdependencies that sustain community structure and function in the ocean.}, + author = {Heal, K.R. and Qin, W. and Ribalet, F. and Bertagnolli, A.D. and Coyote-Maestas, W. and Hmelo, L.R. and Moffett, J.W. and Devol, A.H. and Armbrust, E.V. and Stahl, D.A. and Ingalls, A.E.}, + doi = {10.1073/pnas.1608462114}, + file = {:Users/ribalet/Library/Application Support/Mendeley Desktop/Downloaded/Heal et al. - 2017 - Two distinct pools of Binf12infanalogs reveal community interdependencies in the ocean.pdf:pdf}, + issn = {10916490}, + journal = {Proceedings of the National Academy of Sciences of the United States of America}, + keywords = {B 12,Cobalamin,Cyanobacteria,Pseudocobalamin,Thaumarchaeota}, + number = {2}, + title = {Two distinct pools of B12 analogs reveal community interdependencies in the ocean}, + volume = {114}, + year = {2017} +} + diff --git a/content/publication/heal-2017/featured.png b/content/publication/heal-2017/featured.png new file mode 100644 index 0000000..6f623ba Binary files /dev/null and b/content/publication/heal-2017/featured.png differ diff --git a/content/publication/heal-2017/index.md b/content/publication/heal-2017/index.md new file mode 100644 index 0000000..6352ff2 --- /dev/null +++ b/content/publication/heal-2017/index.md @@ -0,0 +1,13 @@ +--- +title: "Two distinct pools of B12 analogs reveal community interdependencies in the ocean" +date: 2017-01-01 +publishDate: 2020-03-09T17:46:51.931106Z +authors: ["K.R. Heal", "W. Qin", "F. Ribalet", "A.D. Bertagnolli", "W. Coyote-Maestas", "L.R. Hmelo", "J.W. Moffett", "A.H. Devol", "E.V. Armbrust", "D.A. Stahl", "A.E. Ingalls"] +publication_types: ["2"] +abstract: "Organisms within all domains of life require the cofactor cobalamin (vitamin B 12), which is produced only by a subset of bacteria and archaea. On the basis of genomic analyses, cobalamin biosynthesis in marine systems has been inferred in three main groups: select heterotrophic Proteobacteria, chemoautotrophic Thaumarchaeota, and photoautotrophic Cyanobacteria. Culture work demonstrates that many Cyanobacteria do not synthesize cobalamin but rather produce pseudocobalamin, challenging the connection between the occurrence of cobalamin biosynthesis genes and production of the compound in marine ecosystems. Here we show that cobalamin and pseudocobalamin coexist in the surface ocean, have distinct microbial sources, and support different enzymatic demands. Even in the presence of cobalamin, Cyanobacteria synthesize pseudocobalamin likely reflecting their retention of an oxygen-independent pathway to produce pseudocobalamin, which is used as a cofactor in their specialized methionine synthase (MetH). This contrasts a model diatom, Thalassiosira pseudonana, which transported pseudocobalamin into the cell but was unable to use pseudocobalamin in its homolog of MetH. Our genomic and culture analyses showed that marine Thaumarchaeota and select heterotrophic bacteria produce cobalamin. This indicates that cobalamin in the surface ocean is a result of de novo synthesis by heterotrophic bacteria or via modification of closely related compounds like cyanobacterially produced pseudocobalamin. Deeper in the water column, our study implicates Thaumarchaeota as major producers of cobalamin based on genomic potential, cobalamin cell quotas, and abundance. Together, these findings establish the distinctive roles played by abundant prokaryotes in cobalamin-based microbial interdependencies that sustain community structure and function in the ocean." +featured: false +publication: "*Proceedings of the National Academy of Sciences of the United States of America*" +tags: ["B 12", "Cobalamin", "Cyanobacteria", "Pseudocobalamin", "Thaumarchaeota"] +doi: "10.1073/pnas.1608462114" +--- + diff --git a/content/publication/heal-2021/cite.bib b/content/publication/heal-2021/cite.bib new file mode 100644 index 0000000..af9ccf6 --- /dev/null +++ b/content/publication/heal-2021/cite.bib @@ -0,0 +1,10 @@ +@article{Heal2021 + abstract = {Microscopic phytoplankton transform 100 million tons of inorganic carbon into thousands of different organic compounds each day. The structure of each chemical is critical to its biological and ecosystem function, yet the diversity of biomolecules produced by marine microbial communities remained mainly unexplored, especially small polar molecules which are often considered the currency of the microbial loop. Phytoplankton transform inorganic carbon into thousands of biomolecules that represent an important pool of fixed carbon, nitrogen, and sulfur in the surface ocean. Metabolite production differs between phytoplankton, and the flux of these molecules through the microbial food web depends on compound-specific bioavailability to members of a wider microbial community. Yet relatively little is known about the diversity or concentration of metabolites within marine plankton. Here, we compare 313 polar metabolites in 21 cultured phytoplankton species and in natural planktonic communities across environmental gradients to show that bulk community metabolomes reflect the chemical composition of the phytoplankton community. We also show that groups of compounds have similar patterns across space and taxonomy, suggesting that the concentrations of these compounds in the environment are controlled by similar sources and sinks. We quantify several compounds in the surface ocean that represent substantial understudied pools of labile carbon. For example, the N-containing metabolite homarine was up to 3% of particulate carbon and is produced in high concentrations by cultured Synechococcus , and S-containing gonyol accumulated up to 2.5 nM in surface particles and likely originates from dinoflagellates or haptophytes. Our results show that phytoplankton composition directly shapes the carbon composition of the surface ocean. Our findings suggest that in order to access these pools of bioavailable carbon, the wider microbial community must be adapted to phytoplankton community composition. IMPORTANCE Microscopic phytoplankton transform 100 million tons of inorganic carbon into thousands of different organic compounds each day. The structure of each chemical is critical to its biological and ecosystem function, yet the diversity of biomolecules produced by marine microbial communities remained mainly unexplored, especially small polar molecules which are often considered the currency of the microbial loop. Here, we explore the abundance and diversity of small biomolecules in planktonic communities across ecological gradients in the North Pacific and within 21 cultured phytoplankton species. Our work demonstrates that phytoplankton diversity is an important determinant of the chemical composition of the highly bioavailable pool of organic carbon in the ocean, and we highlight understudied yet abundant compounds in both the environment and cultured organisms. These findings add to understanding of how the chemical makeup of phytoplankton shapes marine microbial communities where the ability to sense and use biomolecules depends on the chemical structure.}, + author = {Heal, Katherine R. and Durham, Bryndan P. and Boysen, Angela K. and Carlson, Laura T. and Qin, Wei and Ribalet, Fran{\c{c}ois and White, Angelicque E. and Bundy, Randelle M. and Armbrust, E. Virginia and Ingalls, Anitra E.}, + doi = {10.1128/MSYSTEMS.01334-20}, + journal = {mSystems}, + number = {3}, + title = {Marine Community Metabolomes Carry Fingerprints of Phytoplankton Community Composition}, + volume = {6}, + year = {2021} +} diff --git a/content/publication/heal-2021/featured.png b/content/publication/heal-2021/featured.png new file mode 100644 index 0000000..9490a72 Binary files /dev/null and b/content/publication/heal-2021/featured.png differ diff --git a/content/publication/heal-2021/index.md b/content/publication/heal-2021/index.md new file mode 100644 index 0000000..1cdec8c --- /dev/null +++ b/content/publication/heal-2021/index.md @@ -0,0 +1,14 @@ +--- +title : "Marine Community Metabolomes Carry Fingerprints of Phytoplankton Community Composition" +date : 2021-04-06 +publishDate: 2021-06-01T17:46:51.934135Z +authors : ["Katherine R. Heal", "Bryndan P. Durham", "Angela K. Boysen", "Laura T. Carlson", "Wei Qin", "Francois Ribalet", "Angelicque E. White", "Randelle Bundy", "E. Virginia Armbrust", "Anitra E. Ingalls"] +publication_types : ["2"] +publication : "*mSystems*" +abstract : "Microscopic phytoplankton transform 100 million tons of inorganic carbon into thousands of different organic compounds each day. The structure of each chemical is critical to its biological and ecosystem function, yet the diversity of biomolecules produced by marine microbial communities remained mainly unexplored, especially small polar molecules which are often considered the currency of the microbial loop. Phytoplankton transform inorganic carbon into thousands of biomolecules that represent an important pool of fixed carbon, nitrogen, and sulfur in the surface ocean. Metabolite production differs between phytoplankton, and the flux of these molecules through the microbial food web depends on compound-specific bioavailability to members of a wider microbial community. Yet relatively little is known about the diversity or concentration of metabolites within marine plankton. Here, we compare 313 polar metabolites in 21 cultured phytoplankton species and in natural planktonic communities across environmental gradients to show that bulk community metabolomes reflect the chemical composition of the phytoplankton community. We also show that groups of compounds have similar patterns across space and taxonomy, suggesting that the concentrations of these compounds in the environment are controlled by similar sources and sinks. We quantify several compounds in the surface ocean that represent substantial understudied pools of labile carbon. For example, the N-containing metabolite homarine was up to 3% of particulate carbon and is produced in high concentrations by cultured Synechococcus , and S-containing gonyol accumulated up to 2.5 nM in surface particles and likely originates from dinoflagellates or haptophytes. Our results show that phytoplankton composition directly shapes the carbon composition of the surface ocean. Our findings suggest that in order to access these pools of bioavailable carbon, the wider microbial community must be adapted to phytoplankton community composition. IMPORTANCE Microscopic phytoplankton transform 100 million tons of inorganic carbon into thousands of different organic compounds each day. The structure of each chemical is critical to its biological and ecosystem function, yet the diversity of biomolecules produced by marine microbial communities remained mainly unexplored, especially small polar molecules which are often considered the currency of the microbial loop. Here, we explore the abundance and diversity of small biomolecules in planktonic communities across ecological gradients in the North Pacific and within 21 cultured phytoplankton species. Our work demonstrates that phytoplankton diversity is an important determinant of the chemical composition of the highly bioavailable pool of organic carbon in the ocean, and we highlight understudied yet abundant compounds in both the environment and cultured organisms. These findings add to understanding of how the chemical makeup of phytoplankton shapes marine microbial communities where the ability to sense and use biomolecules depends on the chemical structure." +featured : false +projects : [] +tags : [] +doi : "10.1128/MSYSTEMS.01334-20" +math : false +--- diff --git a/content/publication/henderikx-2020/cite.bib b/content/publication/henderikx-2020/cite.bib new file mode 100644 index 0000000..018cc1f --- /dev/null +++ b/content/publication/henderikx-2020/cite.bib @@ -0,0 +1,17 @@ +@article{HenderikxFreitas2020, +abstract = {Cross-platform observing systems are requisite to capturing the temporal and spatial dynamics of particles in the ocean. We present simultaneous observations of bulk optical properties, including the particulate beam attenuation (cp) and backscattering (bbp) coefficients, and particle size distributions collected in the North Pacific Subtropical Gyre. Clear and coherent diel cycles are observed in all bulk and size-fractionated optical proxies for particle biomass. We show evidence linking diurnal increases in cp and bbp to daytime particle growth and division of cells, with particles <7µm driving the daily cycle of particle production and loss within the mixed layer. Flow cytometry data reveal the nitrogen-fixing cyanobacterium Crocosphaera (∼4−7µm) to be an important driver of cp at the time of sampling, whereas Prochlorococcus dynamics (∼0.5µm) were essential to reproducing temporal variability in bbp. This study is a step towards improved characterization of the particle size range represented by in situ bulk optical properties and a better understanding of the mechanisms that drive variability in particle production in the oligotrophic open ocean.}, +author = {{Henderikx Freitas}, Fernanda and Dugenne, Mathilde and Ribalet, Francois and Hynes, Annette and Barone, Benedetto and Karl, David and White, Angelicque}, +doi = {10.1364/ao.394123}, +issn = {1559-128X}, +journal = {Applied Optics}, +keywords = {Forward scattering,Frequency measurement,Optical measurement,Optical properties,Optical signals,Refractive index}, +month = {jun}, +number = {22}, +pages = {6702--6716}, +publisher = {The Optical Society}, +title = {{Diel variability of bulk optical properties associated with the growth and division of small phytoplankton in the North Pacific Subtropical Gyre}}, +url = {https://www.osapublishing.org/viewmedia.cfm?uri=ao-59-22-6702&seq=0&html=true https://www.osapublishing.org/abstract.cfm?uri=ao-59-22-6702 https://www.osapublishing.org/ao/abstract.cfm?uri=ao-59-22-6702}, +volume = {59}, +year = {2020} +} + diff --git a/content/publication/henderikx-2020/featured.png b/content/publication/henderikx-2020/featured.png new file mode 100644 index 0000000..0b0650b Binary files /dev/null and b/content/publication/henderikx-2020/featured.png differ diff --git a/content/publication/henderikx-2020/index.md b/content/publication/henderikx-2020/index.md new file mode 100644 index 0000000..d88e968 --- /dev/null +++ b/content/publication/henderikx-2020/index.md @@ -0,0 +1,13 @@ +--- +title: "Diel variability of bulk optical properties associated with the growth and division of small phytoplankton in the North Pacific Subtropical Gyre " +date: 2020-07-27 +publishDate: 2020-07-27T17:46:51.934135Z +authors: ["F. Henderikx Freitas", "M. Dugenne", "F. Ribalet", "A. Hynes","B. Barone", "D.M. Karl","A.E. White"] +publication_types: ["2"] +abstract: "Cross-platform observing systems are requisite to capturing the temporal and spatial dynamics of particles in the ocean. We present simultaneous observations of bulk optical properties, including the particulate beam attenuation (cp) and backscattering (bbp) coefficients, and particle size distributions collected in the North Pacific Subtropical Gyre. Clear and coherent diel cycles are observed in all bulk and size-fractionated optical proxies for particle biomass. We show evidence linking diurnal increases in cp and bbp to daytime particle growth and division of cells, with particles <7µm driving the daily cycle of particle production and loss within the mixed layer. Flow cytometry data reveal the nitrogen-fixing cyanobacterium Crocosphaera (∼4−7µm) to be an important driver of cp at the time of sampling, whereas Prochlorococcus dynamics (∼0.5µm) were essential to reproducing temporal variability in bbp. This study is a step towards improved characterization of the particle size range represented by in situ bulk optical properties and a better understanding of the mechanisms that drive variability in particle production in the oligotrophic open ocean." +featured: false +publication: "*Applied Optics*" +url_pdf: "https://doi.org/10.1364/AO.394123" +doi: "10.1364/AO.394123" +--- + diff --git a/content/publication/howard-2017/cite.bib b/content/publication/howard-2017/cite.bib new file mode 100644 index 0000000..e7e2697 --- /dev/null +++ b/content/publication/howard-2017/cite.bib @@ -0,0 +1,15 @@ +@article{Howard2017, + abstract = {In situ oxygen tracers (triple oxygen isotope and oxygen/argon ratios) were used to evaluate meridional trends in surface biological production and export efficiency across ̃8000 km of the tropical and subtropical South Atlantic in March–May 2013. We used observations of picophytoplankton, nanophytoplankton, and microphytoplankton to evaluate community structure and diversity and assessed the relationships of these characteristics with production, export efficiency, and particulate organic carbon (POC) fluxes. Rates of productivity were relatively uniform along most of the transect with net community production (NCP) between 0 and 10 mmol O2 m−2 d−1, gross primary production (GPP) between 40 and 100 mmol O2 m−2 d−1, and NCP/GPP, a measure of export efficiency, ranging from 0.1 to 0.2 (0.05–0.1 in carbon units). However, notable exceptions to this basin-scale homogeneity included two locations with highly enhanced NCP and export efficiency compared to surrounding regions. Export of POC and particulate nitrogen, derived from sediment traps, correlated with GPP across the transect, over which the surface community was dominated numerically by picophytoplankton. NCP, however, did not correlate with POC flux; the mean difference between NCP and POC flux was similar to published estimates of dissolved organic carbon export from the surface ocean. The interrelated rates of production presented in this work contribute to the understanding, building on the framework of better-studied ocean basins, of how carbon is biologically transported between the atmosphere and the deep ocean.}, + author = {Howard, E.M. M. and Durkin, C.A. A. and Hennon, G.M.M. M.M. and Ribalet, F. and Stanley, R.H.R. H.R.}, + doi = {10.1002/2016GB005488}, + file = {:Users/ribalet/Library/Application Support/Mendeley Desktop/Downloaded/Howard et al. - 2017 - Biological production, export efficiency, and phytoplankton communities across 8000 km of the South Atlantic.pdf:pdf}, + issn = {19449224}, + journal = {Global Biogeochemical Cycles}, + keywords = {argon,carbon flux,gross primary production,net community production,oxygen,triple oxygen isotopes}, + number = {7}, + pages = {1066--1088}, + title = {Biological production, export efficiency, and phytoplankton communities across 8000 km of the South Atlantic}, + volume = {31}, + year = {2017} +} + diff --git a/content/publication/howard-2017/featured.png b/content/publication/howard-2017/featured.png new file mode 100644 index 0000000..4629cb8 Binary files /dev/null and b/content/publication/howard-2017/featured.png differ diff --git a/content/publication/howard-2017/index.md b/content/publication/howard-2017/index.md new file mode 100644 index 0000000..db50b2a --- /dev/null +++ b/content/publication/howard-2017/index.md @@ -0,0 +1,13 @@ +--- +title: "Biological production, export efficiency, and phytoplankton communities across 8000 km of the South Atlantic" +date: 2017-01-01 +publishDate: 2020-03-09T17:46:51.928788Z +authors: ["E.M. M. Howard", "C.A. A. Durkin", "G.M.M. M.M. Hennon", "F. Ribalet", "R.H.R. H.R. Stanley"] +publication_types: ["2"] +abstract: "In situ oxygen tracers (triple oxygen isotope and oxygen/argon ratios) were used to evaluate meridional trends in surface biological production and export efficiency across ̃8000 km of the tropical and subtropical South Atlantic in March–May 2013. We used observations of picophytoplankton, nanophytoplankton, and microphytoplankton to evaluate community structure and diversity and assessed the relationships of these characteristics with production, export efficiency, and particulate organic carbon (POC) fluxes. Rates of productivity were relatively uniform along most of the transect with net community production (NCP) between 0 and 10 mmol O2 m−2 d−1, gross primary production (GPP) between 40 and 100 mmol O2 m−2 d−1, and NCP/GPP, a measure of export efficiency, ranging from 0.1 to 0.2 (0.05–0.1 in carbon units). However, notable exceptions to this basin-scale homogeneity included two locations with highly enhanced NCP and export efficiency compared to surrounding regions. Export of POC and particulate nitrogen, derived from sediment traps, correlated with GPP across the transect, over which the surface community was dominated numerically by picophytoplankton. NCP, however, did not correlate with POC flux; the mean difference between NCP and POC flux was similar to published estimates of dissolved organic carbon export from the surface ocean. The interrelated rates of production presented in this work contribute to the understanding, building on the framework of better-studied ocean basins, of how carbon is biologically transported between the atmosphere and the deep ocean." +featured: false +publication: "*Global Biogeochemical Cycles*" +tags: ["argon", "carbon flux", "gross primary production", "net community production", "oxygen", "triple oxygen isotopes"] +doi: "10.1002/2016GB005488" +--- + diff --git a/content/publication/howe-2013/cite.bib b/content/publication/howe-2013/cite.bib new file mode 100644 index 0000000..93ebe07 --- /dev/null +++ b/content/publication/howe-2013/cite.bib @@ -0,0 +1,14 @@ +@article{Howe2013, + abstract = {SQLShare is a Web-based application that emphasizes a simple upload-query-share protocol over conventional database design and uses ad hoc interactive query over general-purpose programming. Here, a case study examines the use of SQLShare as an alternative to script-based scientific workflows for a project in observational biological oceanography. © 1999-2011 IEEE.}, + author = {Howe, B. and Halperin, D. and Ribalet, F. and Chitnis, S. and Armbrust, E.V.}, + doi = {10.1109/MCSE.2013.42}, + file = {:Users/ribalet/Library/Application Support/Mendeley Desktop/Downloaded/Howe et al. - 2013 - Collaborative science workflows in SQL.pdf:pdf}, + issn = {15219615}, + journal = {Computing in Science and Engineering}, + keywords = {database applications,scientific computing,scientific databases,workflow management}, + number = {3}, + title = {Collaborative science workflows in SQL}, + volume = {15}, + year = {2013} +} + diff --git a/content/publication/howe-2013/featured.png b/content/publication/howe-2013/featured.png new file mode 100644 index 0000000..42f57c7 Binary files /dev/null and b/content/publication/howe-2013/featured.png differ diff --git a/content/publication/howe-2013/index.md b/content/publication/howe-2013/index.md new file mode 100644 index 0000000..a90807f --- /dev/null +++ b/content/publication/howe-2013/index.md @@ -0,0 +1,13 @@ +--- +title: "Collaborative science workflows in SQL" +date: 2013-01-01 +publishDate: 2020-03-09T17:46:51.935624Z +authors: ["B. Howe", "D. Halperin", "F. Ribalet", "S. Chitnis", "E.V. Armbrust"] +publication_types: ["2"] +abstract: "SQLShare is a Web-based application that emphasizes a simple upload-query-share protocol over conventional database design and uses ad hoc interactive query over general-purpose programming. Here, a case study examines the use of SQLShare as an alternative to script-based scientific workflows for a project in observational biological oceanography. © 1999-2011 IEEE." +featured: false +publication: "*Computing in Science and Engineering*" +tags: ["database applications", "scientific computing", "scientific databases", "workflow management"] +doi: "10.1109/MCSE.2013.42" +--- + diff --git a/content/publication/hynes_2024/cite.bib b/content/publication/hynes_2024/cite.bib new file mode 100644 index 0000000..6c14a98 --- /dev/null +++ b/content/publication/hynes_2024/cite.bib @@ -0,0 +1,11 @@ +@article{hynes_high-frequency_2024 + abstract = {The Hawaii Ocean Time-series (HOT) at Station ALOHA (22.75°N, 158°W) in the North Pacific Subtropical Gyre (NPSG) serves as a critical vantage point for observing plankton biomass production and its ecological implications. However, the HOT program's near-monthly sampling frequency does not capture shorter time scale variability in phytoplankton populations. To address this gap, we deployed the SeaFlow flow cytometer for continuous monitoring during HOT cruises from 2014 to 2021. This approach allowed us to examine variations in the surface abundance and cell carbon content of specific phytoplankton groups: the cyanobacteria Prochlorococcus, Synechococcus, and Crocosphaera as well as a range of small eukaryotic phytoplankton (≤ 5 μm). Our data showed that daily to monthly variability in Prochlorococcus and Synechococcus abundance matches seasonal and interannual variability, while small eukaryotic phytoplankton and Crocosphaera showed the highest seasonal and interannual fluctuations. The study also found that eukaryotic phytoplankton and Crocosphaera had higher median cellular growth rates (0.076 and 0.090h−1, respectively) compared to Prochlorococcus and Synechococcus (0.037 and 0.045h−1, respectively). These variances in abundance and growth rates indicate that shifts in the community structure significantly impact primary productivity in the NPSG. Our results underscore the importance of daily to monthly phytoplankton dynamics in ecosystem function and carbon cycling.}, + author = {Hynes, Annette M. and Winter, Jordan and Berthiaume, Chris T. and Shimabukuro, Eric and Cain, Kelsy and White, Angelicque and Armbrust, E. Virginia and Ribalet, François}, + doi = {10.1002/lno.12683}, + journal = {Limnology and Oceanography}, + number = {11}, + pages = {2516--2531}, + title = {High-frequency sampling captures variability in phytoplankton population-specific periodicity, growth, and productivity}, + volume = {69}, + year = {2024} +} diff --git a/content/publication/hynes_2024/featured.png b/content/publication/hynes_2024/featured.png new file mode 100644 index 0000000..825f97d Binary files /dev/null and b/content/publication/hynes_2024/featured.png differ diff --git a/content/publication/hynes_2024/index.md b/content/publication/hynes_2024/index.md new file mode 100644 index 0000000..57dc452 --- /dev/null +++ b/content/publication/hynes_2024/index.md @@ -0,0 +1,13 @@ +--- +title : "High-frequency sampling captures variability in phytoplankton population-specific periodicity, growth, and productivity" +date : "2024-12-01T00:00:00" +authors : ["Annette M. Hynes", "Jordan Winter", "Chris T. Berthiaume", "Eric Shimabukuro", "Kelsy Cain", "Angelicque White", "E. Virginia Armbrust", "François Ribalet"] +publication_types : ["2"] +publication : "in *Limnology and Oceanography*" +abstract : "The Hawaii Ocean Time-series (HOT) at Station ALOHA (22.75°N, 158°W) in the North Pacific Subtropical Gyre (NPSG) serves as a critical vantage point for observing plankton biomass production and its ecological implications. However, the HOT program's near-monthly sampling frequency does not capture shorter time scale variability in phytoplankton populations. To address this gap, we deployed the SeaFlow flow cytometer for continuous monitoring during HOT cruises from 2014 to 2021. This approach allowed us to examine variations in the surface abundance and cell carbon content of specific phytoplankton groups: the cyanobacteria Prochlorococcus, Synechococcus, and Crocosphaera as well as a range of small eukaryotic phytoplankton (≤ 5 μm). Our data showed that daily to monthly variability in Prochlorococcus and Synechococcus abundance matches seasonal and interannual variability, while small eukaryotic phytoplankton and Crocosphaera showed the highest seasonal and interannual fluctuations. The study also found that eukaryotic phytoplankton and Crocosphaera had higher median cellular growth rates (0.076 and 0.090h−1, respectively) compared to Prochlorococcus and Synechococcus (0.037 and 0.045h−1, respectively). These variances in abundance and growth rates indicate that shifts in the community structure significantly impact primary productivity in the NPSG. Our results underscore the importance of daily to monthly phytoplankton dynamics in ecosystem function and carbon cycling." +featured : false +projects : [] +tags : [] +doi : "10.1002/lno.12683" +math : false +--- diff --git a/content/publication/hyrkas-2016/cite.bib b/content/publication/hyrkas-2016/cite.bib new file mode 100644 index 0000000..55f39f8 --- /dev/null +++ b/content/publication/hyrkas-2016/cite.bib @@ -0,0 +1,18 @@ +@article{Hyrkas2016, + abstract = {Motivation: Recent technological innovations in flow cytometry now allow oceanographers to collect high-frequency flow cytometry data from particles in aquatic environments on a scale far surpassing conventional flow cytometers. The SeaFlow cytometer continuously profiles microbial phytoplankton populations across thousands of kilometers of the surface ocean. The data streams produced by instruments such as SeaFlow challenge the traditional sample-by-sample approach in cytometric analysis and highlight the need for scalable clustering algorithms to extract population information from these large-scale, high-frequency flow cytometers.Results: We explore how available algorithms commonly used for medical applications perform at classification of such a large-scale, environmental flow cytometry data. We apply large-scale Gaussian mixture models to massive datasets using Hadoop. This approach outperforms current state-of-the-art cytometry classification algorithms in accuracy and can be coupled with manual or automatic partitioning of data into homogeneous sections for further classification gains. We propose the Gaussian mixture model with partitioning approach for classification of large-scale, high-frequency flow cytometry data.}, + author = {Hyrkas, Jeremy and Clayton, Sophie and Ribalet, Francois and Halperin, Daniel and Armbrust, E. Virginia and Howe, Bill}, + doi = {10.1093/bioinformatics/btv594}, + file = {:Users/ribalet/Library/Application Support/Mendeley Desktop/Downloaded/Hyrkas et al. - 2016 - Scalable clustering algorithms for continuous environmental flow cytometry.pdf:pdf}, + journal = {Bioinformatics}, + keywords = {r28958}, + language = {English}, + mendeley-tags = {r28958}, + number = {3}, + pages = {417--423}, + pmid = {26476780}, + title = {Scalable clustering algorithms for continuous environmental flow cytometry}, + url = {http://bioinformatics.oxfordjournals.org/content/32/3/417.abstract}, + volume = {32}, + year = {2016} +} + diff --git a/content/publication/hyrkas-2016/featured.png b/content/publication/hyrkas-2016/featured.png new file mode 100644 index 0000000..95164a6 Binary files /dev/null and b/content/publication/hyrkas-2016/featured.png differ diff --git a/content/publication/hyrkas-2016/index.md b/content/publication/hyrkas-2016/index.md new file mode 100644 index 0000000..9014447 --- /dev/null +++ b/content/publication/hyrkas-2016/index.md @@ -0,0 +1,14 @@ +--- +title: "Scalable clustering algorithms for continuous environmental flow cytometry" +date: 2016-01-01 +publishDate: 2020-03-09T17:46:51.931816Z +authors: ["Jeremy Hyrkas", "Sophie Clayton", "Francois Ribalet", "Daniel Halperin", "E. Virginia Armbrust", "Bill Howe"] +publication_types: ["2"] +abstract: "Motivation: Recent technological innovations in flow cytometry now allow oceanographers to collect high-frequency flow cytometry data from particles in aquatic environments on a scale far surpassing conventional flow cytometers. The SeaFlow cytometer continuously profiles microbial phytoplankton populations across thousands of kilometers of the surface ocean. The data streams produced by instruments such as SeaFlow challenge the traditional sample-by-sample approach in cytometric analysis and highlight the need for scalable clustering algorithms to extract population information from these large-scale, high-frequency flow cytometers.Results: We explore how available algorithms commonly used for medical applications perform at classification of such a large-scale, environmental flow cytometry data. We apply large-scale Gaussian mixture models to massive datasets using Hadoop. This approach outperforms current state-of-the-art cytometry classification algorithms in accuracy and can be coupled with manual or automatic partitioning of data into homogeneous sections for further classification gains. We propose the Gaussian mixture model with partitioning approach for classification of large-scale, high-frequency flow cytometry data." +featured: false +publication: "*Bioinformatics*" +tags: ["r28958"] +url_pdf: "http://bioinformatics.oxfordjournals.org/content/32/3/417.abstract" +doi: "10.1093/bioinformatics/btv594" +--- + diff --git a/content/publication/hyun-2023/cite.bib b/content/publication/hyun-2023/cite.bib new file mode 100644 index 0000000..1ebfe19 --- /dev/null +++ b/content/publication/hyun-2023/cite.bib @@ -0,0 +1,12 @@ +@article{Hyun2023, + abstract = {The ocean is filled with microscopic microalgae, called phytoplankton, which together are responsible for as much photosynthesis as all plants on land combined. Our ability to predict their response to the warming ocean relies on understanding how the dynamics of phytoplankton populations is influenced by changes in environmental conditions. One powerful technique to study the dynamics of phytoplankton is flow cytometry which measures the optical properties of thousands of individual cells per second. Today, oceanographers are able to collect flow cytometry data in real time onboard a moving ship, providing them with fine-scale resolution of the distribution of phytoplankton across thousands of kilometers. One of the current challenges is to understand how these small- and large-scale variations relate to environmental conditions, such as nutrient availability, temperature, light and ocean currents. In this paper we propose a novel sparse mixture of multivariate regressions model to estimate the time-varying phytoplankton subpopulations while simultaneously identifying the specific environmental covariates that are predictive of the observed changes to these subpopulations. We demonstrate the usefulness and interpretability of the approach using both synthetic data and real observations collected on an oceanographic cruise conducted in the northeast Pacific in the spring of 2017.}, + author = {Sangwon Hyun and Mattias Rolf Cape and Francois Ribalet and Jacob Bien}, + doi = {10.1214/22-AOAS1631}, + issn = {1932-6157}, + issue = {1}, + journal = {Annals of Applied Statistics}, + pages = {357-377}, + title = {Modeling cell populations measured by flow cytometry with covariates using sparse mixture of regressions}, + volume = {17}, + year = {2023}, +} diff --git a/content/publication/hyun-2023/featured.png b/content/publication/hyun-2023/featured.png new file mode 100644 index 0000000..7cf4d38 Binary files /dev/null and b/content/publication/hyun-2023/featured.png differ diff --git a/content/publication/hyun-2023/index.md b/content/publication/hyun-2023/index.md new file mode 100644 index 0000000..4ed8594 --- /dev/null +++ b/content/publication/hyun-2023/index.md @@ -0,0 +1,13 @@ +--- +title : "Modeling cell populations measured by flow cytometry with covariates using sparse mixture of regressions" +date : "2023-01-30" +authors : ["Sangwon Hyun", "Mattias Rolf Cape", "Francois Ribalet", "Jacob Bien"] +publication_types : ["2"] +publication : "in *Annals of Applied Statistics*" +abstract : "The ocean is filled with microscopic microalgae, called phytoplankton, which together are responsible for as much photosynthesis as all plants on land combined. Our ability to predict their response to the warming ocean relies on understanding how the dynamics of phytoplankton populations is influenced by changes in environmental conditions. One powerful technique to study the dynamics of phytoplankton is flow cytometry which measures the optical properties of thousands of individual cells per second. Today, oceanographers are able to collect flow cytometry data in real time onboard a moving ship, providing them with fine-scale resolution of the distribution of phytoplankton across thousands of kilometers. One of the current challenges is to understand how these small- and large-scale variations relate to environmental conditions, such as nutrient availability, temperature, light and ocean currents. In this paper we propose a novel sparse mixture of multivariate regressions model to estimate the time-varying phytoplankton subpopulations while simultaneously identifying the specific environmental covariates that are predictive of the observed changes to these subpopulations. We demonstrate the usefulness and interpretability of the approach using both synthetic data and real observations collected on an oceanographic cruise conducted in the northeast Pacific in the spring of 2017." +featured : true +projects : [] +tags : [] +doi : "10.1214/22-AOAS1631" +math : false +--- diff --git a/content/publication/jones-2021/cite.bib b/content/publication/jones-2021/cite.bib new file mode 100644 index 0000000..334ce50 --- /dev/null +++ b/content/publication/jones-2021/cite.bib @@ -0,0 +1,11 @@ +@article{Jones2021, +abstract = {Automated, ship-board flow cytometers provide high-resolution maps of phytoplankton composition over large swaths of the world's oceans. They therefore pave the way for understanding how environmental conditions shape community structure. Identification of community changes along a cruise transect commonly segments the data into distinct regions. However, existing segmentation methods are generally not applicable to flow cytometry data, as these data are recorded as ‘point cloud' data, with hundreds or thousands of particles measured during each time interval. Moreover, nonparametric segmentation methods that do not rely on prior knowledge of the number of species are desirable to map community shifts. We present CytoSegmenter, a kernel-based change-point estimation method for segmenting point cloud data. Our method allows us to represent and summarize a point cloud of data points by a single element in a Hilbert space. The change-point locations can be found using a fast dynamic programming algorithm. Through an analysis of 12 cruises, we demonstrate that CytoSegmenter allows us to locate abrupt changes in phytoplankton community structure. We show that the changes in community structure generally coincide with changes in the temperature and salinity of the ocean. We also illustrate how the main parameter of CytoSegmenter can be easily calibrated using limited auxiliary annotated data. CytoSegmenter is generally applicable for segmenting series of point cloud data from any domain. Moreover, it readily scales to thousands of point clouds, each containing thousands of points. In the context of flow cytometry data collected during research cruises, it does not require prior clustering of particles to define taxa labels, eliminating a potential source of error. This represents an important advance in automating the analysis of large datasets now emerging in biological oceanography and other fields. It also allows for the approach to be applied during research cruises.}, +author = {Jones, Corinne and Clayton, Sophie and Ribalet, Fran{\c{c}}ois and Armbrust, E. Virginia and Harchaoui, Zaid}, +doi = {10.1111/2041-210X.13647}, +journal = {Methods in Ecology and Evolution}, +pages = {1--12}, +title = {A kernel-based change detection method to map shifts in phytoplankton communities measured by flow cytometry}, +volume = {00}, +year = {2021} +} + diff --git a/content/publication/jones-2021/featured.png b/content/publication/jones-2021/featured.png new file mode 100644 index 0000000..87ac4d8 Binary files /dev/null and b/content/publication/jones-2021/featured.png differ diff --git a/content/publication/jones-2021/index.md b/content/publication/jones-2021/index.md new file mode 100644 index 0000000..e811e47 --- /dev/null +++ b/content/publication/jones-2021/index.md @@ -0,0 +1,13 @@ +--- +title: "A kernel-based change detection method to map shifts in phytoplankton communities measured by flow cytometry" +date: 2021-06-25 +publishDate: 2021-05-24T17:46:51.934135Z +authors: ["C. Jones", "S. Clayton", "F. Ribalet", "E.V. Armbrust" , "Z. Harchaoui"] +publication_types: ["2"] +abstract: "Automated, ship-board flow cytometers provide high-resolution maps of phytoplankton composition over large swaths of the world's oceans. They therefore pave the way for understanding how environmental conditions shape community structure. Identification of community changes along a cruise transect commonly segments the data into distinct regions. However, existing segmentation methods are generally not applicable to flow cytometry data, as these data are recorded as ‘point cloud' data, with hundreds or thousands of particles measured during each time interval. Moreover, nonparametric segmentation methods that do not rely on prior knowledge of the number of species are desirable to map community shifts. We present CytoSegmenter, a kernel-based change-point estimation method for segmenting point cloud data. Our method allows us to represent and summarize a point cloud of data points by a single element in a Hilbert space. The change-point locations can be found using a fast dynamic programming algorithm. Through an analysis of 12 cruises, we demonstrate that CytoSegmenter allows us to locate abrupt changes in phytoplankton community structure. We show that the changes in community structure generally coincide with changes in the temperature and salinity of the ocean. We also illustrate how the main parameter of CytoSegmenter can be easily calibrated using limited auxiliary annotated data. CytoSegmenter is generally applicable for segmenting series of point cloud data from any domain. Moreover, it readily scales to thousands of point clouds, each containing thousands of points. In the context of flow cytometry data collected during research cruises, it does not require prior clustering of particles to define taxa labels, eliminating a potential source of error. This represents an important advance in automating the analysis of large datasets now emerging in biological oceanography and other fields. It also allows for the approach to be applied during research cruises." +featured: false +publication: "*Methods in Ecology and Evolution*" +url_pdf: " https://doi.org/10.1111/2041-210X.13647" +doi: "10.1111/2041-210X.13647" +--- + diff --git a/content/publication/joneskellett-2024/cite.bib b/content/publication/joneskellett-2024/cite.bib new file mode 100644 index 0000000..4fc4c88 --- /dev/null +++ b/content/publication/joneskellett-2024/cite.bib @@ -0,0 +1,7 @@ +@article{jones-kellett_amplicon_2024 + abstract = {Marine microbial ecologists seek measurements of organismal abundance and diversity at high taxonomic resolution to understand ecosystem state and function. Conventional flow cytometry accurately estimates microbial cell abundance but only discerns broad groups with distinct optical properties. While amplicon sequencing resolves more comprehensive diversity within microbiomes, it typically only provides relative organismal abundances within samples, not absolute abundance changes. Internal genomic standards offer a solution for absolute amplicon-based measures. Here, we spiked genomic standards into plankton samples from surface seawater, gathered at 46-kilometer intervals along a cruise transect spanning the southern California Current System and the oligotrophic North Pacific Subtropical Gyre. This enabled evaluation of the absolute volumetric gene copy abundances of 16S rRNA Amplicon Sequence Variants (amplified with 515Y-926R universal primers, quantitatively validated with mock communities) and cell abundances of picocyanobacteria with known genomic 16S copy numbers. Comparison of amplicon-derived cell abundances of Prochlorococcus and Synechococcus with flow cytometry data from nearby locations yielded nearly identical results (slope = 1.01; Pearson’s r = 0.9942). Our findings show that this amplicon sequencing protocol combined with genomic internal standards accurately measures absolute cell counts of marine picocyanobacteria in complex field samples. By extension, we expect this approach reasonably estimates volumetric gene copies for other amplified taxa in these samples.}, + author = {Jones-Kellett, Alexandra E and McNichol, Jesse C and Raut, Yubin and Cain, Kelsy R and Ribalet, François and Armbrust, E Virginia and Follows, Michael J and Fuhrman, Jed A}, + doi = {10.1093/ismeco/ycae115}, + journal = {ISME Communications}, + title = {Amplicon {Sequencing} with {Internal} {Standards} {Yields} {Accurate} {Picocyanobacteria} {Cell} {Abundances} as {Validated} with {Flow} {Cytometry}} +} diff --git a/content/publication/joneskellett-2024/featured.png b/content/publication/joneskellett-2024/featured.png new file mode 100644 index 0000000..b501535 Binary files /dev/null and b/content/publication/joneskellett-2024/featured.png differ diff --git a/content/publication/joneskellett-2024/index.md b/content/publication/joneskellett-2024/index.md new file mode 100644 index 0000000..63d6659 --- /dev/null +++ b/content/publication/joneskellett-2024/index.md @@ -0,0 +1,13 @@ +--- +title : "Amplicon sequencing with internal standards yields accurate picocyanobacteria cell abundances as validated with flow cytometry" +date : "2024-12-01T00:00:00" +authors : ["Alex Jones-Kellett", "ra E", "Jesse C McNichol", "Yubin Raut", "Kelsy R Cain", "François Ribalet", "E Virginia Armbrust", "Michael J Follows", "Jed A Fuhrman"] +publication_types : ["2"] +publication : "in *ISME Communications*" +abstract : "Marine microbial ecologists seek measurements of organismal abundance and diversity at high taxonomic resolution to understand ecosystem state and function. Conventional flow cytometry accurately estimates microbial cell abundance but only discerns broad groups with distinct optical properties. While amplicon sequencing resolves more comprehensive diversity within microbiomes, it typically only provides relative organismal abundances within samples, not absolute abundance changes. Internal genomic standards offer a solution for absolute amplicon-based measures. Here, we spiked genomic standards into plankton samples from surface seawater, gathered at 46-kilometer intervals along a cruise transect spanning the southern California Current System and the oligotrophic North Pacific Subtropical Gyre. This enabled evaluation of the absolute volumetric gene copy abundances of 16S rRNA Amplicon Sequence Variants (amplified with 515Y-926R universal primers, quantitatively validated with mock communities) and cell abundances of picocyanobacteria with known genomic 16S copy numbers. Comparison of amplicon-derived cell abundances of Prochlorococcus and Synechococcus with flow cytometry data from nearby locations yielded nearly identical results (slope = 1.01; Pearson’s r = 0.9942). Our findings show that this amplicon sequencing protocol combined with genomic internal standards accurately measures absolute cell counts of marine picocyanobacteria in complex field samples. By extension, we expect this approach reasonably estimates volumetric gene copies for other amplified taxa in these samples." +featured : false +projects : [] +tags : [] +doi : "10.1093/ismeco/ycae115" +math : false +--- diff --git a/content/publication/journal-article/cite.bib b/content/publication/journal-article/cite.bib deleted file mode 100644 index a7da7ac..0000000 --- a/content/publication/journal-article/cite.bib +++ /dev/null @@ -1,8 +0,0 @@ -@article{example2, - title = {An example journal article}, - author={Bighetti, Nelson and Ford, Robert}, - journal = {Journal of Source Themes}, - year = 2015, - volume = 1, - number = 1 -} diff --git a/content/publication/journal-article/featured.jpg b/content/publication/journal-article/featured.jpg deleted file mode 100644 index 15272c0..0000000 Binary files a/content/publication/journal-article/featured.jpg and /dev/null differ diff --git a/content/publication/journal-article/index.md b/content/publication/journal-article/index.md deleted file mode 100644 index 079228a..0000000 --- a/content/publication/journal-article/index.md +++ /dev/null @@ -1,75 +0,0 @@ ---- -title: "An example journal article" -authors: -- admin -- Robert Ford -author_notes: -- "Equal contribution" -- "Equal contribution" -date: "2015-09-01T00:00:00Z" -doi: "" - -# Schedule page publish date (NOT publication's date). -publishDate: "2017-01-01T00:00:00Z" - -# Publication type. -# Accepts a single type but formatted as a YAML list (for Hugo requirements). -# Enter a publication type from the CSL standard. -publication_types: ["article-journal"] - -# Publication name and optional abbreviated publication name. -publication: "*Journal of Source Themes, 1*(1)" -publication_short: "" - -abstract: Lorem ipsum dolor sit amet, consectetur adipiscing elit. Duis posuere tellus ac convallis placerat. Proin tincidunt magna sed ex sollicitudin condimentum. Sed ac faucibus dolor, scelerisque sollicitudin nisi. Cras purus urna, suscipit quis sapien eu, pulvinar tempor diam. Quisque risus orci, mollis id ante sit amet, gravida egestas nisl. Sed ac tempus magna. Proin in dui enim. Donec condimentum, sem id dapibus fringilla, tellus enim condimentum arcu, nec volutpat est felis vel metus. Vestibulum sit amet erat at nulla eleifend gravida. - -# Summary. An optional shortened abstract. -summary: Lorem ipsum dolor sit amet, consectetur adipiscing elit. Duis posuere tellus ac convallis placerat. Proin tincidunt magna sed ex sollicitudin condimentum. - -tags: -- Source Themes -featured: false - -# links: -# - name: "" -# url: "" -url_pdf: http://arxiv.org/pdf/1512.04133v1 -url_code: 'https://github.com/HugoBlox/hugo-blox-builder' -url_dataset: '' -url_poster: '' -url_project: '' -url_slides: '' -url_source: '' -url_video: '' - -# Featured image -# To use, add an image named `featured.jpg/png` to your page's folder. -image: - caption: 'Image credit: [**Unsplash**](https://unsplash.com/photos/jdD8gXaTZsc)' - focal_point: "" - preview_only: false - -# Associated Projects (optional). -# Associate this publication with one or more of your projects. -# Simply enter your project's folder or file name without extension. -# E.g. `internal-project` references `content/project/internal-project/index.md`. -# Otherwise, set `projects: []`. -projects: [] - -# Slides (optional). -# Associate this publication with Markdown slides. -# Simply enter your slide deck's filename without extension. -# E.g. `slides: "example"` references `content/slides/example/index.md`. -# Otherwise, set `slides: ""`. -slides: example ---- - -{{% callout note %}} -Click the *Cite* button above to demo the feature to enable visitors to import publication metadata into their reference management software. -{{% /callout %}} - -{{% callout note %}} -Create your slides in Markdown - click the *Slides* button to check out the example. -{{% /callout %}} - -Add the publication's **full text** or **supplementary notes** here. You can use rich formatting such as including [code, math, and images](https://docs.hugoblox.com/content/writing-markdown-latex/). diff --git a/content/publication/juranek-2020/cite.bib b/content/publication/juranek-2020/cite.bib new file mode 100644 index 0000000..4e3fdeb --- /dev/null +++ b/content/publication/juranek-2020/cite.bib @@ -0,0 +1,10 @@ +@article{Juranek2020, +abstract = {The net balance between photosynthesis and respiration in the surface ocean is a key regulator of ocean-atmosphere carbon dioxide (CO2) partitioning, and by extension, Earth's climate. The slight excess of photosynthesis over community respiration in sunlit waters, known as net community production (NCP), sets the upper bound on the sequestration of carbon via biologically mediated export. Prevailing paradigms suggest a high/low binary where net primary production (NPP), NCP, and export are highest in ecosystems characterized by microplankton (>20 $\mu$m) and lowest in ecosystems dominated by picoplankton (<2 $\mu$m). This bifurcation model neglects the potential importance of nanoplankton (2–20 $\mu$m)—i.e., the “middle” size class—toward global biological pump functioning. Here, we show a relationship between the biomass of nanoplankton and oxygen-based estimates of NCP across natural ecological gradients in the North Pacific Ocean. Using a suite of high-resolution optical imaging approaches including SeaFlow, Imaging FlowCytobot, and laser-based scattering, nanoplankton dynamics are observed to dominate the particle size distribution throughout an $\sim$1,000 km transition between the subtropical and subpolar North Pacific, where NCP rates are threefold to fivefold higher than subtropical values. Based on ecological theory applied to the Darwin size-based ecosystem model, we hypothesize that intermediate size class organisms are capable of high rates of production via an optimization of bottom-up and top-down control inherent to the “middle class.” More broadly, the model indicates the global importance of nanoplankton for ocean biological production.}, +author = {Juranek, Lauren W. and White, Angelicque E. and Dugenne, Mathilde and {Henderikx Freitas}, Fernanda and Dutkiewicz, Stephanie and Ribalet, Francois and Ferr{\'{o}}n, Sara and Armbrust, E. Virginia and Karl, David M.}, +doi = {10.1029/2020GB006702}, +journal = {Global Biogeochemical Cycles}, +number = {12}, +title = {{The Importance of the Phytoplankton “Middle Class” to Ocean Net Community Production}}, +volume = {34}, +year = {2020} +} diff --git a/content/publication/juranek-2020/featured.png b/content/publication/juranek-2020/featured.png new file mode 100644 index 0000000..147c28d Binary files /dev/null and b/content/publication/juranek-2020/featured.png differ diff --git a/content/publication/juranek-2020/index.md b/content/publication/juranek-2020/index.md new file mode 100644 index 0000000..3d6470d --- /dev/null +++ b/content/publication/juranek-2020/index.md @@ -0,0 +1,13 @@ +--- +title: "The Importance of the Phytoplankton “Middle Class” to Ocean Net Community Production" +date: 2020-11-25 +publishDate: 2020-11-25T17:46:51.934135Z +authors: ["L. Juranek", "A. White", "M. Dugenne", "F. Henderikx Freitas", "S. Dutkiewicz", "F. Ribalet", "S. Ferron", "E.V. Armbrust", "D.M. Karl"] +publication_types: ["2"] +abstract: "The net balance between photosynthesis and respiration in the surface ocean is a key regulator of ocean-atmosphere carbon dioxide (CO2) partitioning, and by extension, Earth's climate. The slight excess of photosynthesis over community respiration in sunlit waters, known as net community production (NCP), sets the upper bound on the sequestration of carbon via biologically mediated export. Prevailing paradigms suggest a high/low binary where net primary production (NPP), NCP, and export are highest in ecosystems characterized by microplankton (>20 um) and lowest in ecosystems dominated by picoplankton (<2 um). This bifurcation model neglects the potential importance of nanoplankton (2–20 um)—i.e., the “middle” size class—toward global biological pump functioning. Here, we show a relationship between the biomass of nanoplankton and oxygen-based estimates of NCP across natural ecological gradients in the North Pacific Ocean. Using a suite of high-resolution optical imaging approaches including SeaFlow, Imaging FlowCytobot, and laser-based scattering, nanoplankton dynamics are observed to dominate the particle size distribution throughout a 1,000 km transition between the subtropical and subpolar North Pacific, where NCP rates are threefold to fivefold higher than subtropical values. Based on ecological theory applied to the Darwin size-based ecosystem model, we hypothesize that intermediate size class organisms are capable of high rates of production via an optimization of bottom-up and top-down control inherent to the “middle class.” More broadly, the model indicates the global importance of nanoplankton for ocean biological production." +featured: false +publication: "*Global Biogeochemical Cycles*" +url_pdf: "https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2020GB006702" +doi: "10.1029/2020GB006702" +--- + diff --git a/content/publication/liefer-2024/cite.bib b/content/publication/liefer-2024/cite.bib new file mode 100644 index 0000000..b5ee770 --- /dev/null +++ b/content/publication/liefer-2024/cite.bib @@ -0,0 +1,9 @@ +@article{liefer_latitudinal_2024 + abstract = {The proportions of carbon (C), nitrogen (N), and phosphorus (P) in surface ocean particulate matter deviate greatly from the canonical Redfield Ratio (C:N:P = 106:16:1) in space and time with significant implications for global carbon storage as this matter reaches the deep ocean. Recent work has revealed clear latitudinal patterns in C:N:P, yet the relative importance of ecological, physiological, or biochemical processes in creating these patterns is unclear. We present high-resolution, concurrent measurements of particulate C:N:P, macromolecular composition, environmental conditions, and plankton community composition from a transect spanning a subtropical-subpolar boundary, the North Pacific Transition Zone. We find that the summed contribution of macromolecules to particulate C, N, and P is consistent with, and provides interpretation for, particulate C:N:P patterns. A decline in particulate C:N from the subtropical to subpolar North Pacific largely reflects an increase in the relative contribution of protein compared to carbohydrate and lipid, whereas variation in C:P and N:P correspond to shifts in protein relative to polyphosphate, DNA, and RNA. Possible causes for the corresponding trends in C:N and macromolecular composition include physiological responses and changes in community structure of phytoplankton, which represented approximately 1/3rd of particulate C across the transect. Comparison with culture experiments and an allocation-based model of phytoplankton macromolecular composition suggest that physiological acclimation to changing nutrient supply is the most likely explanation for the latitudinal trend in C:N, offering both a mechanistic interpretation and biochemical basis for large-scale patterns in C:N:P.}, + author = {Liefer, Justin D. and White, Angelicque E. and Finkel, Zoe V. and Irwin, Andrew J. and Dugenne, Mathilde and Inomura, Keisuke and Ribalet, François and Armbrust, E. Virginia and Karl, David M. and Fyfe, Matthew H. and Brown, Christopher M. and Follows, Michael J.}, + doi = {10.1073/pnas.2404460121}, + journal = {Proceedings of the National Academy of Sciences}, + number = {46}, + title = {Latitudinal patterns in ocean {C}:{N}:{P} reflect phytoplankton acclimation and macromolecular composition}, + volume = {121} +} diff --git a/content/publication/liefer-2024/featured.png b/content/publication/liefer-2024/featured.png new file mode 100644 index 0000000..b951c97 Binary files /dev/null and b/content/publication/liefer-2024/featured.png differ diff --git a/content/publication/liefer-2024/index.md b/content/publication/liefer-2024/index.md new file mode 100644 index 0000000..5e296da --- /dev/null +++ b/content/publication/liefer-2024/index.md @@ -0,0 +1,13 @@ +--- +title : "Latitudinal patterns in ocean C:N:P reflect phytoplankton acclimation and macromolecular composition" +date : "2024-12-01T00:00:00" +authors : ["Justin D. Liefer", "Angelicque E. White", "Zoe V. Finkel", "Andrew J. Irwin", "Mathilde Dugenne", "Keisuke Inomura", "François Ribalet", "E. Virginia Armbrust", "David M. Karl", "Matthew H. Fyfe", "Christopher M. Brown", "Michael J. Follows"] +publication_types : ["2"] +publication : "in *Proceedings of the National Academy of Sciences*" +abstract : "The proportions of carbon (C), nitrogen (N), and phosphorus (P) in surface ocean particulate matter deviate greatly from the canonical Redfield Ratio (C:N:P = 106:16:1) in space and time with significant implications for global carbon storage as this matter reaches the deep ocean. Recent work has revealed clear latitudinal patterns in C:N:P, yet the relative importance of ecological, physiological, or biochemical processes in creating these patterns is unclear. We present high-resolution, concurrent measurements of particulate C:N:P, macromolecular composition, environmental conditions, and plankton community composition from a transect spanning a subtropical-subpolar boundary, the North Pacific Transition Zone. We find that the summed contribution of macromolecules to particulate C, N, and P is consistent with, and provides interpretation for, particulate C:N:P patterns. A decline in particulate C:N from the subtropical to subpolar North Pacific largely reflects an increase in the relative contribution of protein compared to carbohydrate and lipid, whereas variation in C:P and N:P correspond to shifts in protein relative to polyphosphate, DNA, and RNA. Possible causes for the corresponding trends in C:N and macromolecular composition include physiological responses and changes in community structure of phytoplankton, which represented approximately 1/3rd of particulate C across the transect. Comparison with culture experiments and an allocation-based model of phytoplankton macromolecular composition suggest that physiological acclimation to changing nutrient supply is the most likely explanation for the latitudinal trend in C:N, offering both a mechanistic interpretation and biochemical basis for large-scale patterns in C:N:P." +featured : false +projects : [] +tags : [] +doi : "10.1073/pnas.2404460121" +math : false +--- diff --git a/content/publication/marchetti-2009/cite.bib b/content/publication/marchetti-2009/cite.bib new file mode 100644 index 0000000..1db5aa7 --- /dev/null +++ b/content/publication/marchetti-2009/cite.bib @@ -0,0 +1,16 @@ +@article{Marchetti2009, + abstract = {Primary productivity in 30-40% of the world's oceans is limited by availability of the micronutrient iron. Regions with chronically low iron concentrations are sporadically pulsed with new iron inputs by way of dust or lateral advection from continental margins. Addition of iron to surface waters in these areas induces massive phytoplankton blooms dominated primarily by pennate diatoms. Here we provide evidence that the bloom-forming pennate diatoms Pseudo-nitzschia and Fragilariopsis use the iron-concentrating protein, ferritin, to safely store iron. Ferritin has not been reported previously in any member of the Stramenopiles, a diverse eukaryotic lineage that includes unicellular algae, macroalgae and plant parasites. Phylogenetic analyses suggest that ferritin may have arisen in this small subset of diatoms through a lateral gene transfer. The crystal structure and functional assays of recombinant ferritin derived from Pseudo-nitzschia multiseries reveal a maxi-ferritin that exhibits ferroxidase activity and binds iron. The protein is predicted to be targeted to the chloroplast to control the distribution and storage of iron for proper functioning of the photosynthetic machinery. Abundance of Pseudo-nitzschia ferritin transcripts is regulated by iron nutritional status, and is closely tied to the loss and recovery of photosynthetic competence. Enhanced iron storage with ferritin allows the oceanic diatom Pseudo-nitzschia granii to undergo several more cell divisions in the absence of iron than the comparably sized, oceanic centric diatom Thalassiosira oceanica. Ferritin in pennate diatoms probably contributes to their success in chronically low-iron regions that receive intermittent iron inputs, and provides an explanation for the importance of these organisms in regulating oceanic CO(2) over geological timescales.}, + author = {Marchetti, Adrian and Parker, Micaela S. and Moccia, Lauren and Lin, Ellen O. and Arrieta, Angele L. and Ribalet, Francois and Murphy, Michael and Maldonado, Maria and Armbrust, E. Virginia}, + doi = {10.1038/nature07539}, + file = {:Users/ribalet/Library/Application Support/Mendeley Desktop/Downloaded/Marchetti et al. - 2009 - Ferritin is used for iron storage in bloom-forming marine pennate diatoms.pdf:pdf}, + isbn = {0028-0836}, + issn = {00280836}, + journal = {Nature}, + number = {7228}, + pages = {467--470}, + pmid = {19037243}, + title = {Ferritin is used for iron storage in bloom-forming marine pennate diatoms}, + volume = {457}, + year = {2009} +} + diff --git a/content/publication/marchetti-2009/featured.png b/content/publication/marchetti-2009/featured.png new file mode 100644 index 0000000..b836ff1 Binary files /dev/null and b/content/publication/marchetti-2009/featured.png differ diff --git a/content/publication/marchetti-2009/index.md b/content/publication/marchetti-2009/index.md new file mode 100644 index 0000000..a88c1e5 --- /dev/null +++ b/content/publication/marchetti-2009/index.md @@ -0,0 +1,12 @@ +--- +title: "Ferritin is used for iron storage in bloom-forming marine pennate diatoms" +date: 2009-01-01 +publishDate: 2020-03-09T17:46:51.938937Z +authors: ["Adrian Marchetti", "Micaela S. Parker", "Lauren Moccia", "Ellen O. Lin", "Angele L. Arrieta", "Francois Ribalet", "Michael Murphy", "Maria Maldonado", "E. Virginia Armbrust"] +publication_types: ["2"] +abstract: "Primary productivity in 30-40% of the world's oceans is limited by availability of the micronutrient iron. Regions with chronically low iron concentrations are sporadically pulsed with new iron inputs by way of dust or lateral advection from continental margins. Addition of iron to surface waters in these areas induces massive phytoplankton blooms dominated primarily by pennate diatoms. Here we provide evidence that the bloom-forming pennate diatoms Pseudo-nitzschia and Fragilariopsis use the iron-concentrating protein, ferritin, to safely store iron. Ferritin has not been reported previously in any member of the Stramenopiles, a diverse eukaryotic lineage that includes unicellular algae, macroalgae and plant parasites. Phylogenetic analyses suggest that ferritin may have arisen in this small subset of diatoms through a lateral gene transfer. The crystal structure and functional assays of recombinant ferritin derived from Pseudo-nitzschia multiseries reveal a maxi-ferritin that exhibits ferroxidase activity and binds iron. The protein is predicted to be targeted to the chloroplast to control the distribution and storage of iron for proper functioning of the photosynthetic machinery. Abundance of Pseudo-nitzschia ferritin transcripts is regulated by iron nutritional status, and is closely tied to the loss and recovery of photosynthetic competence. Enhanced iron storage with ferritin allows the oceanic diatom Pseudo-nitzschia granii to undergo several more cell divisions in the absence of iron than the comparably sized, oceanic centric diatom Thalassiosira oceanica. Ferritin in pennate diatoms probably contributes to their success in chronically low-iron regions that receive intermittent iron inputs, and provides an explanation for the importance of these organisms in regulating oceanic CO(2) over geological timescales." +featured: false +publication: "*Nature*" +doi: "10.1038/nature07539" +--- + diff --git a/content/publication/mattern-2022/cite.bib b/content/publication/mattern-2022/cite.bib new file mode 100644 index 0000000..4ec1a17 --- /dev/null +++ b/content/publication/mattern-2022/cite.bib @@ -0,0 +1,11 @@ +@article{Mattern2022 + abstract = {The rates of cell growth, division, and carbon loss of microbial populations are key parameters for understanding how organisms interact with their environment and how they contribute to the carbon cycle. However, the invasive nature of current analytical methods has hindered efforts to reliably quantify these parameters. In recent years, size-structured matrix population models (MPMs) have gained popularity for estimating division rates of microbial populations by mechanistically describing changes in microbial cell size distributions over time. Motivated by the mechanistic structure of these models, we employ a Bayesian approach to extend size-structured MPMs to capture additional biological processes describing the dynamics of a marine phytoplankton population over the day-night cycle. Our Bayesian framework is able to take prior scientific knowledge into account and generate biologically interpretable results. Using data from an exponentially growing laboratory culture of the cyanobacterium Prochlorococcus, we isolate respiratory and exudative carbon losses as critical parameters for the modeling of their population dynamics. The results suggest that this modeling framework can provide deeper insights into microbial population dynamics provided by size distribution time-series data.}, + author = {Mattern, Jann Paul and Glauninger, Kristof and Britten, Gregory L. and Casey, John R. and Hyun, Sangwon and Wu, Zhen and Armbrust, E. Virginia and Harchaoui, Zaid and Ribalet, Francois}, + doi = {10.1371/JOURNAL.PCBI.1009733}, + journal = {PLOS Computational Biology}, + number = {1}, + pages = {e1009733}, + title = {{A Bayesian approach to modeling phytoplankton population dynamics from size distribution time series}}, + volume = {18}, + year = {2022} +} diff --git a/content/publication/mattern-2022/featured.png b/content/publication/mattern-2022/featured.png new file mode 100644 index 0000000..c452fae Binary files /dev/null and b/content/publication/mattern-2022/featured.png differ diff --git a/content/publication/mattern-2022/index.md b/content/publication/mattern-2022/index.md new file mode 100644 index 0000000..77804ce --- /dev/null +++ b/content/publication/mattern-2022/index.md @@ -0,0 +1,17 @@ ++++ +# +# created by build_publications.py +# +title = "A Bayesian approach to modeling phytoplankton population dynamics from size distribution time series" +date = "2022-02-10T00:00:00" +authors = ["Jann Paul Mattern", "Kristof Glauninger", "Gregory L. Britten", "John R. Casey", "Sangwon Hyun", "Zhen Wu", "E. Virginia Armbrust", "Zaid Harchaoui", "Francois Ribalet"] +publication_types = ["2"] +publication = "in *PLOS Computational Biology*" +abstract = "The rates of cell growth, division, and carbon loss of microbial populations are key parameters for understanding how organisms interact with their environment and how they contribute to the carbon cycle. However, the invasive nature of current analytical methods has hindered efforts to reliably quantify these parameters. In recent years, size-structured matrix population models (MPMs) have gained popularity for estimating division rates of microbial populations by mechanistically describing changes in microbial cell size distributions over time. Motivated by the mechanistic structure of these models, we employ a Bayesian approach to extend size-structured MPMs to capture additional biological processes describing the dynamics of a marine phytoplankton population over the day-night cycle. Our Bayesian framework is able to take prior scientific knowledge into account and generate biologically interpretable results. Using data from an exponentially growing laboratory culture of the cyanobacterium Prochlorococcus, we isolate respiratory and exudative carbon losses as critical parameters for the modeling of their population dynamics. The results suggest that this modeling framework can provide deeper insights into microbial population dynamics provided by size distribution time-series data." +featured = true +projects = [] +tags = [] +url_pdf = "https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009733" +doi = "10.1371/JOURNAL.PCBI.1009733" +math = false ++++ diff --git a/content/publication/mruwat-2020/cite.bib b/content/publication/mruwat-2020/cite.bib new file mode 100644 index 0000000..a370604 --- /dev/null +++ b/content/publication/mruwat-2020/cite.bib @@ -0,0 +1,15 @@ +@article{Mruwat2020, +abstract = {Long-term stability of picocyanobacteria in the open oceans is maintained by a balance between synchronous division and death on daily timescales. Viruses are considered a major source of microbial mortality, however, current methods to measure infection have significant methodological limitations. Here we describe a method that pairs flow-cytometric sorting with a PCR-based polony technique to simultaneously screen thousands of taxonomically resolved individual cells for intracellular virus DNA, enabling sensitive, high-throughput, and direct quantification of infection by different virus lineages. Under controlled conditions with picocyanobacteria-cyanophage models, the method detected infection throughout the lytic cycle and discriminated between varying infection levels. In North Pacific subtropical surface waters, the method revealed that only a small percentage of Prochlorococcus (0.35–1.6%) were infected, predominantly by T4-like cyanophages, and that infection oscillated 2-fold in phase with the diel cycle. This corresponds to 0.35–4.8% of Prochlorococcus mortality daily. Cyanophages were 2–4-fold more abundant than Prochlorococcus, indicating that most encounters did not result in infection and suggesting infection is mitigated via host resistance, reduced phage infectivity and inefficient adsorption. This method will enable quantification of infection for key microbial taxa across oceanic regimes and will help determine the extent that viruses shape microbial communities and ecosystem level processes.}, +author = {Mruwat, Noor and Carlson, Michael C.G. and Goldin, Svetlana and Ribalet, Fran{\c{c}}ois and Kirzner, Shay and Hulata, Yotam and Beckett, Stephen J. and Shitrit, Dror and Weitz, Joshua S. and Armbrust, E. Virginia and Lindell, Debbie}, +doi = {10.1038/s41396-020-00752-6}, +file = {:home/francois/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Mruwat et al. - 2020 - A single-cell polony method reveals low levels of infected Prochlorococcus in oligotrophic waters despite high cy.pdf:pdf}, +issn = {17517370}, +journal = {ISME Journal}, +keywords = {Microbial biooceanography,Microbial ecology,Molecular ecology}, +month = {sep}, +pages = {1--14}, +publisher = {Springer Nature}, +title = {{A single-cell polony method reveals low levels of infected Prochlorococcus in oligotrophic waters despite high cyanophage abundances}}, +url = {https://doi.org/10.1038/s41396-020-00752-6}, +year = {2020} +} diff --git a/content/publication/mruwat-2020/featured.png b/content/publication/mruwat-2020/featured.png new file mode 100644 index 0000000..8dca975 Binary files /dev/null and b/content/publication/mruwat-2020/featured.png differ diff --git a/content/publication/mruwat-2020/index.md b/content/publication/mruwat-2020/index.md new file mode 100644 index 0000000..243d58f --- /dev/null +++ b/content/publication/mruwat-2020/index.md @@ -0,0 +1,13 @@ +--- +title: "A single-cell polony method reveals low levels of infected Prochlorococcus in oligotrophic waters despite high cyanophage abundances" +date: 2020-09-11 +publishDate: 2020-09-11T17:46:51.934135Z +authors: ["N. Mruwat", "M.C.G Carlson", "S. Goldin", "F. Ribalet", "S. Kirzner", "Y. Hulata", "S.J. Beckett", "D. Shitrit", "J. Weitz", "E.V. Armbrust", "L. Debbie"] +publication_types: ["2"] +abstract: "Long-term stability of picocyanobacteria in the open oceans is maintained by a balance between synchronous division and death on daily timescales. Viruses are considered a major source of microbial mortality, however, current methods to measure infection have significant methodological limitations. Here we describe a method that pairs flow-cytometric sorting with a PCR-based polony technique to simultaneously screen thousands of taxonomically resolved individual cells for intracellular virus DNA, enabling sensitive, high-throughput, and direct quantification of infection by different virus lineages. Under controlled conditions with picocyanobacteria-cyanophage models, the method detected infection throughout the lytic cycle and discriminated between varying infection levels. In North Pacific subtropical surface waters, the method revealed that only a small percentage of Prochlorococcus (0.35–1.6%) were infected, predominantly by T4-like cyanophages, and that infection oscillated 2-fold in phase with the diel cycle. This corresponds to 0.35–4.8% of Prochlorococcus mortality daily. Cyanophages were 2–4-fold more abundant than Prochlorococcus, indicating that most encounters did not result in infection and suggesting infection is mitigated via host resistance, reduced phage infectivity and inefficient adsorption. This method will enable quantification of infection for key microbial taxa across oceanic regimes and will help determine the extent that viruses shape microbial communities and ecosystem level processes." +featured: False +publication: "*ISME Journal*" +url_pdf: "https://doi.org/10.1038/s41396-020-00752-6" +doi: "10.1038/s41396-020-00752-6" +--- + diff --git a/content/publication/palevsky-2013/cite.bib b/content/publication/palevsky-2013/cite.bib new file mode 100644 index 0000000..d587a56 --- /dev/null +++ b/content/publication/palevsky-2013/cite.bib @@ -0,0 +1,16 @@ +@article{Palevsky2013, + abstract = {Biological productivity is a key factor controlling the ocean's ability to take up carbon dioxide from the atmosphere. However, the ecological dynamics that drive regions of intense productivity and carbon export are poorly understood. In this study, we present high-spatial-resolution estimates of air-sea CO2 flux, net community production (NCP) rates calculated from O2/Ar ratios, and phytoplankton population abundances determined by continuous underway measurements on a cruise across the Gulf of Alaska in May 2010. The highest rates of NCP (249 ± 40 mmol C m-2 d-1) and oceanic CO2 uptake (air-sea flux of −42.3 ± 6.1 mmol C m-2 d-1) were observed across a transition zone between the high-nitrate low-chlorophyll (HNLC) waters of the Alaskan Gyre and the coastal waters off the Aleutian Islands. While the transition zone comprises 20% of the total area covered in crossing the Gulf of Alaska, it contributed 58% of the total NCP and 67% of the total CO2 uptake observed along the cruise track. A corresponding transition zone phytoplankton bloom was dominated by two small-celled (\textless20 µm) phytoplankton communities, which were distinct from the phytoplankton communities in the surrounding Alaskan Gyre and coastal waters. We hypothesize that mixing between iron-rich coastal waters and iron-limited Alaskan Gyre waters stimulated this bloom and fueled the high NCP and CO2 export observed in the region.}, + author = {Palevsky, Hilary I. and Ribalet, Francois and Swalwell, Jarred E. and Cosca, Catherine E. and Cokelet, Edward D. and Feely, Richard A. and Armbrust, E. Virginia and Quay, Paul D.}, + doi = {10.1002/gbc.20058}, + file = {:Users/ribalet/Library/Application Support/Mendeley Desktop/Downloaded/Palevsky et al. - 2013 - The influence of net community production and phytoplankton community structure on COinf2inf uptake in the Gulf.pdf:pdf}, + isbn = {1944-9224}, + issn = {08866236}, + journal = {Global Biogeochemical Cycles}, + keywords = {Gulf of Alaska,biological pump,carbon cycle,net community production,phytoplankton}, + number = {3}, + pages = {664--676}, + title = {The influence of net community production and phytoplankton community structure on CO2 uptake in the Gulf of Alaska}, + volume = {27}, + year = {2013} +} + diff --git a/content/publication/palevsky-2013/featured.png b/content/publication/palevsky-2013/featured.png new file mode 100644 index 0000000..4d4fefa Binary files /dev/null and b/content/publication/palevsky-2013/featured.png differ diff --git a/content/publication/palevsky-2013/index.md b/content/publication/palevsky-2013/index.md new file mode 100644 index 0000000..338d058 --- /dev/null +++ b/content/publication/palevsky-2013/index.md @@ -0,0 +1,13 @@ +--- +title: "The influence of net community production and phytoplankton community structure on CO2 uptake in the Gulf of Alaska" +date: 2013-01-01 +publishDate: 2020-03-09T17:46:51.934699Z +authors: ["Hilary I. Palevsky", "Francois Ribalet", "Jarred E. Swalwell", "Catherine E. Cosca", "Edward D. Cokelet", "Richard A. Feely", "E. Virginia Armbrust", "Paul D. Quay"] +publication_types: ["2"] +abstract: "Biological productivity is a key factor controlling the ocean's ability to take up carbon dioxide from the atmosphere. However, the ecological dynamics that drive regions of intense productivity and carbon export are poorly understood. In this study, we present high-spatial-resolution estimates of air-sea CO2 flux, net community production (NCP) rates calculated from O2/Ar ratios, and phytoplankton population abundances determined by continuous underway measurements on a cruise across the Gulf of Alaska in May 2010. The highest rates of NCP (249 ± 40 mmol C m-2 d-1) and oceanic CO2 uptake (air-sea flux of −42.3 ± 6.1 mmol C m-2 d-1) were observed across a transition zone between the high-nitrate low-chlorophyll (HNLC) waters of the Alaskan Gyre and the coastal waters off the Aleutian Islands. While the transition zone comprises 20% of the total area covered in crossing the Gulf of Alaska, it contributed 58% of the total NCP and 67% of the total CO2 uptake observed along the cruise track. A corresponding transition zone phytoplankton bloom was dominated by two small-celled (textless20 µm) phytoplankton communities, which were distinct from the phytoplankton communities in the surrounding Alaskan Gyre and coastal waters. We hypothesize that mixing between iron-rich coastal waters and iron-limited Alaskan Gyre waters stimulated this bloom and fueled the high NCP and CO2 export observed in the region." +featured: false +publication: "*Global Biogeochemical Cycles*" +tags: ["Gulf of Alaska", "biological pump", "carbon cycle", "net community production", "phytoplankton"] +doi: "10.1002/gbc.20058" +--- + diff --git a/content/publication/park-2023/cite.bib b/content/publication/park-2023/cite.bib new file mode 100644 index 0000000..1011866 --- /dev/null +++ b/content/publication/park-2023/cite.bib @@ -0,0 +1,11 @@ +@article{park_siderophore_2023 + abstract = {Siderophores are strong iron-binding molecules produced and utilized by microbes to acquire the limiting nutrient iron (Fe) from their surroundings. Despite their importance as a component of the iron-binding ligand pool in seawater, data on the distribution of siderophores and the microbes that use them are limited. Here, we measured the concentrations and types of dissolved siderophores during two cruises in April 2016 and June 2017 that transited from the iron-replete, low-macronutrient North Pacific Subtropical Gyre through the North Pacific Transition Zone (NPTZ) to the iron-deplete, high-macronutrient North Pacific Subarctic Frontal Zone (SAFZ). Surface siderophore concentrations in 2017 were higher in the NPTZ (4.0–13.9 pM) than the SAFZ (1.2–5.1 pM), which may be partly attributed to stimulated siderophore production by environmental factors such as dust-derived iron concentrations (up to 0.51 nM). Multiple types of siderophores were identified on both cruises, including ferrioxamines, amphibactins, and iron-free forms of photoreactive siderophores, which suggest active production and use of diverse siderophores across latitude and depth. Siderophore biosynthesis and uptake genes and transcripts were widespread across latitude, and higher abundances of these genes and transcripts at higher latitudes may reflect active siderophore-mediated iron uptake by the local bacterial community across the North Pacific. The variability in the taxonomic composition of bacterial communities that transcribe putative ferrioxamine, amphibactin, and salmochelin transporter genes at different latitudes further suggests that the microbial groups involved in active siderophore production and usage change depending on local conditions.}, + author = {Park, Jiwoon and Durham, Bryndan P. and Key, Rebecca S. and Groussman, Ryan D. and Bartolek, Zinka and Pinedo-Gonzalez, Paulina and Hawco, Nicholas J. and John, Seth G. and Carlson, Michael C. G. and Lindell, Debbie and Juranek, Lauren W. and Ferrón, Sara and Ribalet, Francois and Armbrust, E. Virginia and Ingalls, Anitra E. and Bundy, Randelle M.}, + doi = {10.1002/lno.12373}, + journal = {Limnology and Oceanography}, + number = {7}, + pages = {1636--1653}, + title = {Siderophore production and utilization by marine bacteria in the {North} {Pacific} {Ocean}}, + volume = {68}, + year = {2023} +} diff --git a/content/publication/park-2023/featured.png b/content/publication/park-2023/featured.png new file mode 100644 index 0000000..5d2d978 Binary files /dev/null and b/content/publication/park-2023/featured.png differ diff --git a/content/publication/park-2023/index.md b/content/publication/park-2023/index.md new file mode 100644 index 0000000..9d661c7 --- /dev/null +++ b/content/publication/park-2023/index.md @@ -0,0 +1,13 @@ +--- +title : "Siderophore production and utilization by marine bacteria in the {North} {Pacific} {Ocean" +date : "2023-12-01T00:00:00" +authors : ["Jiwoon Park", "Bryndan P. Durham", "Rebecca S. Key", "Ryan D. Groussman", "Zinka Bartolek", "Paulina Pinedo-Gonzalez", "Nicholas J. Hawco", "Seth G. John", "Michael C. G. Carlson", "Debbie Lindell", "Lauren W. Juranek", "Sara Ferrón", "Francois Ribalet", "E. Virginia Armbrust", "Anitra E. Ingalls", "R Bundy", "elle M."] +publication_types : ["2"] +publication : "in *Limnology and Oceanography*" +abstract : "Siderophores are strong iron-binding molecules produced and utilized by microbes to acquire the limiting nutrient iron (Fe) from their surroundings. Despite their importance as a component of the iron-binding ligand pool in seawater, data on the distribution of siderophores and the microbes that use them are limited. Here, we measured the concentrations and types of dissolved siderophores during two cruises in April 2016 and June 2017 that transited from the iron-replete, low-macronutrient North Pacific Subtropical Gyre through the North Pacific Transition Zone (NPTZ) to the iron-deplete, high-macronutrient North Pacific Subarctic Frontal Zone (SAFZ). Surface siderophore concentrations in 2017 were higher in the NPTZ (4.0–13.9 pM) than the SAFZ (1.2–5.1 pM), which may be partly attributed to stimulated siderophore production by environmental factors such as dust-derived iron concentrations (up to 0.51 nM). Multiple types of siderophores were identified on both cruises, including ferrioxamines, amphibactins, and iron-free forms of photoreactive siderophores, which suggest active production and use of diverse siderophores across latitude and depth. Siderophore biosynthesis and uptake genes and transcripts were widespread across latitude, and higher abundances of these genes and transcripts at higher latitudes may reflect active siderophore-mediated iron uptake by the local bacterial community across the North Pacific. The variability in the taxonomic composition of bacterial communities that transcribe putative ferrioxamine, amphibactin, and salmochelin transporter genes at different latitudes further suggests that the microbial groups involved in active siderophore production and usage change depending on local conditions." +featured : false +projects : [] +tags : [] +doi : "10.1002/lno.12373" +math : false +--- diff --git a/content/publication/preprint/featured.jpg b/content/publication/preprint/featured.jpg deleted file mode 100644 index 8fdeeee..0000000 Binary files a/content/publication/preprint/featured.jpg and /dev/null differ diff --git a/content/publication/preprint/index.md b/content/publication/preprint/index.md deleted file mode 100644 index ccb94da..0000000 --- a/content/publication/preprint/index.md +++ /dev/null @@ -1,68 +0,0 @@ ---- -title: "An example preprint / working paper" -authors: -- admin -date: "2019-04-07T00:00:00Z" -doi: "" - -# Schedule page publish date (NOT publication's date). -publishDate: "2017-01-01T00:00:00Z" - -# Publication type. -# Accepts a single type but formatted as a YAML list (for Hugo requirements). -# Enter a publication type from the CSL standard. -publication_types: ["article"] - -# Publication name and optional abbreviated publication name. -publication: "" -publication_short: "" - -abstract: Lorem ipsum dolor sit amet, consectetur adipiscing elit. Duis posuere tellus ac convallis placerat. Proin tincidunt magna sed ex sollicitudin condimentum. Sed ac faucibus dolor, scelerisque sollicitudin nisi. Cras purus urna, suscipit quis sapien eu, pulvinar tempor diam. Quisque risus orci, mollis id ante sit amet, gravida egestas nisl. Sed ac tempus magna. Proin in dui enim. Donec condimentum, sem id dapibus fringilla, tellus enim condimentum arcu, nec volutpat est felis vel metus. Vestibulum sit amet erat at nulla eleifend gravida. - -# Summary. An optional shortened abstract. -summary: Lorem ipsum dolor sit amet, consectetur adipiscing elit. Duis posuere tellus ac convallis placerat. Proin tincidunt magna sed ex sollicitudin condimentum. - -tags: -- Source Themes -featured: false - -links: -- name: Custom Link - url: http://example.org -url_pdf: http://arxiv.org/pdf/1512.04133v1 -url_code: 'https://github.com/HugoBlox/hugo-blox-builder' -url_dataset: '#' -url_poster: '#' -url_project: '' -url_slides: '' -url_source: '#' -url_video: '#' - -# Featured image -# To use, add an image named `featured.jpg/png` to your page's folder. -image: - caption: 'Image credit: [**Unsplash**](https://unsplash.com/photos/s9CC2SKySJM)' - focal_point: "" - preview_only: false - -# Associated Projects (optional). -# Associate this publication with one or more of your projects. -# Simply enter your project's folder or file name without extension. -# E.g. `internal-project` references `content/project/internal-project/index.md`. -# Otherwise, set `projects: []`. -projects: -- internal-project - -# Slides (optional). -# Associate this publication with Markdown slides. -# Simply enter your slide deck's filename without extension. -# E.g. `slides: "example"` references `content/slides/example/index.md`. -# Otherwise, set `slides: ""`. -slides: example ---- - -{{% callout note %}} -Create your slides in Markdown - click the *Slides* button to check out the example. -{{% /callout %}} - -Add the publication's **full text** or **supplementary notes** here. You can use rich formatting such as including [code, math, and images](https://docs.hugoblox.com/content/writing-markdown-latex/). diff --git a/content/publication/ribalet-2007/cite.bib b/content/publication/ribalet-2007/cite.bib new file mode 100644 index 0000000..fe05e61 --- /dev/null +++ b/content/publication/ribalet-2007/cite.bib @@ -0,0 +1,17 @@ +@article{Ribalet2007a, + abstract = {Several marine diatoms produce polyunsaturated aldehydes (PUAs) that have been shown to be toxic to a wide variety of model organisms, from bacteria to invertebrates. However, very little information is available on their effect on phytoplankton. Here, we expand previous studies to six species of marine phytoplankton, belonging to different taxonomic groups that are well represented in marine plankton. The effect of three PUAs, 2E,4E-decadienal, 2E,4E-octadienal and 2E,4E-heptadienal, was assessed on growth, cell membrane permeability, flow cytometric properties and morphology. A concentration-dependent reduction in the growth rate was observed for all cultures exposed to PUAs with longer-chained aldehydes having stronger effects on growth than shorter-chained aldehydes. Clear differences were observed among the different species. The prymnesiophyte Isochrysis galbana was the most sensitive species to PUA exposure with a lower threshold for an observed effect triggered by mean concentrations of 0.10 $μ$mol L-1for 2E,4E-decadienal, 1.86 $μ$mol L-1for 2E,4E-octadienal and 3.06 $μ$mol L-1for 2E,4E-heptadienal, and a 50% growth inhibition (EC50) with respect to the control at 0.99, 2.25 and 5.90 $μ$mol L-1for the three PUAs, respectively. Alternatively, the chlorophyte Tetraselmis suecica and the diatom Skeletonema marinoi (formerly S. costatum) were the most resistant species with 50% growth inhibition occurring at concentrations at least two to three times higher than I. galbana. In all species, the three PUAs caused changes in flow cytometric measures of cell size and cell granulosity and increased membrane permeability, assessed using the viability stain SYTOX Green. For example, after 48 h 51.6 ± 2.6% of I. galbana cells and 15.0 ± 1.8% of S. marinoi cells were not viable. Chromatin fragmentation was observed in the dinoflagellate Amphidinium carterae while clear DNA degradation was observed in the chlorophyte Dunaliella tertiolecta. Concentrations used are in a significant range for affecting growth and performance of phytoplankton living in close vicinity of PUA-producing algae. Thus, PUAs may act as allelochemicals by mediating interactions among planktonic organisms.}, + author = {Ribalet, François and Berges, John A. and Ianora, Adrianna and Casotti, Raffaella}, + doi = {10.1016/j.aquatox.2007.09.006}, + file = {:Users/ribalet/Library/Application Support/Mendeley Desktop/Downloaded/Ribalet et al. - 2007 - Growth inhibition of cultured marine phytoplankton by toxic algal-derived polyunsaturated aldehydes.pdf:pdf}, + isbn = {0166-445X}, + issn = {0166445X}, + journal = {Aquatic Toxicology}, + keywords = {Allelochemicals,Diatoms,EC 50,EC50,Growth inhibition,Toxicity,Viability}, + number = {3}, + pages = {219--227}, + pmid = {17942163}, + title = {Growth inhibition of cultured marine phytoplankton by toxic algal-derived polyunsaturated aldehydes}, + volume = {85}, + year = {2007} +} + diff --git a/content/publication/ribalet-2007/featured.png b/content/publication/ribalet-2007/featured.png new file mode 100644 index 0000000..7133cd0 Binary files /dev/null and b/content/publication/ribalet-2007/featured.png differ diff --git a/content/publication/ribalet-2007/index.md b/content/publication/ribalet-2007/index.md new file mode 100644 index 0000000..9c50f51 --- /dev/null +++ b/content/publication/ribalet-2007/index.md @@ -0,0 +1,13 @@ +--- +title: "Growth inhibition of cultured marine phytoplankton by toxic algal-derived polyunsaturated aldehydes" +date: 2007-01-01 +publishDate: 2020-03-09T17:46:51.942188Z +authors: ["François Ribalet", "John A. Berges", "Adrianna Ianora", "Raffaella Casotti"] +publication_types: ["2"] +abstract: "Several marine diatoms produce polyunsaturated aldehydes (PUAs) that have been shown to be toxic to a wide variety of model organisms, from bacteria to invertebrates. However, very little information is available on their effect on phytoplankton. Here, we expand previous studies to six species of marine phytoplankton, belonging to different taxonomic groups that are well represented in marine plankton. The effect of three PUAs, 2E,4E-decadienal, 2E,4E-octadienal and 2E,4E-heptadienal, was assessed on growth, cell membrane permeability, flow cytometric properties and morphology. A concentration-dependent reduction in the growth rate was observed for all cultures exposed to PUAs with longer-chained aldehydes having stronger effects on growth than shorter-chained aldehydes. Clear differences were observed among the different species. The prymnesiophyte Isochrysis galbana was the most sensitive species to PUA exposure with a lower threshold for an observed effect triggered by mean concentrations of 0.10 $μ$mol L-1for 2E,4E-decadienal, 1.86 $μ$mol L-1for 2E,4E-octadienal and 3.06 $μ$mol L-1for 2E,4E-heptadienal, and a 50% growth inhibition (EC50) with respect to the control at 0.99, 2.25 and 5.90 $μ$mol L-1for the three PUAs, respectively. Alternatively, the chlorophyte Tetraselmis suecica and the diatom Skeletonema marinoi (formerly S. costatum) were the most resistant species with 50% growth inhibition occurring at concentrations at least two to three times higher than I. galbana. In all species, the three PUAs caused changes in flow cytometric measures of cell size and cell granulosity and increased membrane permeability, assessed using the viability stain SYTOX Green. For example, after 48 h 51.6 ± 2.6% of I. galbana cells and 15.0 ± 1.8% of S. marinoi cells were not viable. Chromatin fragmentation was observed in the dinoflagellate Amphidinium carterae while clear DNA degradation was observed in the chlorophyte Dunaliella tertiolecta. Concentrations used are in a significant range for affecting growth and performance of phytoplankton living in close vicinity of PUA-producing algae. Thus, PUAs may act as allelochemicals by mediating interactions among planktonic organisms." +featured: false +publication: "*Aquatic Toxicology*" +tags: ["Allelochemicals", "Diatoms", "EC 50", "EC50", "Growth inhibition", "Toxicity", "Viability"] +doi: "10.1016/j.aquatox.2007.09.006" +--- + diff --git a/content/publication/ribalet-2007b/cite.bib b/content/publication/ribalet-2007b/cite.bib new file mode 100644 index 0000000..700c67e --- /dev/null +++ b/content/publication/ribalet-2007b/cite.bib @@ -0,0 +1,17 @@ +@article{Ribalet2007b, + abstract = {Skeletonema marinoi produces 2,4-heptadienal, 2,4-octadienal, and 2,4,7-octatrienal, the latter only in traces. In nutrient-replete cultures, the production of potentially defensive polyunsaturated aldehydes (PUA) increases from the exponential to the stationary phase of growth from 1.2 fmol cell-1(±0.4 fmol cell-1SD) to 4.2 fmol cell-1(±1.0 fmol cell-1SD), with 2,4-heptadienal as the dominant aldehyde. The plasticity of PUA production with age of the culture supports the hypothesis of a direct link between toxin production and cell physiological state. N- and P-limited cells in stationary phase produced 1.4 and 1.8 fold higher amounts of PUA than control cultures and 10.7 and 4.6 times higher PUAs when compared to their own exponential growth phase, respectively. The increase in PUA production in the nutrient-limited cultures was not paralleled by an increase in the total amount of precursor fatty acids indicating that physiological stress might trigger an enhanced expression or activity of the enzymes responsible for PUA production, i.e. chemical defense increase in aged and nutrient-stressed diatoms. If this holds true during blooms, grazers feeding at the end of a bloom would be more affected than early-bloom grazers.}, + author = {Ribalet, François and Wichard, Thomas and Pohnert, Georg and Ianora, Adrianna and Miralto, Antonio and Casotti, Raffaella}, + doi = {10.1016/j.phytochem.2007.05.012}, + file = {:Users/ribalet/Library/Application Support/Mendeley Desktop/Downloaded/Ribalet et al. - 2007 - Age and nutrient limitation enhance polyunsaturated aldehyde production in marine diatoms.pdf:pdf}, + isbn = {0031-9422}, + issn = {00319422}, + journal = {Phytochemistry}, + keywords = {Chemical defense,Growth phase,Harmful algal blooms,Nutrient limitation,Polyunsaturated fatty acids,Skeletonema}, + number = {15}, + pages = {2059--2067}, + pmid = {17575990}, + title = {Age and nutrient limitation enhance polyunsaturated aldehyde production in marine diatoms}, + volume = {68}, + year = {2007} +} + diff --git a/content/publication/ribalet-2007b/featured.png b/content/publication/ribalet-2007b/featured.png new file mode 100644 index 0000000..f0c6b17 Binary files /dev/null and b/content/publication/ribalet-2007b/featured.png differ diff --git a/content/publication/ribalet-2007b/index.md b/content/publication/ribalet-2007b/index.md new file mode 100644 index 0000000..3fe4a34 --- /dev/null +++ b/content/publication/ribalet-2007b/index.md @@ -0,0 +1,13 @@ +--- +title: "Age and nutrient limitation enhance polyunsaturated aldehyde production in marine diatoms" +date: 2007-01-01 +publishDate: 2020-03-09T17:46:51.943245Z +authors: ["François Ribalet", "Thomas Wichard", "Georg Pohnert", "Adrianna Ianora", "Antonio Miralto", "Raffaella Casotti"] +publication_types: ["2"] +abstract: "Skeletonema marinoi produces 2,4-heptadienal, 2,4-octadienal, and 2,4,7-octatrienal, the latter only in traces. In nutrient-replete cultures, the production of potentially defensive polyunsaturated aldehydes (PUA) increases from the exponential to the stationary phase of growth from 1.2 fmol cell-1(±0.4 fmol cell-1SD) to 4.2 fmol cell-1(±1.0 fmol cell-1SD), with 2,4-heptadienal as the dominant aldehyde. The plasticity of PUA production with age of the culture supports the hypothesis of a direct link between toxin production and cell physiological state. N- and P-limited cells in stationary phase produced 1.4 and 1.8 fold higher amounts of PUA than control cultures and 10.7 and 4.6 times higher PUAs when compared to their own exponential growth phase, respectively. The increase in PUA production in the nutrient-limited cultures was not paralleled by an increase in the total amount of precursor fatty acids indicating that physiological stress might trigger an enhanced expression or activity of the enzymes responsible for PUA production, i.e. chemical defense increase in aged and nutrient-stressed diatoms. If this holds true during blooms, grazers feeding at the end of a bloom would be more affected than early-bloom grazers." +featured: false +publication: "*Phytochemistry*" +tags: ["Chemical defense", "Growth phase", "Harmful algal blooms", "Nutrient limitation", "Polyunsaturated fatty acids", "Skeletonema"] +doi: "10.1016/j.phytochem.2007.05.012" +--- + diff --git a/content/publication/ribalet-2008/cite.bib b/content/publication/ribalet-2008/cite.bib new file mode 100644 index 0000000..720ef17 --- /dev/null +++ b/content/publication/ribalet-2008/cite.bib @@ -0,0 +1,14 @@ +@article{Ribalet2008, + abstract = {Bioactive polyunsaturated aldehydes (PUAs) are produced by several marine phytoplankton (mainly diatoms) and have been shown to have a detrimental effect on a wide variety of organisms, including phytoplankton and invertebrates. However, their potential impact on marine bacteria has been largely neglected. We assess here the effect of three PUAs produced by marine diatoms: 2E,4E-decadienal, 2E,4E-octadienal and 2E,4E-heptadienal, on the growth of 33 marine bacterial strains, including 16 strains isolated during a bloom of the PUA-producing diatom Skeletonema marinoi in the Northern Adriatic Sea. A concentration-dependent growth reduction was observed for 19 bacterial strains at concentrations ranging from 3 to 145 $μ$mol L -1 . Surprisingly, Eudora adriatica strain MOLA358 (Flavobacteriaceae) and Alteromonas hispanica strain MOLA151 (Alteromonadaceae) showed growth stimulation upon exposure to PUAs at concentrations between 13 and 18 $μ$mol L -1 . The remaining 12 strains were unaffected by even very high PUA concentrations. Strains isolated during the diatom bloom showed remarkable resistance to PUA exposures, with only two out of 16 strains showing growth inhibition at PUA concentrations below 106, 130, and 145 $μ$mol L -1 for 2E,4E-decadienal, 2E,4E-octadienal and 2E,4E-heptadienal, respectively. No correlation between taxonomical position and sensitivity to PUA was observed. Considering that many bacteria thrive in close vicinity of diatom cells, it is likely that these compounds may shape the structure of associated bacterial communities by representing a selection force. This is even more relevant during the final stages of blooms, when senescence and nutrient limitation increase the potential production and release of aldehydes. © 2007 Elsevier B.V. All rights reserved.}, + author = {Ribalet, Francois and Intertaglia, Laurent and Lebaron, Phillipe and Casotti, Raffaella}, + doi = {10.1016/j.aquatox.2007.11.005}, + file = {:Users/ribalet/Library/Application Support/Mendeley Desktop/Downloaded/Ribalet et al. - 2008 - Differential effect of three polyunsaturated aldehydes on marine bacterial isolates.pdf:pdf}, + issn = {0166445X}, + journal = {Aquatic Toxicology}, + keywords = {Allelochemicals,Diatoms,Growth,LOEC,Marine bacteria,Polyunsaturated aldehydes,Toxicity}, + number = {2}, + title = {Differential effect of three polyunsaturated aldehydes on marine bacterial isolates}, + volume = {86}, + year = {2008} +} + diff --git a/content/publication/ribalet-2008/featured.png b/content/publication/ribalet-2008/featured.png new file mode 100644 index 0000000..dc6c2fc Binary files /dev/null and b/content/publication/ribalet-2008/featured.png differ diff --git a/content/publication/ribalet-2008/index.md b/content/publication/ribalet-2008/index.md new file mode 100644 index 0000000..8d967d2 --- /dev/null +++ b/content/publication/ribalet-2008/index.md @@ -0,0 +1,13 @@ +--- +title: "Differential effect of three polyunsaturated aldehydes on marine bacterial isolates" +date: 2008-01-01 +publishDate: 2020-03-09T17:46:51.940255Z +authors: ["Francois Ribalet", "Laurent Intertaglia", "Phillipe Lebaron", "Raffaella Casotti"] +publication_types: ["2"] +abstract: "Bioactive polyunsaturated aldehydes (PUAs) are produced by several marine phytoplankton (mainly diatoms) and have been shown to have a detrimental effect on a wide variety of organisms, including phytoplankton and invertebrates. However, their potential impact on marine bacteria has been largely neglected. We assess here the effect of three PUAs produced by marine diatoms: 2E,4E-decadienal, 2E,4E-octadienal and 2E,4E-heptadienal, on the growth of 33 marine bacterial strains, including 16 strains isolated during a bloom of the PUA-producing diatom Skeletonema marinoi in the Northern Adriatic Sea. A concentration-dependent growth reduction was observed for 19 bacterial strains at concentrations ranging from 3 to 145 $μ$mol L -1 . Surprisingly, Eudora adriatica strain MOLA358 (Flavobacteriaceae) and Alteromonas hispanica strain MOLA151 (Alteromonadaceae) showed growth stimulation upon exposure to PUAs at concentrations between 13 and 18 $μ$mol L -1 . The remaining 12 strains were unaffected by even very high PUA concentrations. Strains isolated during the diatom bloom showed remarkable resistance to PUA exposures, with only two out of 16 strains showing growth inhibition at PUA concentrations below 106, 130, and 145 $μ$mol L -1 for 2E,4E-decadienal, 2E,4E-octadienal and 2E,4E-heptadienal, respectively. No correlation between taxonomical position and sensitivity to PUA was observed. Considering that many bacteria thrive in close vicinity of diatom cells, it is likely that these compounds may shape the structure of associated bacterial communities by representing a selection force. This is even more relevant during the final stages of blooms, when senescence and nutrient limitation increase the potential production and release of aldehydes. © 2007 Elsevier B.V. All rights reserved." +featured: false +publication: "*Aquatic Toxicology*" +tags: ["Allelochemicals", "Diatoms", "Growth", "LOEC", "Marine bacteria", "Polyunsaturated aldehydes", "Toxicity"] +doi: "10.1016/j.aquatox.2007.11.005" +--- + diff --git a/content/publication/ribalet-2009/cite.bib b/content/publication/ribalet-2009/cite.bib new file mode 100644 index 0000000..c215b92 --- /dev/null +++ b/content/publication/ribalet-2009/cite.bib @@ -0,0 +1,14 @@ +@article{Ribalet2009, + abstract = {Diatoms have evolved a silicified cell wall that provides an efficient barrier against herbivores. These microalgae also produce chemical compounds such as polyunsaturated aldehydes (PUAs) that can potentially impair recruitment and cause malformations in the offspring of such grazers. We measured silica content as an indication of cell wall thickness, organic nutrient cell quotas, PUAs and polyunsaturated fatty acid cell content in Skeletonema marinoi grown under N-, P- and Si-limitation in continuous cultures. A 7.5 fold increase in PUA production was observed (27.5 fmol cell -1 ) in Si-limited cells with respect to the controls, while Si content decreased by 50%. PUA production decreased in nitrogen-limited cells to 0.14 fmol cell -1 and increased 3 times in phosphorus-limited cells (7.53 fmol cell -1 ), while silica content increased by 20% in both cases. The substrate to product ratio suggested that production of the PUAs heptadienal and octadienal was limited by the amount of substrate under P- and Si-limitation, and by enzyme activity under N-limitation. Octatrienal production was likely limited by enzyme activity in all growth conditions. The high PUA levels produced under Si-limitation, when cells have a thinner cell wall, suggests a compensatory alternation of mechanical and chemical defense mechanisms.}, + author = {Ribalet, François and Vidoudez, Charles and Cassin, Daniele and Pohnert, Georg and Ianora, Adrianna and Miralto, Antonio and Casotti, Raffaella}, + doi = {10.1016/j.protis.2009.01.003}, + file = {:Users/ribalet/Library/Application Support/Mendeley Desktop/Downloaded/Ribalet et al. - 2009 - High Plasticity in the Production of Diatom-derived Polyunsaturated Aldehydes under Nutrient Limitation Physiolo.pdf:pdf}, + issn = {14344610}, + journal = {Protist}, + keywords = {Skeletonema marinoi,defense,diatoms,nutrient limitation,polyunsaturated aldehydes}, + number = {3}, + title = {High Plasticity in the Production of Diatom-derived Polyunsaturated Aldehydes under Nutrient Limitation: Physiological and Ecological Implications}, + volume = {160}, + year = {2009} +} + diff --git a/content/publication/ribalet-2009/featured.png b/content/publication/ribalet-2009/featured.png new file mode 100644 index 0000000..b591c76 Binary files /dev/null and b/content/publication/ribalet-2009/featured.png differ diff --git a/content/publication/ribalet-2009/index.md b/content/publication/ribalet-2009/index.md new file mode 100644 index 0000000..5ecb0bb --- /dev/null +++ b/content/publication/ribalet-2009/index.md @@ -0,0 +1,13 @@ +--- +title: "High Plasticity in the Production of Diatom-derived Polyunsaturated Aldehydes under Nutrient Limitation: Physiological and Ecological Implications" +date: 2009-01-01 +publishDate: 2020-03-09T17:46:51.939574Z +authors: ["François Ribalet", "Charles Vidoudez", "Daniele Cassin", "Georg Pohnert", "Adrianna Ianora", "Antonio Miralto", "Raffaella Casotti"] +publication_types: ["2"] +abstract: "Diatoms have evolved a silicified cell wall that provides an efficient barrier against herbivores. These microalgae also produce chemical compounds such as polyunsaturated aldehydes (PUAs) that can potentially impair recruitment and cause malformations in the offspring of such grazers. We measured silica content as an indication of cell wall thickness, organic nutrient cell quotas, PUAs and polyunsaturated fatty acid cell content in Skeletonema marinoi grown under N-, P- and Si-limitation in continuous cultures. A 7.5 fold increase in PUA production was observed (27.5 fmol cell -1 ) in Si-limited cells with respect to the controls, while Si content decreased by 50%. PUA production decreased in nitrogen-limited cells to 0.14 fmol cell -1 and increased 3 times in phosphorus-limited cells (7.53 fmol cell -1 ), while silica content increased by 20% in both cases. The substrate to product ratio suggested that production of the PUAs heptadienal and octadienal was limited by the amount of substrate under P- and Si-limitation, and by enzyme activity under N-limitation. Octatrienal production was likely limited by enzyme activity in all growth conditions. The high PUA levels produced under Si-limitation, when cells have a thinner cell wall, suggests a compensatory alternation of mechanical and chemical defense mechanisms." +featured: false +publication: "*Protist*" +tags: ["Skeletonema marinoi", "defense", "diatoms", "nutrient limitation", "polyunsaturated aldehydes"] +doi: "10.1016/j.protis.2009.01.003" +--- + diff --git a/content/publication/ribalet-2010/cite.bib b/content/publication/ribalet-2010/cite.bib new file mode 100644 index 0000000..993ec32 --- /dev/null +++ b/content/publication/ribalet-2010/cite.bib @@ -0,0 +1,14 @@ +@article{Ribalet2010, + abstract = {In terrestrial ecosystems, transitional areas between different plant communities (ecotones) are formed by steep environmental gradients and are commonly characterized by high species diversity and primary productivity, which in turn influences the foodweb structure of these regions. Whether comparable zones of elevated diversity and productivity characterize ecotones in the oceans remains poorly understood. Here we describe a previously hidden hotspot of phytoplankton diversity and productivity in a narrow but seasonally persistent transition zone at the intersection of iron-poor, nitrate-rich offshore waters and iron-rich, nitrate-poor coastal waters of the Northeast Pacific Ocean. Novel continuous measurements of phytoplankton cell abundance and composition identified a complex succession of blooms of five distinct size classes of phytoplankton populations within a 100-km - wide transition zone. The blooms appear to be fueled by natural iron enrichment of offshore communities as they are transported toward the coast. The observed succession of phytoplankton populations is likely driven by spatial gradients in iron availability or time since iron enrichment. Regardless of the underlying mechanism, the resulting communities have a strong impact on the regional biogeochemistry as evidenced by the low partial pressure of CO 2 and the nearly complete depletion of nutrients. Enhanced phytoplankton productivity and diversity associated with steep environmental gradients are expected wherever water masses with complementary nutrient compositions mix to create a region more favorable for phytoplankton growth. The ability to detect and track these important but poorly characterized marine ecotones is critical for understanding their impact on productivity and ecosystem structure in the oceans.}, + author = {Ribalet, François and Marchetti, Adrian and Hubbard, Kate A. and Brown, Katherin and Durkin, Colleen .A. and Morales, Rhonda and Robert, Marie and Swalwell, Jarred E. and Tortell, Philippe D. and Armbrust, E. Virginia}, + doi = {10.1073/pnas.1005638107}, + file = {:Users/ribalet/Library/Application Support/Mendeley Desktop/Downloaded/Ribalet et al. - 2010 - Unveiling a phytoplankton hotspot at a narrow boundary between coastal and offshore waters.pdf:pdf}, + issn = {10916490}, + journal = {Proceedings of the National Academy of Sciences of the United States of America}, + keywords = {Ecotone,Flow cytometry,High-nitrate,Iron,Transition zone,low-chlorophyll}, + number = {38}, + title = {Unveiling a phytoplankton hotspot at a narrow boundary between coastal and offshore waters}, + volume = {107}, + year = {2010} +} + diff --git a/content/publication/ribalet-2010/featured.png b/content/publication/ribalet-2010/featured.png new file mode 100644 index 0000000..d620f5e Binary files /dev/null and b/content/publication/ribalet-2010/featured.png differ diff --git a/content/publication/ribalet-2010/index.md b/content/publication/ribalet-2010/index.md new file mode 100644 index 0000000..3702907 --- /dev/null +++ b/content/publication/ribalet-2010/index.md @@ -0,0 +1,13 @@ +--- +title: "Unveiling a phytoplankton hotspot at a narrow boundary between coastal and offshore waters" +date: 2010-01-01 +publishDate: 2020-03-09T17:46:51.937854Z +authors: ["François Ribalet", "Adrian Marchetti", "Kate A. Hubbard", "Katherin Brown", "Colleen .A. Durkin", "Rhonda Morales", "Marie Robert", "Jarred E. Swalwell", "Philippe D. Tortell", "E. Virginia Armbrust"] +publication_types: ["2"] +abstract: "In terrestrial ecosystems, transitional areas between different plant communities (ecotones) are formed by steep environmental gradients and are commonly characterized by high species diversity and primary productivity, which in turn influences the foodweb structure of these regions. Whether comparable zones of elevated diversity and productivity characterize ecotones in the oceans remains poorly understood. Here we describe a previously hidden hotspot of phytoplankton diversity and productivity in a narrow but seasonally persistent transition zone at the intersection of iron-poor, nitrate-rich offshore waters and iron-rich, nitrate-poor coastal waters of the Northeast Pacific Ocean. Novel continuous measurements of phytoplankton cell abundance and composition identified a complex succession of blooms of five distinct size classes of phytoplankton populations within a 100-km - wide transition zone. The blooms appear to be fueled by natural iron enrichment of offshore communities as they are transported toward the coast. The observed succession of phytoplankton populations is likely driven by spatial gradients in iron availability or time since iron enrichment. Regardless of the underlying mechanism, the resulting communities have a strong impact on the regional biogeochemistry as evidenced by the low partial pressure of CO 2 and the nearly complete depletion of nutrients. Enhanced phytoplankton productivity and diversity associated with steep environmental gradients are expected wherever water masses with complementary nutrient compositions mix to create a region more favorable for phytoplankton growth. The ability to detect and track these important but poorly characterized marine ecotones is critical for understanding their impact on productivity and ecosystem structure in the oceans." +featured: false +publication: "*Proceedings of the National Academy of Sciences of the United States of America*" +tags: ["Ecotone", "Flow cytometry", "High-nitrate", "Iron", "Transition zone", "low-chlorophyll"] +doi: "10.1073/pnas.1005638107" +--- + diff --git a/content/publication/ribalet-2011/cite.bib b/content/publication/ribalet-2011/cite.bib new file mode 100644 index 0000000..a6c58ba --- /dev/null +++ b/content/publication/ribalet-2011/cite.bib @@ -0,0 +1,13 @@ +@article{Ribalet2011, + abstract = {Motivation: Flow cytometry is a widely used technique among biologists to study the abundances of populations of microscopic algae living in aquatic environments. A new generation of high-frequency flow cytometers collects up to several hundred samples per day and can run continuously for several weeks. Automated computational methods are needed to analyze the different phytoplankton populations present in each sample. Software packages in the programming environment R provide powerful tools for conducting such analyses. Results: We introduce flowPhyto, an R package that performs aggregate statistics on virtually unlimited collections of raw flow cytometry files and provides a memory efficient, parallelized solution for analyzing high-throughput flow cytometric data.}, + author = {Ribalet, Francois and Schruth, David and Armbrust, E. Virginia}, + doi = {10.1093/bioinformatics/btr003}, + file = {:Users/ribalet/Library/Application Support/Mendeley Desktop/Downloaded/Ribalet, Schruth, Armbrust - 2011 - flowPhyto Enabling automated analysis of microscopic algae from continuous flow cytometric data.pdf:pdf}, + issn = {13674803}, + journal = {Bioinformatics}, + number = {5}, + title = {flowPhyto: Enabling automated analysis of microscopic algae from continuous flow cytometric data}, + volume = {27}, + year = {2011} +} + diff --git a/content/publication/ribalet-2011/featured.png b/content/publication/ribalet-2011/featured.png new file mode 100644 index 0000000..b9af536 Binary files /dev/null and b/content/publication/ribalet-2011/featured.png differ diff --git a/content/publication/ribalet-2011/index.md b/content/publication/ribalet-2011/index.md new file mode 100644 index 0000000..d03d2b8 --- /dev/null +++ b/content/publication/ribalet-2011/index.md @@ -0,0 +1,12 @@ +--- +title: "flowPhyto: Enabling automated analysis of microscopic algae from continuous flow cytometric data" +date: 2011-01-01 +publishDate: 2020-03-09T17:46:51.936231Z +authors: ["Francois Ribalet", "David Schruth", "E. Virginia Armbrust"] +publication_types: ["2"] +abstract: "Motivation: Flow cytometry is a widely used technique among biologists to study the abundances of populations of microscopic algae living in aquatic environments. A new generation of high-frequency flow cytometers collects up to several hundred samples per day and can run continuously for several weeks. Automated computational methods are needed to analyze the different phytoplankton populations present in each sample. Software packages in the programming environment R provide powerful tools for conducting such analyses. Results: We introduce flowPhyto, an R package that performs aggregate statistics on virtually unlimited collections of raw flow cytometry files and provides a memory efficient, parallelized solution for analyzing high-throughput flow cytometric data." +featured: false +publication: "*Bioinformatics*" +doi: "10.1093/bioinformatics/btr003" +--- + diff --git a/content/publication/ribalet-2014/cite.bib b/content/publication/ribalet-2014/cite.bib new file mode 100644 index 0000000..e31652a --- /dev/null +++ b/content/publication/ribalet-2014/cite.bib @@ -0,0 +1,14 @@ +@article{Ribalet2014, + abstract = {Diatoms are able to react to biotic and abiotic stress, such as competition, predation and unfavorable growth conditions, by producing bioactive compounds including polyunsaturated aldehydes (PUAs). PUAs have been shown to act against grazers and either enhance or inhibit the growth of different phytoplankton and bacteria both in culture and in the field. Presence of nanomolar concentrations of dissolved PUAs in seawater has been reported in the North Adriatic Sea (Mediterranean), suggesting that these compounds are released in seawater following diatom cell lysis. However, the origin of the PUAs and their effects on natural phytoplankton assemblages remain unclear. Here we present data from four oceanographic cruises that took place during diatom blooms in the northern Adriatic Sea where concentrations of particulate and dissolved PUAs were monitored along with phytoplankton cell lysis. Cell lysis was positively correlated with both concentrations of particulate and dissolved PUAs (R = 0.69 and R = 0.77, respectively), supporting the hypothesis that these compounds are released by cell lysis. However, the highest concentration of dissolved PUAs (2.53 nM) was measured when cell lysis was high (0.24 d(-1)) but no known PUA-producing diatoms were detected, suggesting either that other organisms can produce PUAs or that PUA-producing enzymes retain activity extracellularly after diatom cells have lysed. Although in situ concentrations of dissolved PUAs were one to three orders of magnitude lower than those typically used in laboratory culture experiments, we argue that concentrations produced in the field could induce similar effects to those observed in culture and therefore may help shape plankton community composition and function in the oceans.}, + author = {Ribalet, François and Bastianini, Mauro and Vidoudez, Charles and Acri, Francesco and Berges, John and Ianora, Adrianna and Miralto, Antonio and Pohnert, Georg and Romano, Giovanna and Wichard, Thomas and Casotti, Raffaella}, + doi = {10.1371/journal.pone.0085947}, + file = {:Users/ribalet/Library/Application Support/Mendeley Desktop/Downloaded/Ribalet et al. - 2014 - Phytoplankton cell lysis associated with polyunsaturated aldehyde release in the northern Adriatic Sea.pdf:pdf}, + issn = {19326203}, + journal = {PLoS ONE}, + number = {1}, + pmid = {24497933}, + title = {Phytoplankton cell lysis associated with polyunsaturated aldehyde release in the northern Adriatic Sea}, + volume = {9}, + year = {2014} +} + diff --git a/content/publication/ribalet-2014/featured.png b/content/publication/ribalet-2014/featured.png new file mode 100644 index 0000000..158954c Binary files /dev/null and b/content/publication/ribalet-2014/featured.png differ diff --git a/content/publication/ribalet-2014/index.md b/content/publication/ribalet-2014/index.md new file mode 100644 index 0000000..8a130a8 --- /dev/null +++ b/content/publication/ribalet-2014/index.md @@ -0,0 +1,12 @@ +--- +title: "Phytoplankton cell lysis associated with polyunsaturated aldehyde release in the northern Adriatic Sea" +date: 2014-01-01 +publishDate: 2020-03-09T17:46:51.933493Z +authors: ["François Ribalet", "Mauro Bastianini", "Charles Vidoudez", "Francesco Acri", "John Berges", "Adrianna Ianora", "Antonio Miralto", "Georg Pohnert", "Giovanna Romano", "Thomas Wichard", "Raffaella Casotti"] +publication_types: ["2"] +abstract: "Diatoms are able to react to biotic and abiotic stress, such as competition, predation and unfavorable growth conditions, by producing bioactive compounds including polyunsaturated aldehydes (PUAs). PUAs have been shown to act against grazers and either enhance or inhibit the growth of different phytoplankton and bacteria both in culture and in the field. Presence of nanomolar concentrations of dissolved PUAs in seawater has been reported in the North Adriatic Sea (Mediterranean), suggesting that these compounds are released in seawater following diatom cell lysis. However, the origin of the PUAs and their effects on natural phytoplankton assemblages remain unclear. Here we present data from four oceanographic cruises that took place during diatom blooms in the northern Adriatic Sea where concentrations of particulate and dissolved PUAs were monitored along with phytoplankton cell lysis. Cell lysis was positively correlated with both concentrations of particulate and dissolved PUAs (R = 0.69 and R = 0.77, respectively), supporting the hypothesis that these compounds are released by cell lysis. However, the highest concentration of dissolved PUAs (2.53 nM) was measured when cell lysis was high (0.24 d(-1)) but no known PUA-producing diatoms were detected, suggesting either that other organisms can produce PUAs or that PUA-producing enzymes retain activity extracellularly after diatom cells have lysed. Although in situ concentrations of dissolved PUAs were one to three orders of magnitude lower than those typically used in laboratory culture experiments, we argue that concentrations produced in the field could induce similar effects to those observed in culture and therefore may help shape plankton community composition and function in the oceans." +featured: false +publication: "*PLoS ONE*" +doi: "10.1371/journal.pone.0085947" +--- + diff --git a/content/publication/ribalet-2015/cite.bib b/content/publication/ribalet-2015/cite.bib new file mode 100644 index 0000000..7127086 --- /dev/null +++ b/content/publication/ribalet-2015/cite.bib @@ -0,0 +1,17 @@ +@article{Ribalet2015, + abstract = {Theoretical studies predict that competition for limited resources reduces biodiversity to the point of ecological instability, whereas strong predator/prey interactions enhance the number of coexisting species and limit fluctuations in abundances. In open ocean ecosystems, competition for low availability of essential nutrients results in relatively few abundant microbial species. The remarkable stability in overall cell abundance of the dominant photosynthetic cyanobacterium Prochlorococcus is assumed to reflect a simple food web structure strongly controlled by grazers and/or viruses. This hypothesized link between stability and ecological interactions, however, has been difficult to test with open ocean microbes because sampling methods commonly have poor temporal and spatial resolution. Here we use continuous techniques on two different winter-time cruises to show that Prochlorococcus cell production and mortality rates are tightly synchronized to the day/night cycle across the subtropical Pacific Ocean. In warmer waters, we observed harmonic oscillations in cell production and mortality rates, with a peak in mortality rate consistently occurring ∼6 h after the peak in cell production. Essentially no cell mortality was observed during daylight. Our results are best explained as a synchronized two-component trophic interaction with the per-capita rates of Prochlorococcus consumption driven either directly by the day/night cycle or indirectly by Prochlorococcus cell production. Light-driven synchrony of food web dynamics in which most of the newly produced Prochlorococcus cells are consumed each night likely enforces ecosystem stability across vast expanses of the open ocean.}, + author = {Ribalet, Francois and Swalwell, Jarred and Clayton, Sophie and Jiménez, Valeria and Sudek, Sebastian and Lin, Yajuan and Johnson, Zackary I. and Worden, Alexandra Z. and Armbrust, E. Virginia}, + doi = {10.1073/pnas.1424279112}, + file = {:Users/ribalet/Downloads/pnas.1424279112.sapp.pdf:pdf;:Users/ribalet/Library/Application Support/Mendeley Desktop/Downloaded/Ribalet et al. - 2015 - Light-driven synchrony of Prochlorococcus growth and mortality in the subtropical Pacific gyre(2).pdf:pdf}, + issn = {0027-8424}, + journal = {Proceedings of the National Academy of Sciences}, + keywords = {Cell division,Cyanobacteria,Flow cytometry,Mortality,SeaFlow}, + month = {jun}, + number = {26}, + pages = {8008--8012}, + title = {Light-driven synchrony of Prochlorococcus growth and mortality in the subtropical Pacific gyre}, + url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1424279112}, + volume = {112}, + year = {2015} +} + diff --git a/content/publication/ribalet-2015/featured.png b/content/publication/ribalet-2015/featured.png new file mode 100644 index 0000000..217fe69 Binary files /dev/null and b/content/publication/ribalet-2015/featured.png differ diff --git a/content/publication/ribalet-2015/index.md b/content/publication/ribalet-2015/index.md new file mode 100644 index 0000000..2d36d51 --- /dev/null +++ b/content/publication/ribalet-2015/index.md @@ -0,0 +1,14 @@ +--- +title: "Light-driven synchrony of Prochlorococcus growth and mortality in the subtropical Pacific gyre" +date: 2015-06-01 +publishDate: 2020-03-09T17:46:51.932643Z +authors: ["Francois Ribalet", "Jarred Swalwell", "Sophie Clayton", "Valeria Jiménez", "Sebastian Sudek", "Yajuan Lin", "Zackary I. Johnson", "Alexandra Z. Worden", "E. Virginia Armbrust"] +publication_types: ["2"] +abstract: "Theoretical studies predict that competition for limited resources reduces biodiversity to the point of ecological instability, whereas strong predator/prey interactions enhance the number of coexisting species and limit fluctuations in abundances. In open ocean ecosystems, competition for low availability of essential nutrients results in relatively few abundant microbial species. The remarkable stability in overall cell abundance of the dominant photosynthetic cyanobacterium Prochlorococcus is assumed to reflect a simple food web structure strongly controlled by grazers and/or viruses. This hypothesized link between stability and ecological interactions, however, has been difficult to test with open ocean microbes because sampling methods commonly have poor temporal and spatial resolution. Here we use continuous techniques on two different winter-time cruises to show that Prochlorococcus cell production and mortality rates are tightly synchronized to the day/night cycle across the subtropical Pacific Ocean. In warmer waters, we observed harmonic oscillations in cell production and mortality rates, with a peak in mortality rate consistently occurring ∼6 h after the peak in cell production. Essentially no cell mortality was observed during daylight. Our results are best explained as a synchronized two-component trophic interaction with the per-capita rates of Prochlorococcus consumption driven either directly by the day/night cycle or indirectly by Prochlorococcus cell production. Light-driven synchrony of food web dynamics in which most of the newly produced Prochlorococcus cells are consumed each night likely enforces ecosystem stability across vast expanses of the open ocean." +featured: false +publication: "*Proceedings of the National Academy of Sciences*" +tags: ["Cell division", "Cyanobacteria", "Flow cytometry", "Mortality", "SeaFlow"] +url_pdf: "http://www.pnas.org/lookup/doi/10.1073/pnas.1424279112" +doi: "10.1073/pnas.1424279112" +--- + diff --git a/content/publication/ribalet-2019/cite.bib b/content/publication/ribalet-2019/cite.bib new file mode 100644 index 0000000..724a486 --- /dev/null +++ b/content/publication/ribalet-2019/cite.bib @@ -0,0 +1,18 @@ +@article{Ribalet2019, + abstract = {SeaFlow is an underway flow cytometer that provides continuous shipboard observations of the abundance and optical properties of small phytoplankton (\textless5 $μ$m in equivalent spherical diameter, ESD). Here we present data sets consisting of SeaFlow-based cell abundance, forward light scatter, and pigment fluorescence of individual cells, as well as derived estimates of ESD and cellular carbon content of picophytoplankton, which includes the cyanobacteria Prochlorococcus, Synechococcus and small-sized Crocosphaera (\textless5 $μ$m ESD), and picophytoplankton and nanophytoplankton (2–5 $μ$m ESD). Data were collected in surface waters (≈5 m depth) from 27 oceanographic cruises carried out in the Northeast Pacific Ocean between 2010 and 2018. Thirteen cruises provide high spatial resolution (≈1 km) measurements across 32,500 km of the Northeast Pacific Ocean and 14 near-monthly cruises beginning in 2015 provide seasonal distributions at the long-term sampling site (Station ALOHA) of the Hawaii Ocean Time-Series. These data sets expand our knowledge of the current spatial and temporal distributions of picophytoplankton in the surface ocean.}, + author = {Ribalet, François and Berthiaume, Chris and Hynes, Annette and Swalwell, Jarred and Carlson, Michael and Clayton, Sophie and Hennon, Gwenn and Poirier, Camille and Shimabukuro, Eric and White, Angelicque and Armbrust, E. Virginia}, + doi = {10.1038/s41597-019-0292-2}, + file = {:Users/ribalet/Library/Application Support/Mendeley Desktop/Downloaded/Ribalet et al. - 2019 - SeaFlow data v1, high-resolution abundance, size and biomass of small phytoplankton in the North Pacific.pdf:pdf}, + issn = {2052-4463}, + journal = {Scientific Data}, + keywords = {Marine biology,Microbial ecology}, + month = {dec}, + number = {1}, + pages = {277}, + publisher = {Nature Publishing Group}, + title = {SeaFlow data v1, high-resolution abundance, size and biomass of small phytoplankton in the North Pacific}, + url = {http://www.nature.com/articles/s41597-019-0292-2}, + volume = {6}, + year = {2019} +} + diff --git a/content/publication/ribalet-2019/featured.png b/content/publication/ribalet-2019/featured.png new file mode 100644 index 0000000..c199c35 Binary files /dev/null and b/content/publication/ribalet-2019/featured.png differ diff --git a/content/publication/ribalet-2019/index.md b/content/publication/ribalet-2019/index.md new file mode 100644 index 0000000..15b3947 --- /dev/null +++ b/content/publication/ribalet-2019/index.md @@ -0,0 +1,14 @@ +--- +title: "SeaFlow data v1, high-resolution abundance, size and biomass of small phytoplankton in the North Pacific" +date: 2019-12-01 +publishDate: 2020-03-09T17:46:51.928149Z +authors: ["François Ribalet", "Chris Berthiaume", "Annette Hynes", "Jarred Swalwell", "Michael Carlson", "Sophie Clayton", "Gwenn Hennon", "Camille Poirier", "Eric Shimabukuro", "Angelicque White", "E. Virginia Armbrust"] +publication_types: ["2"] +abstract: "SeaFlow is an underway flow cytometer that provides continuous shipboard observations of the abundance and optical properties of small phytoplankton (< 5 μm in equivalent spherical diameter, ESD). Here we present data sets consisting of SeaFlow-based cell abundance, forward light scatter, and pigment fluorescence of individual cells, as well as derived estimates of ESD and cellular carbon content of picophytoplankton, which includes the cyanobacteria Prochlorococcus, Synechococcus and small-sized Crocosphaera (< 5 μm ESD), and picophytoplankton and nanophytoplankton (2–5 μm ESD). Data were collected in surface waters (≈5 m depth) from 27 oceanographic cruises carried out in the Northeast Pacific Ocean between 2010 and 2018. Thirteen cruises provide high spatial resolution (≈1 km) measurements across 32,500 km of the Northeast Pacific Ocean and 14 near-monthly cruises beginning in 2015 provide seasonal distributions at the long-term sampling site (Station ALOHA) of the Hawaii Ocean Time-Series. These data sets expand our knowledge of the current spatial and temporal distributions of picophytoplankton in the surface ocean." +featured: true +publication: "*Scientific Data*" +tags: ["Marine biology", "Microbial ecology"] +url_pdf: "http://www.nature.com/articles/s41597-019-0292-2" +doi: "10.1038/s41597-019-0292-2" +--- + diff --git a/content/publication/smyth-2023/cite.bib b/content/publication/smyth-2023/cite.bib new file mode 100644 index 0000000..64d39f1 --- /dev/null +++ b/content/publication/smyth-2023/cite.bib @@ -0,0 +1,13 @@ +@Article{Smyth2023, + author = {Smyth, Timothy and Moffat, David and Tarran, Glen and Sathyendranath, Shubha and Ribalet, Francois and Casey, John}, + journal = {Frontiers in Marine Science}, + title = {Determining drivers of phytoplankton carbon to chlorophyll ratio at {Atlantic} {Basin} scale}, + year = {2023}, + issn = {2296-7745}, + volume = {10}, + abstract = {We demonstrate the ability of flow cytometry to determine species specific cellular carbon and chlorophyll content in vivo by using laboratory cultures of phytoplankton encompassing a wide range of cell sizes. When applied to the large Atlantic Meridional Transect flow cytometry dataset, we reveal patterns in the species-specific phytoplankton carbon (C), chlorophyll (Chl) and C:Chl ratio. For Prochlorococcus the range of C:Chl is between 2 – 604; for Synechococcus 0.5 – 558. Using a Random Forest machine learning approach, we show that predictability of phytoplankton C:Chl, dominated by the prevalence of Prochlorococcus, is largely driven by silicate and nitrite concentration in the Atlantic Ocean.}, + doi = {10.3389/fmars.2023.1191216}, + file = {:Smyth2023.pdf:PDF}, + url = {https://www.frontiersin.org/articles/10.3389/fmars.2023.1191216}, + urldate = {2023-07-11}, +} diff --git a/content/publication/smyth-2023/featured.png b/content/publication/smyth-2023/featured.png new file mode 100644 index 0000000..ecb2fa1 Binary files /dev/null and b/content/publication/smyth-2023/featured.png differ diff --git a/content/publication/smyth-2023/index.md b/content/publication/smyth-2023/index.md new file mode 100644 index 0000000..e319df5 --- /dev/null +++ b/content/publication/smyth-2023/index.md @@ -0,0 +1,15 @@ +--- +title : "Determining drivers of phytoplankton carbon to chlorophyll ratio at Atlantic Basin scale" +date : "2023-07-11" +publishDate : 2023-07-11T17:46:51.936845Z +authors : ["Timothy Smyth", "David Moffat", "Glen Tarran", "Shubha Sathyendranath", "François Ribalet", "John Casey"] +publication_types : ["2"] +abstract : "We demonstrate the ability of flow cytometry to determine species specific cellular carbon and chlorophyll content in vivo by using laboratory cultures of phytoplankton encompassing a wide range of cell sizes. When applied to the large Atlantic Meridional Transect flow cytometry dataset, we reveal patterns in the species-specific phytoplankton carbon (C), chlorophyll (Chl) and C:Chl ratio. For Prochlorococcus the range of C:Chl is between 2 – 604; for Synechococcus 0.5 – 558. Using a Random Forest machine learning approach, we show that predictability of phytoplankton C:Chl, dominated by the prevalence of Prochlorococcus, is largely driven by silicate and nitrite concentration in the Atlantic Ocean." +featured : true +projects : [] +tags : [] +publication : "*Frontiers in Marine Science*" +doi: "10.3389/fmars.2023.1191216" +math : false +--- + diff --git a/content/publication/swalwell-2011/cite.bib b/content/publication/swalwell-2011/cite.bib new file mode 100644 index 0000000..59eda8d --- /dev/null +++ b/content/publication/swalwell-2011/cite.bib @@ -0,0 +1,13 @@ +@article{Swalwell2011, + abstract = {Current automated flow cytometers primarily target the dynamics of phytoplankton communities in coastal environments and lack the sensitivity to resolve the spatial distribution of Prochlorococcus, the smallest phytoplankton that dominates the open ocean. Here we present SeaFlow, a novel flow cytometer developed for continuous real-time observations of natural assemblages of small phytoplankton cells, including Prochlorococcus. Unlike other flow cytometers, SeaFlow does not use sheath fluid. Instead, a virtual-core is used to determine the position of a particle in the stream of seawater. By eliminating sheath fluid, SeaFlow can continuously sample the seawater stream directly from a ship's intake system. Image analysis is used to automatically align the laser with the optical system and then monitor and correct for drift. SeaFlow performs rapid quantification (up to 24,000 cells per second) of multidimensional characteristics of phytoplankton cells in the pico- to nanophytoplankton size range (0.5-20 $μ$m) to analyze the equivalent of 480 traditional flow cytometry samples per day while on board a research vessel. Data analysis tools have been created to automatically cluster and count phytoplankton populations with geo-referenced data visualization. SeaFlow makes it possible to explore surface phytoplankton dynamics at a spatial scale ranging from a few meters to thousands of kilometers. An example data set is presented from a 450-km long transect near the Hawaiian Islands with the continuous data aggregated in 3 min intervals. © 2011, by the American Society of Limnology and Oceanography, Inc.}, + author = {Swalwell, Jarred E. and Ribalet, François and Armbrust, E. Virginia}, + doi = {10.4319/lom.2011.9.466}, + file = {:Users/ribalet/Library/Application Support/Mendeley Desktop/Downloaded/Swalwell, Ribalet, Armbrust - 2011 - Seaflow A novel underway flow-cytometer for continuous observations of phytoplankton in the ocean.pdf:pdf}, + issn = {15415856}, + journal = {Limnology and Oceanography: Methods}, + number = {OCTOBER}, + title = {Seaflow: A novel underway flow-cytometer for continuous observations of phytoplankton in the ocean}, + volume = {9}, + year = {2011} +} + diff --git a/content/publication/swalwell-2011/featured.png b/content/publication/swalwell-2011/featured.png new file mode 100644 index 0000000..2a5dece Binary files /dev/null and b/content/publication/swalwell-2011/featured.png differ diff --git a/content/publication/swalwell-2011/index.md b/content/publication/swalwell-2011/index.md new file mode 100644 index 0000000..1e22493 --- /dev/null +++ b/content/publication/swalwell-2011/index.md @@ -0,0 +1,12 @@ +--- +title: "Seaflow: A novel underway flow-cytometer for continuous observations of phytoplankton in the ocean" +date: 2011-01-01 +publishDate: 2020-03-09T17:46:51.936845Z +authors: ["Jarred E. Swalwell", "François Ribalet", "E. Virginia Armbrust"] +publication_types: ["2"] +abstract: "Current automated flow cytometers primarily target the dynamics of phytoplankton communities in coastal environments and lack the sensitivity to resolve the spatial distribution of Prochlorococcus, the smallest phytoplankton that dominates the open ocean. Here we present SeaFlow, a novel flow cytometer developed for continuous real-time observations of natural assemblages of small phytoplankton cells, including Prochlorococcus. Unlike other flow cytometers, SeaFlow does not use sheath fluid. Instead, a virtual-core is used to determine the position of a particle in the stream of seawater. By eliminating sheath fluid, SeaFlow can continuously sample the seawater stream directly from a ship's intake system. Image analysis is used to automatically align the laser with the optical system and then monitor and correct for drift. SeaFlow performs rapid quantification (up to 24,000 cells per second) of multidimensional characteristics of phytoplankton cells in the pico- to nanophytoplankton size range (0.5-20 μm) to analyze the equivalent of 480 traditional flow cytometry samples per day while on board a research vessel. Data analysis tools have been created to automatically cluster and count phytoplankton populations with geo-referenced data visualization. SeaFlow makes it possible to explore surface phytoplankton dynamics at a spatial scale ranging from a few meters to thousands of kilometers. An example data set is presented from a 450-km long transect near the Hawaiian Islands with the continuous data aggregated in 3 min intervals." +featured: false +publication: "*Limnology and Oceanography: Methods*" +doi: "10.4319/lom.2011.9.466" +--- + diff --git a/content/publication/thyssen-2022/cite.bib b/content/publication/thyssen-2022/cite.bib new file mode 100644 index 0000000..2184fbf --- /dev/null +++ b/content/publication/thyssen-2022/cite.bib @@ -0,0 +1,8 @@ +@article{thyssen_interoperable_2022 + abstract = {The recent development of biological sensors has extended marine plankton studies from conducting laboratory bench work to in vivo and real-time observations. Flow cytometry (FCM) has shed new light on marine microorganisms since the 1980s through its single-cell approach and robust detection of the smallest cells. FCM records valuable optical properties of light scattering and fluorescence from cells passing in a single file in front of a narrow-collimated light source, recording tens of thousands of cells within a few minutes. Depending on the instrument settings, the sampling strategy, and the automation level, it resolves the spatial and temporal distribution of microbial marine prokaryotes and eukaryotes. Cells are usually classified and grouped on cytograms by experts and are still lacking standards, reducing data sharing capacities. Therefore, the need to make FCM data sets FAIR (Findability, Accessibility, Interoperability, and Reusability of digital assets) is becoming critical. In this paper, we present a consensus vocabulary for the 13 most common marine microbial groups observed with FCM using blue and red-light excitation. The authors designed a common layout on two-dimensional log-transformed cytograms reinforced by a decision tree that facilitates the characterization of groups. The proposed vocabulary aims at standardising data analysis and definitions, to promote harmonisation and comparison of data between users and instruments. This represents a much-needed step towards FAIRification of flow cytometric data collected in various marine environments.}, + author = {Thyssen, Melilotus and Grégori, Gérald and Créach, Véronique and Lahbib, Soumaya and Dugenne, Mathilde and Aardema, Hedy M. and Artigas, Luis Felipe and Huang, Bangqin and Barani, Aude and Beaugeard, Laureen and Bellaaj-Zouari, Amel and Beran, Alfred and Casotti, Raffaella and Del Amo, Yolanda and Denis, Michel and Dubelaar, George B.J. and Endres, Sonja and Haraguchi, Lumi and Karlson, Bengt and Lambert, Christophe and Louchart, Arnaud and Marie, Dominique and Moncoiffé, Gwenaëlle and Pecqueur, David and Ribalet, François and Rijkeboer, Machteld and Silovic, Tina and Silva, Ricardo and Marro, Sophie and Sosik, Heidi M. and Sourisseau, Marc and Tarran, Glen and Van Oostende, Nicolas and Zhao, Li and Zheng, Shan}, + doi = {10.3389/FMARS.2022.975877}, + journal = {Frontiers in Marine Science}, + title = {Interoperable vocabulary for marine microbial flow cytometry}, + volume = {9} +} diff --git a/content/publication/thyssen-2022/featured.png b/content/publication/thyssen-2022/featured.png new file mode 100644 index 0000000..e2c03c6 Binary files /dev/null and b/content/publication/thyssen-2022/featured.png differ diff --git a/content/publication/thyssen-2022/index.md b/content/publication/thyssen-2022/index.md new file mode 100644 index 0000000..b79b2d3 --- /dev/null +++ b/content/publication/thyssen-2022/index.md @@ -0,0 +1,13 @@ +--- +title : "Interoperable vocabulary for marine microbial flow cytometry" +date : "2024-12-01T00:00:00" +authors : ["Melilotus Thyssen", "Gérald Grégori", "Véronique Créach", "Soumaya Lahbib", "Mathilde Dugenne", "Hedy M. Aardema", "Luis Felipe Artigas", "Bangqin Huang", "Aude Barani", "Laureen Beaugeard", "Amel Bellaaj-Zouari", "Alfred Beran", "Raffaella Casotti", "Yol Del Amo", "a", "Michel Denis", "George B.J. Dubelaar", "Sonja Endres", "Lumi Haraguchi", "Bengt Karlson", "Christophe Lambert", "Arnaud Louchart", "Dominique Marie", "Gwenaëlle Moncoiffé", "David Pecqueur", "François Ribalet", "Machteld Rijkeboer", "Tina Silovic", "Ricardo Silva", "Sophie Marro", "Heidi M. Sosik", "Marc Sourisseau", "Glen Tarran", "Nicolas Van Oostende", "Li Zhao", "Shan Zheng"] +publication_types : ["2"] +publication : "in *Frontiers in Marine Science*" +abstract : "The recent development of biological sensors has extended marine plankton studies from conducting laboratory bench work to in vivo and real-time observations. Flow cytometry (FCM) has shed new light on marine microorganisms since the 1980s through its single-cell approach and robust detection of the smallest cells. FCM records valuable optical properties of light scattering and fluorescence from cells passing in a single file in front of a narrow-collimated light source, recording tens of thousands of cells within a few minutes. Depending on the instrument settings, the sampling strategy, and the automation level, it resolves the spatial and temporal distribution of microbial marine prokaryotes and eukaryotes. Cells are usually classified and grouped on cytograms by experts and are still lacking standards, reducing data sharing capacities. Therefore, the need to make FCM data sets FAIR (Findability, Accessibility, Interoperability, and Reusability of digital assets) is becoming critical. In this paper, we present a consensus vocabulary for the 13 most common marine microbial groups observed with FCM using blue and red-light excitation. The authors designed a common layout on two-dimensional log-transformed cytograms reinforced by a decision tree that facilitates the characterization of groups. The proposed vocabulary aims at standardising data analysis and definitions, to promote harmonisation and comparison of data between users and instruments. This represents a much-needed step towards FAIRification of flow cytometric data collected in various marine environments." +featured : false +projects : [] +tags : [] +doi : "10.3389/FMARS.2022.975877" +math : false +--- diff --git a/content/publication/vardi-2006/cite.bib b/content/publication/vardi-2006/cite.bib new file mode 100644 index 0000000..6c7b381 --- /dev/null +++ b/content/publication/vardi-2006/cite.bib @@ -0,0 +1,16 @@ +@article{Vardi2006, + abstract = {Diatoms are an important group of eukaryotic phytoplankton, responsible for about 20% of global primary productivity. Study of the functional role of chemical signaling within phytoplankton assemblages is still in its infancy although recent reports in diatoms suggest the existence of chemical-based defense strategies. Here, we demonstrate how the accurate perception of diatom-derived reactive aldehydes can determine cell fate in diatoms. In particular, the aldehyde (2E,4E/Z)-decadienal (DD) can trigger intracellular calcium transients and the generation of nitric oxide (NO) by a calcium-dependent NO synthase-like activity, which results in cell death. However, pretreatment of cells with sublethal doses of aldehyde can induce resistance to subsequent lethal doses, which is reflected in an altered calcium signature and kinetics of NO production. We also present evidence for a DD-derived NO-based intercellular signaling system for the perception of stressed bystander cells. Based on these findings, we propose the existence of a sophisticated stress surveillance system in diatoms, which has important implications for understanding the cellular mechanisms responsible for acclimation versus death during phytoplankton bloom successions.}, + author = {Vardi, Assaf and Formiggini, Fabio and Casotti, Raffaella and De Martino, Alessandra and Ribalet, François and Miralto, Antonio and Bowler, Chris}, + doi = {10.1371/journal.pbio.0040060}, + file = {:Users/ribalet/Library/Application Support/Mendeley Desktop/Downloaded/Vardi et al. - 2006 - A stress surveillance system based on calcium and nitric oxide in marine diatoms.pdf:pdf}, + isbn = {1544-9173}, + issn = {15457885}, + journal = {PLoS Biology}, + number = {3}, + pages = {0411--0419}, + pmid = {16475869}, + title = {A stress surveillance system based on calcium and nitric oxide in marine diatoms}, + volume = {4}, + year = {2006} +} + diff --git a/content/publication/vardi-2006/featured.png b/content/publication/vardi-2006/featured.png new file mode 100644 index 0000000..04d0b17 Binary files /dev/null and b/content/publication/vardi-2006/featured.png differ diff --git a/content/publication/vardi-2006/index.md b/content/publication/vardi-2006/index.md new file mode 100644 index 0000000..64f56de --- /dev/null +++ b/content/publication/vardi-2006/index.md @@ -0,0 +1,12 @@ +--- +title: "A stress surveillance system based on calcium and nitric oxide in marine diatoms" +date: 2006-01-01 +publishDate: 2020-03-09T17:46:51.944300Z +authors: ["Assaf Vardi", "Fabio Formiggini", "Raffaella Casotti", "Alessandra De Martino", "François Ribalet", "Antonio Miralto", "Chris Bowler"] +publication_types: ["2"] +abstract: "Diatoms are an important group of eukaryotic phytoplankton, responsible for about 20% of global primary productivity. Study of the functional role of chemical signaling within phytoplankton assemblages is still in its infancy although recent reports in diatoms suggest the existence of chemical-based defense strategies. Here, we demonstrate how the accurate perception of diatom-derived reactive aldehydes can determine cell fate in diatoms. In particular, the aldehyde (2E,4E/Z)-decadienal (DD) can trigger intracellular calcium transients and the generation of nitric oxide (NO) by a calcium-dependent NO synthase-like activity, which results in cell death. However, pretreatment of cells with sublethal doses of aldehyde can induce resistance to subsequent lethal doses, which is reflected in an altered calcium signature and kinetics of NO production. We also present evidence for a DD-derived NO-based intercellular signaling system for the perception of stressed bystander cells. Based on these findings, we propose the existence of a sophisticated stress surveillance system in diatoms, which has important implications for understanding the cellular mechanisms responsible for acclimation versus death during phytoplankton bloom successions." +featured: false +publication: "*PLoS Biology*" +doi: "10.1371/journal.pbio.0040060" +--- + diff --git a/content/publication/wilson-2017/cite.bib b/content/publication/wilson-2017/cite.bib new file mode 100644 index 0000000..bc83ce1 --- /dev/null +++ b/content/publication/wilson-2017/cite.bib @@ -0,0 +1,12 @@ +@article{Wilson2017, + abstract = {The temporal dynamics of phytoplankton growth and activity have large impacts on fluxes of matter and energy, yet obtaining in situ metabolic measurements of sufficient resolution for even dominant microorganisms remains a considerable challenge. We performed Lagrangian diel sampling with synoptic measurements of population abundances, dinitrogen (N2) fixation, mortality, productivity, export and transcription in a bloom of Crocosphaera over eight days in the North Pacific Subtropical Gyre (NPSG). Quantitative transcriptomic analyses revealed clear diel oscillations in transcript abundances for 34% of Crocosphaera genes identified, reflecting a systematic progression of gene expression in diverse metabolic pathways. Significant time-lagged correspondence was evident between nifH transcript abundance and maximal N2 fixation, as well as sepF transcript abundance and cell division, demonstrating the utility of transcriptomics to predict the occurrence and timing of physiological and biogeochemical processes in natural populations. Indirect estimates of carbon fixation by Crocosphaera were equivalent to 11% of net community production, suggesting that under bloom conditions this diazotroph has a considerable impact on the wider carbon cycle. Our cross-scale synthesis of molecular, population and community-wide data underscores the tightly coordinated in situ metabolism of the keystone N2-fixing cyanobacterium Crocosphaera, as well as the broader ecosystem-wide implications of its activities.}, + author = {Wilson, S.T. and Aylward, F.O. and Ribalet, F. and Barone, B. and Casey, J.R. and Connell, P.E. and Eppley, J.M. and Ferron, S. and Fitzsimmons, J.N. and Hayes, C.T. and Romano, A.E. and Turk-Kubo, K.A. and Vislova, A. and Virginia Armbrust, E. and Caron, D.A. and Church, M.J. and Zehr, J.P. and Karl, D.M. and De Long, E.F.}, + doi = {10.1038/nmicrobiol.2017.118}, + file = {:Users/ribalet/Library/Application Support/Mendeley Desktop/Downloaded/Wilson et al. - 2017 - Coordinated regulation of growth, activity and transcription in natural populations of the unicellular nitrogen-f.pdf:pdf}, + issn = {20585276}, + journal = {Nature Microbiology}, + title = {Coordinated regulation of growth, activity and transcription in natural populations of the unicellular nitrogen-fixing cyanobacterium Crocosphaera}, + volume = {2}, + year = {2017} +} + diff --git a/content/publication/wilson-2017/featured.png b/content/publication/wilson-2017/featured.png new file mode 100644 index 0000000..9ff6b3f Binary files /dev/null and b/content/publication/wilson-2017/featured.png differ diff --git a/content/publication/wilson-2017/index.md b/content/publication/wilson-2017/index.md new file mode 100644 index 0000000..3cb3b46 --- /dev/null +++ b/content/publication/wilson-2017/index.md @@ -0,0 +1,12 @@ +--- +title: "Coordinated regulation of growth, activity and transcription in natural populations of the unicellular nitrogen-fixing cyanobacterium Crocosphaera" +date: 2017-01-01 +publishDate: 2020-03-09T17:46:51.930164Z +authors: ["S.T. Wilson", "F.O. Aylward", "F. Ribalet", "B. Barone", "J.R. Casey", "P.E. Connell", "J.M. Eppley", "S. Ferron", "J.N. Fitzsimmons", "C.T. Hayes", "A.E. Romano", "K.A. Turk-Kubo", "A. Vislova", "E. Virginia Armbrust", "D.A. Caron", "M.J. Church", "J.P. Zehr", "D.M. Karl", "E.F. De Long"] +publication_types: ["2"] +abstract: "The temporal dynamics of phytoplankton growth and activity have large impacts on fluxes of matter and energy, yet obtaining in situ metabolic measurements of sufficient resolution for even dominant microorganisms remains a considerable challenge. We performed Lagrangian diel sampling with synoptic measurements of population abundances, dinitrogen (N2) fixation, mortality, productivity, export and transcription in a bloom of Crocosphaera over eight days in the North Pacific Subtropical Gyre (NPSG). Quantitative transcriptomic analyses revealed clear diel oscillations in transcript abundances for 34% of Crocosphaera genes identified, reflecting a systematic progression of gene expression in diverse metabolic pathways. Significant time-lagged correspondence was evident between nifH transcript abundance and maximal N2 fixation, as well as sepF transcript abundance and cell division, demonstrating the utility of transcriptomics to predict the occurrence and timing of physiological and biogeochemical processes in natural populations. Indirect estimates of carbon fixation by Crocosphaera were equivalent to 11% of net community production, suggesting that under bloom conditions this diazotroph has a considerable impact on the wider carbon cycle. Our cross-scale synthesis of molecular, population and community-wide data underscores the tightly coordinated in situ metabolism of the keystone N2-fixing cyanobacterium Crocosphaera, as well as the broader ecosystem-wide implications of its activities." +featured: false +publication: "*Nature Microbiology*" +doi: "10.1038/nmicrobiol.2017.118" +--- + diff --git a/content/publication/wilson-2019/cite.bib b/content/publication/wilson-2019/cite.bib new file mode 100644 index 0000000..cb8dcc7 --- /dev/null +++ b/content/publication/wilson-2019/cite.bib @@ -0,0 +1,17 @@ +@article{Wilson2019, + abstract = {From June to August 2018, the eruption of Kīlauea volcano on the island of Hawai‘i injected millions of cubic meters of molten lava into the nutrient-poor waters of the North Pacific Subtropical Gyre.The lava-impacted seawater was characterized by high concentrations of metals and nutrients that stimulated phytoplankton growth, resulting in an extensive plume of chlorophyll a that was detectable by satellite. Chemical and molecular evidence revealed that this biological response hinged on unexpectedly high concentrations of nitrate, despite the negligible quantities of nitrogen in basaltic lava. We hypothesize that the high nitrate was caused by buoyant plumes of nutrient-rich deep waters created by the substantial input of lava into the ocean. This large-scale ocean fertilization was therefore a unique perturbation event that revealed how marine ecosystems respond to exogenous inputs of nutrients.}, + author = {Wilson, Samuel T. and Hawco, Nicholas J. and Armbrust, E. Virginia and Barone, Benedetto and Björkman, Karin M. and Boysen, Angela K. and Burgos, Macarena and Burrell, Timothy J. and Casey, John R. and DeLong, Edward F. and Dugenne, Mathilde and Dutkiewicz, Stephanie and Dyhrman, Sonya T. and Ferrón, Sara and Follows, Michael J. and Foreman, Rhea K. and Funkey, Carolina P. and Harke, Matthew J. and Henke, Britt A. and Hill, Christopher N. and Hynes, Annette M. and Ingalls, Anitra E. and Jahn, Oliver and Kelly, Rachel L. and Knapp, Angela N. and Letelier, Ricardo M. and Ribalet, Francois and Shimabukuro, Eric M. and Tabata, Ryan K. S. and Turk-Kubo, Kendra A. and White, Angelique E. and Zehr, Jonathan P. and John, Seth and Karl, David M.}, + doi = {10.1126/SCIENCE.AAX4767}, + file = {:Users/ribalet/Library/Application Support/Mendeley Desktop/Downloaded/Wilson et al. - 2019 - Kīlauea lava fuels phytoplankton bloom in the North Pacific Ocean.pdf:pdf}, + issn = {0036-8075}, + journal = {Science}, + month = {sep}, + number = {6457}, + pages = {1040--1044}, + publisher = {American Association for the Advancement of Science}, + title = {Kīlauea lava fuels phytoplankton bloom in the North Pacific Ocean}, + url = {https://science.sciencemag.org/content/365/6457/1040?utm_campaign=toc_sci-mag_2019-09-05&et_rid=40171609&et_cid=2975480}, + volume = {365}, + year = {2019} +} + diff --git a/content/publication/wilson-2019/featured.png b/content/publication/wilson-2019/featured.png new file mode 100644 index 0000000..6b53cc4 Binary files /dev/null and b/content/publication/wilson-2019/featured.png differ diff --git a/content/publication/wilson-2019/index.md b/content/publication/wilson-2019/index.md new file mode 100644 index 0000000..4a3b20a --- /dev/null +++ b/content/publication/wilson-2019/index.md @@ -0,0 +1,13 @@ +--- +title: "Kīlauea lava fuels phytoplankton bloom in the North Pacific Ocean" +date: 2019-09-01 +publishDate: 2020-03-09T17:46:51.926845Z +authors: ["Samuel T. Wilson", "Nicholas J. Hawco", "E. Virginia Armbrust", "Benedetto Barone", "Karin M. Björkman", "Angela K. Boysen", "Macarena Burgos", "Timothy J. Burrell", "John R. Casey", "Edward F. DeLong", "Mathilde Dugenne", "Stephanie Dutkiewicz", "Sonya T. Dyhrman", "Sara Ferrón", "Michael J. Follows", "Rhea K. Foreman", "Carolina P. Funkey", "Matthew J. Harke", "Britt A. Henke", "Christopher N. Hill", "Annette M. Hynes", "Anitra E. Ingalls", "Oliver Jahn", "Rachel L. Kelly", "Angela N. Knapp", "Ricardo M. Letelier", "Francois Ribalet", "Eric M. Shimabukuro", "Ryan K. S. Tabata", "Kendra A. Turk-Kubo", "Angelique E. White", "Jonathan P. Zehr", "Seth John", "David M. Karl"] +publication_types: ["2"] +abstract: "From June to August 2018, the eruption of Kīlauea volcano on the island of Hawai‘i injected millions of cubic meters of molten lava into the nutrient-poor waters of the North Pacific Subtropical Gyre.The lava-impacted seawater was characterized by high concentrations of metals and nutrients that stimulated phytoplankton growth, resulting in an extensive plume of chlorophyll a that was detectable by satellite. Chemical and molecular evidence revealed that this biological response hinged on unexpectedly high concentrations of nitrate, despite the negligible quantities of nitrogen in basaltic lava. We hypothesize that the high nitrate was caused by buoyant plumes of nutrient-rich deep waters created by the substantial input of lava into the ocean. This large-scale ocean fertilization was therefore a unique perturbation event that revealed how marine ecosystems respond to exogenous inputs of nutrients." +featured: false +publication: "*Science*" +url_pdf: "https://science.sciencemag.org/content/365/6457/1040?utm_campaign=toc_sci-mag_2019-09-05&et_rid=40171609&et_cid=2975480" +doi: "10.1126/SCIENCE.AAX4767" +--- + diff --git a/content/research/_index.md b/content/research/_index.md new file mode 100644 index 0000000..3d52641 --- /dev/null +++ b/content/research/_index.md @@ -0,0 +1,18 @@ +--- +title: The Role of Phytoplankton in a Changing Planet +subtitle : Integrating High-Resolution Observations and Modeling + + +# Listing view +view: card + +# Optional header image (relative to `assets/media/` folder). +banner: + caption: '' + image: cruisetracks.jpg + text: +--- +
+Our research group focuses on understanding the critical role of marine phytoplankton in ocean ecosystems and climate change. By developing innovative technologies like the SeaFlow cytometer, we conduct high-resolution observations of phytoplankton population dynamics across ocean transition zones, capturing unprecedented spatial and temporal data. Our approach integrates advanced computational modeling, including matrix population models, to track phytoplankton activities and understand how environmental pressures reshape marine ecosystems. Our group aims to improve climate change predictions by integrating high-resolution biological data into Earth system models, with a particular emphasis on understanding how small-sized phytoplankton respond to and influence environmental shifts. Ultimately, our interdisciplinary research seeks to enhance our understanding of ocean-climate feedbacks and inform critical climate mitigation strategies. +
+
\ No newline at end of file diff --git a/content/research/climate/featured.png b/content/research/climate/featured.png new file mode 100644 index 0000000..aca1acf Binary files /dev/null and b/content/research/climate/featured.png differ diff --git a/content/research/climate/index.md b/content/research/climate/index.md new file mode 100644 index 0000000..b6bfe8d --- /dev/null +++ b/content/research/climate/index.md @@ -0,0 +1,7 @@ +--- +title: Climate Change and its Impact on Phytoplankton Population Dynamics +date: "2022-03-01" +--- + + +content to be added soon diff --git a/content/research/flowrate/featured.png b/content/research/flowrate/featured.png new file mode 100644 index 0000000..b244e0a Binary files /dev/null and b/content/research/flowrate/featured.png differ diff --git a/content/research/flowrate/index.md b/content/research/flowrate/index.md new file mode 100644 index 0000000..ae9e58c --- /dev/null +++ b/content/research/flowrate/index.md @@ -0,0 +1,9 @@ +--- +title: Matrix Population Models for Estimating Phytoplankton Growth and Turnover Rates +date: "2024-03-01" +--- + +This research builds upon the achievements of the SeaFlow project (2021-2024), which involved analyzing flow cytometry data from over 100 cruises. Our primary focus is on estimating cell growth and turnover rates across various phytoplankton populations, two critical traits that influence how organisms interact with their environment. Leveraging the size-structured matrix population model developed by our team, our initial phase generated 180 estimates of *Prochlorococcus* growth rates. The goal of this new proposal is to estimate not only cell growth but also cell mortality, carbon loss, and carbon fixation across all phytoplankton populations captured by SeaFlow. This comprehensive approach will offer critical insights into both the drivers (growth and productivity) and consequences (loss and turnover) of ecological processes driven by these phytoplankton populations. This knowledge will be instrumental in predicting how primary production and ecosystem health may change in response to environmental shifts. + +### Funding sources +Project supported by grants from the [Simons Foundation](https://www.simonsfoundation.org/life-sciences/microbial-oceanography/) diff --git a/content/research/gradients/featured.png b/content/research/gradients/featured.png new file mode 100644 index 0000000..6904572 Binary files /dev/null and b/content/research/gradients/featured.png differ diff --git a/content/research/gradients/index.md b/content/research/gradients/index.md new file mode 100644 index 0000000..b9eefe7 --- /dev/null +++ b/content/research/gradients/index.md @@ -0,0 +1,7 @@ +--- +title: Phytoplankton Dynamics in Ocean Transition Zones +date: "2020-03-01" +--- + + +content to be added soon \ No newline at end of file diff --git a/content/software/CytoSegmenter/featured.png b/content/software/CytoSegmenter/featured.png new file mode 100644 index 0000000..c060292 Binary files /dev/null and b/content/software/CytoSegmenter/featured.png differ diff --git a/content/software/CytoSegmenter/index.md b/content/software/CytoSegmenter/index.md new file mode 100644 index 0000000..8dcd481 --- /dev/null +++ b/content/software/CytoSegmenter/index.md @@ -0,0 +1,7 @@ +--- +title: CytoSegmenter +date: "2020-11-01" +--- +[Cytosegmenter](https://github.com/cjones6/cytosegmenter) is a kernel-based change detection method to map shifts in phytoplankton communities measured by flow cytometry. Detailed information can be found in [Jones et al. (2020)](https://doi.org/10.1111/2041-210X.13647). + +In this project in collaboration with Dr. Corinne Jones and UW Pr. Zaid Harchaoui, we applied a new method to segment flow cytometry data on phytoplankton measured during research cruises. Understanding how phytoplankton communities vary in time and space across ocean basins is critical for predicting how marine ecosystems will respond to future climate change. We propose an approach to segmenting sequences of point clouds into distinct segments. The software first generates Hilbertian embeddings for each point cloud. It then segments the data by applying a kernel-based change-point detection method on the embeddings. To estimate the number of change points we propose using auxiliary labeled data. \ No newline at end of file diff --git a/content/software/_index.md b/content/software/_index.md new file mode 100644 index 0000000..323b750 --- /dev/null +++ b/content/software/_index.md @@ -0,0 +1,15 @@ +--- +title: Computational Tools + +# Listing view +view: compact + +# Optional header image (relative to `assets/media/` folder). +banner: + caption: '' + image: cell-laser.jpg +--- + +Our research group generates large-scale, basin-wide flow-cytometry data to understand temporal and spatial variability in phytoplankton communities. By developing computational tools and statistical models, we aim to understand how these tiny organisms grow, interact with their environment, and contribute to the global carbon cycle. Our ultimate goal is to shed light on the crucial role phytoplankton play in the ocean ecosystem and predict how they will respond to a changing climate. + +
\ No newline at end of file diff --git a/content/software/flowMix/featured.png b/content/software/flowMix/featured.png new file mode 100644 index 0000000..5497627 Binary files /dev/null and b/content/software/flowMix/featured.png differ diff --git a/content/software/flowMix/index.md b/content/software/flowMix/index.md new file mode 100644 index 0000000..20080f3 --- /dev/null +++ b/content/software/flowMix/index.md @@ -0,0 +1,9 @@ +--- +title: flowMix +date: "2023-01-03" +--- +[flowMix](https://github.com/seaflow-uw/flowmix) is a statistical approach to model cell populations measured by flow cytometry with covariates using sparse mixture of regressions. Detailed information can be found in [Hyun et al. (2023)](https://doi.org/10.1214/22-AOAS1631). + +In this project led by Dr. Sangwon Hyun, we apply a sparse mixture of multivariate regressions model for flow cytometry data. The main motivating application is continuous-time flow cytometry data collected in the ocean, over space and time. we propose a novel sparse mixture of multivariate regressions model to estimate the time-varying phytoplankton subpopulations while simultaneously identifying the specific environmental covariates that are predictive of the observed changes to these subpopulations. + +A short vignette [here](http://htmlpreview.github.io/?https://github.com/sangwon-hyun/flowmix/blob/master/flowmix/vignettes/flowmix.html) shows how to use the package. diff --git a/content/software/mpm/featured.png b/content/software/mpm/featured.png new file mode 100644 index 0000000..fe1b9be Binary files /dev/null and b/content/software/mpm/featured.png differ diff --git a/content/software/mpm/index.md b/content/software/mpm/index.md new file mode 100644 index 0000000..a871f1c --- /dev/null +++ b/content/software/mpm/index.md @@ -0,0 +1,7 @@ +--- +title: flowRate +date: "2022-01-01" +--- +[flowRate](https://github.com/seaflow-uw/mpm-workflow) is a size-structured matrix population model to estimate rates of cell division, carbon fixation and carbon loss in phytoplankton measured by flow cytometry. Detailed information can be found in [Glauninger et al. (2022)](https://doi.org/10.1371/journal.pcbi.1009733) + +The rates of cell growth, division, and carbon loss of microbial populations in their natural habitat are key parameters for understanding how organisms interact with their environment and how they contribute to the carbon cycle. However, the invasive nature of current analytical methods has hindered efforts to reliably quantify these parameters. In [Glauninger et al. (2022)](https://doi.org/10.1371/journal.pcbi.1009733), we present a flexible Bayesian formulation of size-structured matrix population model for testing a set of underlying assumptions describing microbial population dynamics. We incorporate the model into a Bayesian framework that not only takes into account prior scientific knowledge but also generates biologically interpretable results. \ No newline at end of file diff --git a/content/software/popcycle/featured.png b/content/software/popcycle/featured.png new file mode 100644 index 0000000..7f5f8d5 Binary files /dev/null and b/content/software/popcycle/featured.png differ diff --git a/content/software/popcycle/index.md b/content/software/popcycle/index.md new file mode 100644 index 0000000..54648ed --- /dev/null +++ b/content/software/popcycle/index.md @@ -0,0 +1,13 @@ +--- +title: Popcycle +date: "2014-12-01" +--- +[Popcycle](https://github.com/seaflow-uw/popcycle) is an R package that offers a reproducible approach to process, calibrate and curate flow cytometry data collected by SeaFlow. Detailed information can be found in the [Ribalet et al. (2019)](https://doi.org/10.1038/s41597-019-0292-2). + + The software package performs 3 key analyses +1. ```Gating```: Classification of phytoplankton cell populations using a mixture of manual gating and a semi-supervized clusterting algorithm. This involves identifying and classifying different phytoplankton populations, such as Prochlorococcus, Synechococcus, and Crocosphaera, based on their optical properties (forward scatter, chlorophyll fluorescence, and phycoerythrin fluorescence). +2. ```Light scatter conversion```: Convert light scattering of each particle to cell diameter ([fsc-size-calibration](https://github.com/seaflow-uw/fsc-size-calibration)) and carbon content ([fsc-poc-calibration](https://github.com/seaflow-uw/fsc-poc-calibration)).This is achieved by applying Mie light scattering theory to a simplified optical model and using an optimization procedure to minimize differences between measured forward scatter and the scatter intensity predicted by Mie light scatter of homogeneous spherical particles +3. ```Population data```: Perform aggregate statistics along with error propagation for the different populations.This includes calculating cell abundance, median, 25th and 75th percentiles of optical properties, equivalent spherical diameter (ESD), and carbon quotas for each population, along with measurement errors based on uncertainties in the virtual core volume and light scatter conversion. + +The cell population identification (```gated``` data) and diameter and carbon content (```calibrated``` data) of each OPP are saved as separate text files with a similar file structure as the raw data. The metadata, gating scheme, and aggregated statistics for each step are saved to a SQL database using SQLite3. + diff --git a/content/tour/index.md b/content/tour/index.md deleted file mode 100644 index 28554db..0000000 --- a/content/tour/index.md +++ /dev/null @@ -1,54 +0,0 @@ ---- -title: Tour -date: 2022-10-24 - -type: landing - -sections: - - block: slider - content: - slides: - - title: 👋 Welcome to the group - content: Take a look at what we're working on... - align: center - background: - image: - filename: coders.jpg - filters: - brightness: 0.7 - position: right - color: '#666' - - title: Lunch & Learn ☕️ - content: 'Share your knowledge with the group and explore exciting new topics together!' - align: left - background: - image: - filename: contact.jpg - filters: - brightness: 0.7 - position: center - color: '#555' - - title: World-Class Semiconductor Lab - content: 'Just opened last month!' - align: right - background: - image: - filename: welcome.jpg - filters: - brightness: 0.5 - position: center - color: '#333' - link: - icon: graduation-cap - icon_pack: fas - text: Join Us - url: ../contact/ - design: - # Slide height is automatic unless you force a specific height (e.g. '400px') - slide_height: '' - is_fullscreen: true - # Automatically transition through slides? - loop: false - # Duration of transition between slides (in ms) - interval: 2000 ---- diff --git a/go.sum b/go.sum new file mode 100644 index 0000000..0aee5cb --- /dev/null +++ b/go.sum @@ -0,0 +1,8 @@ +github.com/HugoBlox/hugo-blox-builder/modules/blox-bootstrap/v5 v5.9.8-0.20241012174104-661cadc17327 h1:aKhll1k3EctTWSvLZYrkhz4ehSqo1+OX5Ho7LvfZR/0= +github.com/HugoBlox/hugo-blox-builder/modules/blox-bootstrap/v5 v5.9.8-0.20241012174104-661cadc17327/go.mod h1:+Itucnia7M8NWxaEys257x/34K4+POiBlR1yYCTrzBM= +github.com/HugoBlox/hugo-blox-builder/modules/blox-core v0.3.1/go.mod h1:So8+V2U+TNxlXmcpZfdDX0muLh3PdJ7z92h30sv3bZg= +github.com/HugoBlox/hugo-blox-builder/modules/blox-plugin-decap-cms v0.1.2-0.20231108143325-448ed0e3bd2b h1:pOYZJXK2hahVeW/FcVuBoFdvtR3DpsDDZVcbGnMNEdQ= +github.com/HugoBlox/hugo-blox-builder/modules/blox-plugin-decap-cms v0.1.2-0.20231108143325-448ed0e3bd2b/go.mod h1:Njlsj3S1Z833TdX1nacJZzsiwGGhOq4Nilzo2BH/wQ8= +github.com/HugoBlox/hugo-blox-builder/modules/blox-plugin-netlify v1.1.2-0.20240509231741-c3d23d929bc6 h1:QIQqCc9DnS/PjhHCnyzxe5yhUMUYtJDMpRoaBtBk3VY= +github.com/HugoBlox/hugo-blox-builder/modules/blox-plugin-netlify v1.1.2-0.20240509231741-c3d23d929bc6/go.mod h1:C7jfxMLv1bEUqbM9XDSmEpfOpS8w06OgqNDEcbuRgL4= +github.com/HugoBlox/hugo-blox-builder/modules/blox-seo v0.2.3/go.mod h1:NsESu6cEms1DgH84icCyylElg2Zu8A0f7Fma5JR0LZE= diff --git a/preview.png b/preview.png deleted file mode 100644 index 74fccae..0000000 Binary files a/preview.png and /dev/null differ