index.json

[{"authors":["admin"],"categories":null,"content":"I am a researcher in the evolve.zoo lab in the Department of Zoology at the University of Oxford. My interests include cancer phylodynamics, pathogen population genetics, spatial genetics, and host-pathogen evolutionary relationships. Related interests include bioinformatics, oncology, and applications in translational medicine.\nPrior to Oxford I was based at the Natural History Museum in London working on the parasitic blood-fluke Schistosoma. During this time I undertook many field expeditions, leading teams in remote areas of Laos, Cambodia, Malaysia and Indonesia. I later moved my focus to China, working on the Schistosomiasis Control Programme there. My parasitological work resulted in the discovery and naming of several new species and insights into the health and biodiversity impacts of hydro-power dams in the Mekong Basin. I identified two new foci of schistosomiasis transmission to humans in Cambodia and Laos, greatly expanding the risk-map for Mekong schistosomiasis and was the first to report the transmission of this disease outside the Mekong river.\nI began my postdoctoral career as an NERC Fellow, following this I was PI on three Project grants awarded to me by the Wellcome Trust. I also held a China National Science Foundation Project Grant, and numerous small awards. I have taught Molecular Ecology at West China Medical School, and for a short time as a visitor at Kingston University (London).\n","date":1549324800,"expirydate":-62135596800,"kind":"taxonomy","lang":"en","lastmod":1567641600,"objectID":"2525497d367e79493fd32b198b28f040","permalink":"http://InfrPopGen.github.io/authors/admin/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/admin/","section":"authors","summary":"I am a researcher in the evolve.zoo lab in the Department of Zoology at the University of Oxford. My interests include cancer phylodynamics, pathogen population genetics, spatial genetics, and host-pathogen evolutionary relationships. Related interests include bioinformatics, oncology, and applications in translational medicine.\nPrior to Oxford I was based at the Natural History Museum in London working on the parasitic blood-fluke Schistosoma. During this time I undertook many field expeditions, leading teams in remote areas of Laos, Cambodia, Malaysia and Indonesia.","tags":null,"title":"Stephen Attwood","type":"authors"},{"authors":null,"categories":null,"content":"Flexibility This feature can be used for publishing content such as:\n Online courses Project or software documentation Tutorials  The courses folder may be renamed. For example, we can rename it to docs for software/project documentation or tutorials for creating an online course.\nDelete tutorials To remove these pages, delete the courses folder and see below to delete the associated menu link.\nUpdate site menu After renaming or deleting the courses folder, you may wish to update any [[main]] menu links to it by editing your menu configuration at config/_default/menus.toml.\nFor example, if you delete this folder, you can remove the following from your menu configuration:\n[[main]] name = \u0026#34;Courses\u0026#34; url = \u0026#34;courses/\u0026#34; weight = 50 Or, if you are creating a software documentation site, you can rename the courses folder to docs and update the associated Courses menu configuration to:\n[[main]] name = \u0026#34;Docs\u0026#34; url = \u0026#34;docs/\u0026#34; weight = 50 Update the docs menu If you use the docs layout, note that the name of the menu in the front matter should be in the form [menu.X] where X is the folder name. Hence, if you rename the courses/example/ folder, you should also rename the menu definitions in the front matter of files within courses/example/ from [menu.example] to [menu.\u0026lt;NewFolderName\u0026gt;].\n","date":1536451200,"expirydate":-62135596800,"kind":"section","lang":"en","lastmod":1536451200,"objectID":"59c3ce8e202293146a8a934d37a4070b","permalink":"http://InfrPopGen.github.io/courses/example/","publishdate":"2018-09-09T00:00:00Z","relpermalink":"/courses/example/","section":"courses","summary":"Learn how to use Academic's docs layout for publishing online courses, software documentation, and tutorials.","tags":null,"title":"Overview","type":"docs"},{"authors":null,"categories":null,"content":"In this tutorial, I'll share my top 10 tips for getting started with Academic:\nTip 1 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.\nNullam vel molestie justo. Curabitur vitae efficitur leo. In hac habitasse platea dictumst. Sed pulvinar mauris dui, eget varius purus congue ac. Nulla euismod, lorem vel elementum dapibus, nunc justo porta mi, sed tempus est est vel tellus. Nam et enim eleifend, laoreet sem sit amet, elementum sem. Morbi ut leo congue, maximus velit ut, finibus arcu. In et libero cursus, rutrum risus non, molestie leo. Nullam congue quam et volutpat malesuada. Sed risus tortor, pulvinar et dictum nec, sodales non mi. Phasellus lacinia commodo laoreet. Nam mollis, erat in feugiat consectetur, purus eros egestas tellus, in auctor urna odio at nibh. Mauris imperdiet nisi ac magna convallis, at rhoncus ligula cursus.\nCras aliquam rhoncus ipsum, in hendrerit nunc mattis vitae. Duis vitae efficitur metus, ac tempus leo. Cras nec fringilla lacus. Quisque sit amet risus at ipsum pharetra commodo. Sed aliquam mauris at consequat eleifend. Praesent porta, augue sed viverra bibendum, neque ante euismod ante, in vehicula justo lorem ac eros. Suspendisse augue libero, venenatis eget tincidunt ut, malesuada at lorem. Donec vitae bibendum arcu. Aenean maximus nulla non pretium iaculis. Quisque imperdiet, nulla in pulvinar aliquet, velit quam ultrices quam, sit amet fringilla leo sem vel nunc. Mauris in lacinia lacus.\nSuspendisse a tincidunt lacus. Curabitur at urna sagittis, dictum ante sit amet, euismod magna. Sed rutrum massa id tortor commodo, vitae elementum turpis tempus. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Aenean purus turpis, venenatis a ullamcorper nec, tincidunt et massa. Integer posuere quam rutrum arcu vehicula imperdiet. Mauris ullamcorper quam vitae purus congue, quis euismod magna eleifend. Vestibulum semper vel augue eget tincidunt. Fusce eget justo sodales, dapibus odio eu, ultrices lorem. Duis condimentum lorem id eros commodo, in facilisis mauris scelerisque. Morbi sed auctor leo. Nullam volutpat a lacus quis pharetra. Nulla congue rutrum magna a ornare.\nAliquam in turpis accumsan, malesuada nibh ut, hendrerit justo. Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus. Quisque sed erat nec justo posuere suscipit. Donec ut efficitur arcu, in malesuada neque. Nunc dignissim nisl massa, id vulputate nunc pretium nec. Quisque eget urna in risus suscipit ultricies. Pellentesque odio odio, tincidunt in eleifend sed, posuere a diam. Nam gravida nisl convallis semper elementum. Morbi vitae felis faucibus, vulputate orci placerat, aliquet nisi. Aliquam erat volutpat. Maecenas sagittis pulvinar purus, sed porta quam laoreet at.\nTip 2 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.\nNullam vel molestie justo. Curabitur vitae efficitur leo. In hac habitasse platea dictumst. Sed pulvinar mauris dui, eget varius purus congue ac. Nulla euismod, lorem vel elementum dapibus, nunc justo porta mi, sed tempus est est vel tellus. Nam et enim eleifend, laoreet sem sit amet, elementum sem. Morbi ut leo congue, maximus velit ut, finibus arcu. In et libero cursus, rutrum risus non, molestie leo. Nullam congue quam et volutpat malesuada. Sed risus tortor, pulvinar et dictum nec, sodales non mi. Phasellus lacinia commodo laoreet. Nam mollis, erat in feugiat consectetur, purus eros egestas tellus, in auctor urna odio at nibh. Mauris imperdiet nisi ac magna convallis, at rhoncus ligula cursus.\nCras aliquam rhoncus ipsum, in hendrerit nunc mattis vitae. Duis vitae efficitur metus, ac tempus leo. Cras nec fringilla lacus. Quisque sit amet risus at ipsum pharetra commodo. Sed aliquam mauris at consequat eleifend. Praesent porta, augue sed viverra bibendum, neque ante euismod ante, in vehicula justo lorem ac eros. Suspendisse augue libero, venenatis eget tincidunt ut, malesuada at lorem. Donec vitae bibendum arcu. Aenean maximus nulla non pretium iaculis. Quisque imperdiet, nulla in pulvinar aliquet, velit quam ultrices quam, sit amet fringilla leo sem vel nunc. Mauris in lacinia lacus.\nSuspendisse a tincidunt lacus. Curabitur at urna sagittis, dictum ante sit amet, euismod magna. Sed rutrum massa id tortor commodo, vitae elementum turpis tempus. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Aenean purus turpis, venenatis a ullamcorper nec, tincidunt et massa. Integer posuere quam rutrum arcu vehicula imperdiet. Mauris ullamcorper quam vitae purus congue, quis euismod magna eleifend. Vestibulum semper vel augue eget tincidunt. Fusce eget justo sodales, dapibus odio eu, ultrices lorem. Duis condimentum lorem id eros commodo, in facilisis mauris scelerisque. Morbi sed auctor leo. Nullam volutpat a lacus quis pharetra. Nulla congue rutrum magna a ornare.\nAliquam in turpis accumsan, malesuada nibh ut, hendrerit justo. Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus. Quisque sed erat nec justo posuere suscipit. Donec ut efficitur arcu, in malesuada neque. Nunc dignissim nisl massa, id vulputate nunc pretium nec. Quisque eget urna in risus suscipit ultricies. Pellentesque odio odio, tincidunt in eleifend sed, posuere a diam. Nam gravida nisl convallis semper elementum. Morbi vitae felis faucibus, vulputate orci placerat, aliquet nisi. Aliquam erat volutpat. Maecenas sagittis pulvinar purus, sed porta quam laoreet at.\n","date":1557010800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1557010800,"objectID":"74533bae41439377bd30f645c4677a27","permalink":"http://InfrPopGen.github.io/courses/example/example1/","publishdate":"2019-05-05T00:00:00+01:00","relpermalink":"/courses/example/example1/","section":"courses","summary":"In this tutorial, I'll share my top 10 tips for getting started with Academic:\nTip 1 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.","tags":null,"title":"Example Page 1","type":"docs"},{"authors":null,"categories":null,"content":"Here are some more tips for getting started with Academic:\nTip 3 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.\nNullam vel molestie justo. Curabitur vitae efficitur leo. In hac habitasse platea dictumst. Sed pulvinar mauris dui, eget varius purus congue ac. Nulla euismod, lorem vel elementum dapibus, nunc justo porta mi, sed tempus est est vel tellus. Nam et enim eleifend, laoreet sem sit amet, elementum sem. Morbi ut leo congue, maximus velit ut, finibus arcu. In et libero cursus, rutrum risus non, molestie leo. Nullam congue quam et volutpat malesuada. Sed risus tortor, pulvinar et dictum nec, sodales non mi. Phasellus lacinia commodo laoreet. Nam mollis, erat in feugiat consectetur, purus eros egestas tellus, in auctor urna odio at nibh. Mauris imperdiet nisi ac magna convallis, at rhoncus ligula cursus.\nCras aliquam rhoncus ipsum, in hendrerit nunc mattis vitae. Duis vitae efficitur metus, ac tempus leo. Cras nec fringilla lacus. Quisque sit amet risus at ipsum pharetra commodo. Sed aliquam mauris at consequat eleifend. Praesent porta, augue sed viverra bibendum, neque ante euismod ante, in vehicula justo lorem ac eros. Suspendisse augue libero, venenatis eget tincidunt ut, malesuada at lorem. Donec vitae bibendum arcu. Aenean maximus nulla non pretium iaculis. Quisque imperdiet, nulla in pulvinar aliquet, velit quam ultrices quam, sit amet fringilla leo sem vel nunc. Mauris in lacinia lacus.\nSuspendisse a tincidunt lacus. Curabitur at urna sagittis, dictum ante sit amet, euismod magna. Sed rutrum massa id tortor commodo, vitae elementum turpis tempus. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Aenean purus turpis, venenatis a ullamcorper nec, tincidunt et massa. Integer posuere quam rutrum arcu vehicula imperdiet. Mauris ullamcorper quam vitae purus congue, quis euismod magna eleifend. Vestibulum semper vel augue eget tincidunt. Fusce eget justo sodales, dapibus odio eu, ultrices lorem. Duis condimentum lorem id eros commodo, in facilisis mauris scelerisque. Morbi sed auctor leo. Nullam volutpat a lacus quis pharetra. Nulla congue rutrum magna a ornare.\nAliquam in turpis accumsan, malesuada nibh ut, hendrerit justo. Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus. Quisque sed erat nec justo posuere suscipit. Donec ut efficitur arcu, in malesuada neque. Nunc dignissim nisl massa, id vulputate nunc pretium nec. Quisque eget urna in risus suscipit ultricies. Pellentesque odio odio, tincidunt in eleifend sed, posuere a diam. Nam gravida nisl convallis semper elementum. Morbi vitae felis faucibus, vulputate orci placerat, aliquet nisi. Aliquam erat volutpat. Maecenas sagittis pulvinar purus, sed porta quam laoreet at.\nTip 4 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.\nNullam vel molestie justo. Curabitur vitae efficitur leo. In hac habitasse platea dictumst. Sed pulvinar mauris dui, eget varius purus congue ac. Nulla euismod, lorem vel elementum dapibus, nunc justo porta mi, sed tempus est est vel tellus. Nam et enim eleifend, laoreet sem sit amet, elementum sem. Morbi ut leo congue, maximus velit ut, finibus arcu. In et libero cursus, rutrum risus non, molestie leo. Nullam congue quam et volutpat malesuada. Sed risus tortor, pulvinar et dictum nec, sodales non mi. Phasellus lacinia commodo laoreet. Nam mollis, erat in feugiat consectetur, purus eros egestas tellus, in auctor urna odio at nibh. Mauris imperdiet nisi ac magna convallis, at rhoncus ligula cursus.\nCras aliquam rhoncus ipsum, in hendrerit nunc mattis vitae. Duis vitae efficitur metus, ac tempus leo. Cras nec fringilla lacus. Quisque sit amet risus at ipsum pharetra commodo. Sed aliquam mauris at consequat eleifend. Praesent porta, augue sed viverra bibendum, neque ante euismod ante, in vehicula justo lorem ac eros. Suspendisse augue libero, venenatis eget tincidunt ut, malesuada at lorem. Donec vitae bibendum arcu. Aenean maximus nulla non pretium iaculis. Quisque imperdiet, nulla in pulvinar aliquet, velit quam ultrices quam, sit amet fringilla leo sem vel nunc. Mauris in lacinia lacus.\nSuspendisse a tincidunt lacus. Curabitur at urna sagittis, dictum ante sit amet, euismod magna. Sed rutrum massa id tortor commodo, vitae elementum turpis tempus. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Aenean purus turpis, venenatis a ullamcorper nec, tincidunt et massa. Integer posuere quam rutrum arcu vehicula imperdiet. Mauris ullamcorper quam vitae purus congue, quis euismod magna eleifend. Vestibulum semper vel augue eget tincidunt. Fusce eget justo sodales, dapibus odio eu, ultrices lorem. Duis condimentum lorem id eros commodo, in facilisis mauris scelerisque. Morbi sed auctor leo. Nullam volutpat a lacus quis pharetra. Nulla congue rutrum magna a ornare.\nAliquam in turpis accumsan, malesuada nibh ut, hendrerit justo. Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus. Quisque sed erat nec justo posuere suscipit. Donec ut efficitur arcu, in malesuada neque. Nunc dignissim nisl massa, id vulputate nunc pretium nec. Quisque eget urna in risus suscipit ultricies. Pellentesque odio odio, tincidunt in eleifend sed, posuere a diam. Nam gravida nisl convallis semper elementum. Morbi vitae felis faucibus, vulputate orci placerat, aliquet nisi. Aliquam erat volutpat. Maecenas sagittis pulvinar purus, sed porta quam laoreet at.\n","date":1557010800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1557010800,"objectID":"1c2b5a11257c768c90d5050637d77d6a","permalink":"http://InfrPopGen.github.io/courses/example/example2/","publishdate":"2019-05-05T00:00:00+01:00","relpermalink":"/courses/example/example2/","section":"courses","summary":"Here are some more tips for getting started with Academic:\nTip 3 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.","tags":null,"title":"Example Page 2","type":"docs"},{"authors":["S.W. Attwood"],"categories":["Synopsis","immunology","phylogenetics","virology"],"content":"    Note If there is unfamiliar terminology here, then it may help to read these posts in order, starting with \u0026ldquo;Is SARS-CoV-2 evolving?\u0026rdquo; of 18th May 2020. Definitions of terms are in bold to help in finding them.\nPhylogenetics can give clues about how SARS-CoV-2 battles the anti-viral responses of its hosts―two recent papers considered the C-\u0026gt;U hypermutation which, like other coronaviruses, is a feature of the SARS-CoV-2 genome. Peter Simmonds\u0026rsquo; preprint focused on treating the low CpG content of the CoV genomes as a phylogenetic character that tells us something about events in their history, and the paper by Salvatore Giorgio et al (2020) gives further examination of the anti-viral aspects. Simmonds noted that there are about four times the number of C-\u0026gt;U transitions in the SARS-CoV-2 genome than expected by chance, which is high even among RNA viruses, and that around half of non-synonymous mutations are C-\u0026gt;U substitutions―suggesting they might be important in the evolution of the virus (but see below). This excess increases 10-fold if the C-\u0026gt;U is flanked by a certain motif (i.e. specific sequence pattern), which Simmonds noted are favoured by certain APOBEC proteins. Some APOBECs are thought able to introduce mutations to RNA viral genomes by deamination of cytidines, with the mutations introduced as an anti-viral defence. The fact that these viruses show low GC content, but the G+A content is relatively normal, would fit with an APOBEC acting on the genomic (positive) strand of the virus, exposed in the cytoplasm, before replication complex formation―otherwise both strands would be present, and susceptible to mutation as the genome is replicated―the GA content would then fall with the GC. The same idea (lack of symmetry) argues against the mutations being errors of the viral RdRp (RNA-dependent RNA-polymerase, the enzyme that the viruses uses to copy its own genome). APOBEC RNA-editing would also explain the strangely high dN/dS ratio in SARS-CoV-2 because it would not be shaped by natural selection. Indeed, we would have APOBEC introducing variants and natural selection removing any that were deleterious. Of course, we can imagine that these viruses would evolve to avoid using sequences that APOBECs target; however, there is a diverse family of APOBECs and they vary among host species. Simmonds observed that the hypermutation is greatest in close relatives of SARS-CoV-2 and reduces as more divergent lineages are considered; this could be because the human SARS-CoVs have only recently begun to infect humans, whereas the seasonal CoVs that have long circulated in humans have adapted to our APOBECs and restored their GC content. The implication is that SARS-CoV and SARS-CoV-2 are still adapted to bat APOBECs (or to whatever the ancestral hosts were). Giorgio et al. take the story a little further, and look at another deanimase family, the ADARs, as well as APOBEC; they found frequently overrepresented stop codons in transcribed viral RNAs rather than genomic, which supported an anti-viral role for these enzymes.\nAs we tend to learn most from papers that attract criticism, I should mention the paper in MBE by Xia (2020) here. Xia came up with a nice idea (those are often the ones that are most questioned), as he found CpG levels in some canine alphacoronaviruses as low as in SARS-CoV-2, the record holder for low CpG among these CoVs (although human seasonal cold virus CoV HKU1 might be lower). He reasoned that the ancestor of SARS-CoV-2 may have been subjected to a canine immune environment, and on that basis argued that SARS-CoV-2 jumped from bats to some canine and then to humans. In a recent (aren't they all?) preprint Digard et al (2020) aligned nearly 200 genomes of SARS-CoVs and various coronaviruses transmitting in animals. They found that although CpG levels were lowest in human and canine coronaviruses and highest in bat and rodent, there was much range overlap, which makes Xia's nice idea more shaky. These authors all noted that the low CpG may well be to avoid the action of Zinc-finger Antiviral Protein (ZAP), which binds to viral RNAs at their CpG motifs (an addition to the APOBEC explanation). Interestingly, Digard's group found almost normal CpG levels at two loci, E ORF and the coding region of ORF10 (an ORF is an Open Reading Frame, the coding part of a gene that can be translated, but viruses can have overlapping ORFs, or \u0026ldquo;sub-ORFs\u0026rdquo; if you like, that's not an official term!). These two loci also showed much less CpG suppression than the rest of their genomes in bat- and pangolin-CoVs sampled nearly a decade ago. The implication is that selection had not removed this pattern over the years, and so it is a derived trait that was selected for before SARS-CoVs began to transmit widely among humans. In support of this, a phylogenetic tree estimated with only E ORF sequences for the 7 human-CoVs and 96 bat-CoVs showed the human-CoVs scattered among the bat-CoV lineages and with CpG levels matching their closest bat-CoV relatives. They suggest that the high CpG in E ORF might be because it is transcribed late in the infection process, when attack by ZAP is less of a problem. By the way, Xia is also the author of DAMBE which I used in most of my 1990s papers! It's worth checking out, if you don't know it―not now the best for phylogenetics but its other features are handy.\nThe E ORF story is a good example of how phylogenetics can help us understand the anti-viral reponses during infection, and the strategies SARS-CoV-2 has been using to avoid them as it evolved and moved from host to host. Now let's look at some sequencing studies on the immune response itself.\nAPOBECS are part of the interferon-induced innate immune response (they have links with adaptive response too, but that is another topic), but Galson et al (2020) use sequencing data, and a nearest-neighbour kind of clustering algorithm, to directly explore the humoral immune response to SARS-CoV-2. They compared the IGHA and IGHG B-Cell Receptor (BCR) sequences for 19 patients with those for healthy individuals. The numbers of mutations showed a bimodal frequency plot (i.e. two humps), which suggests an expanding population―i.e. a population of B-cells that had only just \u0026ldquo;switched\u0026rdquo; on to the presence of the virus. Nevertheless, the larger clonal expansions revealed by the sequence network showed many mutations, which fits with their having activated from memory of a previously encountered antigen. Convergent BCR sequences were also seen, with very similar sequences among different patients, and even between UK and US studies; this convergence is good news for vaccine development, as it implies that a vaccine that works across diverse lineages of virus is feasible. We also saw signs of activation from memory.\nTo counter that possibly good news, Cheng et al. (2020)\u0026lsquo;s preprint is potentially worrying, but models are never perfect so\u0026hellip;. These authors modelled the shape (and charge) of the \u0026ldquo;spike\u0026rdquo; protein, which is what the virus uses to recognise ACE2 receptors on our cells and trigger the process of cell entry. The models indicated a 20 amino acid motif in spike that mimics a superantigen called staphylococcal entero-toxin B (SEB), which is known to be the trigger for toxic shock or the cytokine storm in humans. In SARS-CoV-2 the motif appears to be palindromic so, when the reverse direction is also included, this doubles the stretch of sequence to match with the superantigen peptide. The superantigen motif is not found in any other SARS coronavirus, such as SARS-CoV from the 2002-2004 outbreak. Probably most controversially the models indicate that some Single Nucleotide Polymorphisms (SNPs, or substitutions at a single site that persist in a population at non-negligible frequencies) currently circulating in Europe and the US may increase the superantigenicity of the SEB-like motif. Among these is the infamous D641G, which I have to write about next, which may interact with MHCII to strengthen the association with T-cell receptors involved in cytokine storm initiation. The authors suggest that this may explain the higher rates of cytokine storm in Europe and US and the appearance in Europe of SARS-CoV-2 related inflammatory syndrome in children. It is important to note that without a heap of empirical evidence to back these suggestions, the indications of computer models are just that, indications only. After all, there are many possible explanations for many things!\nPS Just for fun, you may want to think about what the implications are of C-\u0026gt;G hypermutation, especially by APOBECs, on phylogenetics (i.e. on estimating evolutionary trees). How might that affect our SARS-CoV-2 evolutionary trees?\nTop image: \u0026ldquo;Heatmap of the 777 convergent COVID-19-associated clonotypes (observed between 4 or more COVID-19 participants)\u0026rdquo; by Galson, J. D.; Schaetzle, S.; Bashford-Rogers, R. J. M.; Raybould, M. I. J.; Kovaltsuk, A.; Kilpatrick, G. J.; Minter, R.; Finch, D. K.; Dias, J.; James, L.; Thomas, G., et al. 2020, used under CC.\n","date":1591539304,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1591539304,"objectID":"c72d6aaf9e7e5eb4d30685bc8f238e09","permalink":"http://InfrPopGen.github.io/blog/sars_evol_immunity/","publishdate":"2020-06-07T15:15:04+01:00","relpermalink":"/blog/sars_evol_immunity/","section":"blog","summary":"Did the emerging SARS-CoV-2 virus show adaptation to humans? Can phylogenetics reveal aspects of the human response to infection? Well, the short answers are probably not, and yes! Anyway, please read on!","tags":["genomics","virology","immunology","phylogenetics","evolution","SARS-CoV-2"],"title":"Evolution of the human–virus interaction in COVID-19","type":"blog"},{"authors":[" The COVID-19 Genomics UK (COG-UK) consortium"],"categories":null,"content":"","date":1590969600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1590969600,"objectID":"08ab9d55690b258572d58735240abe31","permalink":"http://InfrPopGen.github.io/publication/the-covid-19-genomics-ukcogu-kconsortium-2020/","publishdate":"2020-06-07T12:32:26.865278Z","relpermalink":"/publication/the-covid-19-genomics-ukcogu-kconsortium-2020/","section":"publication","summary":"","tags":null,"title":"An integrated national scale SARS-CoV-2 genomic surveillance network","type":"publication"},{"authors":["S.W. Attwood"],"categories":["Review","epidemiology","phylogenetics","virology"],"content":"    An April 28th paper featuring a SARS-CoV-2 phylogenetic tree provoked the ire of many evolutionary virologists―the paper (Forster et al. 2020) appeared in Proceedings of the National Academy of Sciences USA (PNAS) which is a prestigious journal, so what could have upset the evolutionary biology community so much? Alarm bells probably began to ring at this point in the abstract \u0026lsquo;The network faithfully traces routes of infections for documented coronavirus disease 2019 (COVID-19) cases, indicating that phylogenetic networks can likewise be successfully used to help trace undocumented COVID-19 infection sources\u0026rsquo;. First problem is that SARS-CoV-2 transmits itself on average once a week, but it accumulates variants around once a fortnight, so there is not the resolution to unravel a series of transmissions close together in time. A bigger problem is sampling―the authors infer a chain of transmission from China to Germany to Italy to Mexico, but this is not at all certain. If a \u0026ldquo;German\u0026rdquo; variant was quite common in China (or Italy) but was not often sampled because, for example, sampling was biased to cases in a particular city hospital and by chance this variant was common in a rural area, then it can appear that a variant arose in Germany and passed to Italy, when in fact it came from a third country. Last but not least, the authors observed certain variants in certain parts of the world that defined lineages on their tree (East Asian, European, and US/Australian) and they proposed that this divergence was due to selection for variants that favoured the virus in each particular part of the world. In fact there was no reason to imagine selection and adaptation because founder effects can explain their tree, without any selection. As people caught flights around the world, some variants went with them and some did not, and some were transmitted onward in the other countries and some were not. The result was founding populations in each region that differed, each with its own spectrum of variants and their frequencies, but all shaped by chance. As the outbreaks grew into a pandemic, these differences were amplified, because a common variant is more likely to be involved in a transmission event (so making it more common), to produce the differences that Forster et al. attributed to selection. A variant a low frequency is more likely to be lost by chance, for example only a few self-isolating cases need to be effective. We call this accidental loss genetic drift because the variant frequencies drift by chance (selection isn't pushing them). Some variants are lost by chance, and some might reach quite high percentages in the populations.\nTang et al. 2020 attracted similar criticism when they inferred selection for the virus during its first entry into the human population. The first problem was, again that one lineage had been inferred to be spreading faster and coming to dominate the population. The authors defined two \u0026ldquo;strains\u0026rdquo; (we prefer to call them lineages, until a very convincing case has been made for real biological differences among them) on the basis of posession of two variants (one of which was non-synonymous, i.e. it changed the amino acid coded for). The S (for serine) lineage lacked the variants (relative to the ancestral genome, which should be oldest SARS-CoV-2 genome we can find or infer, but this is a separate problem, see below) and the L (for leucine) lineage had them. Consequently, Tang et al. regarded the \u0026ldquo;S-strain\u0026rdquo; as ancestral, and L as derived from it. As L was derived, but more common (then ~70% of isolates sequenced) than S, the authors assumed that L had arisen and outcompeted S. The assumption that S is \u0026ldquo;evolutionarily older and less aggressive\u0026rdquo; can be questioned, as we did above with regard to founder effects. A second problem here is that of sampling bias, because only detected cases get sequenced, and detected cases are often related to one another (i.e. not independent samples). For example, a particular hospital might have good links with a sequencing consortium and so many genomes are sequenced from its locality, our database are also biased towards cases in cities. On top of this, the scope and depth of sampling varies by country―by early March most of the cases were in China, but 60% of the genomic data were coming from cases elsewhere.\nThe second problem is a little more subtle. The authors aimed to detect selection using the number of non-synonymous (dN) to synonymous (dS) substitutions (substitutions are mutations that stick in a population through the time we sample). If part of the genome (called a locus) has a low dN/dS it could be that purifying selection is removing genomes with altered amino acid sequences, so as to keep the locus unchanged, except for synonymous changes that only affect the RNA sequence, not the protein. We might then regard such conserved loci as important to success of the virus in some way. The first problem with this relates to sequencing errors; these are rare, because unlike real mutations they can't be transmitted, and have a higher non-synonymous to synonymous ratio because, again unlike real mutations, they have equal chance of occurring at a first codon as at a third codon. Consequently, such errors can cause an apparent excess of low-frequency non-synonymous substitutions which will mimic purifying selection. Second, because in a population there are always more non-synonymous substitutions than synonymous ones, and because most mutations are rare, there is more chance of sampling a synonymous substitution many times; this makes non-synonymous mutations look rarer than they really are.\nFinally, there was a view that Tang et al. had a problem with their rooting. The root of a phylogenetic tree (or a cluster of branches on a tree, which can be called a clade) is where you decide to put the origin of all the organisms, phylogenetics calls the things on a tree taxa (singular taxon), so the root is the ancestor of all the taxa on the tree. The derived taxa on the authors\u0026rsquo; tree should be those with a substitution relative to the sequence for the last common ancestor of the epidemic in China; however, it looked like they had used the Most Recent Common Ancestor (MRCA) not of the epidemic, but of the virus (SARS-CoV-2) and its closest known relative, the bat-CoV (bat coronavirus) RaTG13. The evolutionary distance back to this MRCA (the one with the bat-CoV) is much greater than that to the MRCA of the epidemic, because the time scales are decades, not months. The bigger distance allows back mutations (back to the ancestral state) to occur, so we won't be able to tell which substitutions are derived and which are not. The problem of back mutation will affect new synonymous mutations more than new non-synonymous ones because synonymous sites have higher substitution rates. The back mutation is back to the real common ancestor of the epidemic, and can be removal of slightly harmful mutations by positive selection, but it looks like a derived mutation away from the MRCA with the bat-CoV. So we can see the effect of not using the MRCA of the epidemic as the root, in a study where we are looking for selection in the epidemic (not the wrong root, but the wrong root for this particular analysis)―the effect is that the faux \u0026ldquo;derived\u0026rdquo; substitutions make it look like we have an excess of high-frequency synonymous substitutions when we don't, and to a potentially false conclusion of purifying selection.\nThe authors also identified \u0026ldquo;derived\u0026rdquo; variants that they presented as favouring transmission or virulence, but this was not convincing to many researchers. You can read more about these problems in MacLean et al 2020 and for a general warning of the pitfalls relating to inferring selection and new virulent strains of SARS-CoV-2, this is a good read Villabona-Arenas, Hanage \u0026amp; Tully, 2020. I think the general rule is, try not to get lost in your own analysis. Imagine you are someone else, a critical reviewer, and ask, what else could explain what I am seeing, aside from what I want to be true?\nPublish what you see, not what you think is there!\nTop image: \u0026ldquo;The logo of the ARTIC network\u0026rdquo; Credit: ARTIC Network\n","date":1589830110,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1589830110,"objectID":"975b42397e4cf56ef46e17b7bc65a107","permalink":"http://InfrPopGen.github.io/blog/sars2_evolving/","publishdate":"2020-05-18T20:28:30+01:00","relpermalink":"/blog/sars2_evolving/","section":"blog","summary":"What we can tell about SARS-CoV-2 from the observed genetic variation? and why there is controversy about whether or not the virus has evolved into different strains:","tags":["genomics","virology","epidemiology","phylogenetics","evolution","SARS-CoV-2"],"title":"Is SARS-CoV-2 evolving?","type":"blog"},{"authors":["S.W. Attwood"],"categories":["Research Advance","epidemiology"],"content":"    This investigation into the re-emergence of Bluetongue virus serotype 8 (BTV-8) in France 2015 is a fine example of phylogenetic epidemiology in action. In the 2006 outbreak BTV spread to affect 16 countries and killed many livestock animals, particularly sheep, with losses to European agriculture in the billions of Euros. BTV is an arthropod-borne virus of ruminants and was considered successfully controlled through vaccination by early 2010, but is now enzootic to France. Consequently, David Pascall, Kyriaki Nomikou, and colleagues in Glasgow and across Europe, sought to explain the unexpected outbreak in France by applying phylogenetics to a data-set of 164 complete BTV-8 genomes sampled throughout the first (2006-2009) and second (2015) outbreaks. Cessation of vaccination in 2010 was followed by a steady decline in seropositivity in cattle until 2014; thus a reintroduction (rather than cryptic sub-clinical transmission) appeared likely. To avoid culture effects most samples were taken directly from infected cattle. The phylogeny showed genomes of the second outbreak to be monophyletic (all in one clade or lineage, with no other genomes mixed in) and entirely nested within those of the first. Notably, the branch linking the two outbreaks was suspiciously short given the substitution rate of BTV-8 and the five years between the outbreaks. The ancestral sequence was reconstructed for the second outbreak and found to differ at only 4 sites from its closest relative in the first epidemic, whereas samples collected in 2006 differed from those in 2008 by up to 56 sites. Indeed root-to-tip regression (of tree branch lengths against sampling times), applied to a tree that included the reconstructed ancestor of the second outbreak, dated the ancestor as having been circulating in late March 2008. The authors were able to effectively rule out dormancy in some life-stage of the arthropod vector, and latency in some accessory host, because five years was just too long. Noting that BTV has been detected in the semen of viraemic bulls and rams, the authors proposed that the 2015 outbreak may have arisen from use of frozen semen, embryos or colostrum, which is a common practice in livestock farming. The study has been published in PLoS Biology and is available open-access directly from the publisher here.\nTop image: \u0026ldquo;Timescaled phylogenetic tree of BTV-8 samples collected during the European outbreaks between 2006 and 2018\u0026rdquo; by Pascall DJ, Nomikou K, Bréard E, Zientara S, Filipe AdS, Hoffmann B, et al. 2020, used under CC.\n","date":1588585726,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1588585726,"objectID":"ccf757108d3d1feaad8b5cbbf98497fc","permalink":"http://InfrPopGen.github.io/blog/frozenevol/","publishdate":"2020-05-04T10:48:46+01:00","relpermalink":"/blog/frozenevol/","section":"blog","summary":"This investigation into the recrudescence of Bluetongue virus serotype 8 (BTV-8) in France in 2015 is a fine example of phylogenetic epidemiology going detective to explain the reappearance of this virus, once thought erradiacted. Of course, this also reminds us of how we need to think of all potential sources of re-emergence if we hope to rid the world of SARS-CoV-2, viruses are persistent:","tags":["genomics","virology","epidemiology"],"title":"A virus goes missing―genomics explains reappearance of lost virus","type":"blog"},{"authors":["Ben P. Jones","Billie F. Norman","Hannah E. Borrett","Stephen W. Attwood","Mohammed M. H. Mondal","Anthony J. Walker","Joanne P. Webster","P. R. V. Jayanthe Rajapakse","Scott P. Lawton"],"categories":null,"content":"","date":1580515200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1580515200,"objectID":"9dc349e8a42a311d23d804e2ab4e9f6b","permalink":"http://InfrPopGen.github.io/publication/jones-divergence-2020/","publishdate":"2020-05-04T11:26:45.234213Z","relpermalink":"/publication/jones-divergence-2020/","section":"publication","summary":"Schistosoma spindale and Schistosoma indicum are ruminant-infecting trematodes of the Schistosoma indicum group that are widespread across Southeast Asia. Though neglected, these parasites can cause major pathology and mortality to livestock leading to significant welfare and socio-economic issues, predominantly amongst poor subsistence farmers and their families. Here we used mitogenomic analysis to determine the relationships between these two sympatric species of schistosome and to characterise S. spindale diversity in order to identify possible cryptic speciation. The mitochondrial genomes of S. spindale and S. indicum were assembled and genetic analyses revealed high levels of diversity within the S. indicum group. Evidence of functional changes in mitochondrial genes indicated adaptation to environmental change associated with speciation events in S. spindale around 2.5 million years ago. We discuss our results in terms of their theoretical and applied implications.","tags":null,"title":"Divergence across mitochondrial genomes of sympatric members of the Schistosoma indicum group and clues into the evolution of Schistosoma spindale","type":"publication"},{"authors":["S.W. Attwood"],"categories":["professional activity"],"content":"Download my recent Publons record file\n","date":1576959762,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1576959762,"objectID":"5ebc58f5802fcca6c5b89adf92a14af1","permalink":"http://InfrPopGen.github.io/files/publons/","publishdate":"2019-12-21T20:22:42Z","relpermalink":"/files/publons/","section":"files","summary":"My recent Publons record (my almost complete editorial activity), which I thought was better than just putting a test-file here!","tags":["professional activity","editing","peer-review"],"title":"Publons","type":"files"},{"authors":["S.W. Attwood"],"categories":["oncology","Research Advance","Pre-clinical"],"content":"    The study found that the more cancer cells in a tumour communicate with one another the more similar or complementary and co-dependent they become in terms of the molecular pathways they use and resources they exploit in order to feed and grow. The effect of this coupling is that the cells gradually fall into the same niche, and this has the effect of increasing cell to cell competition (because now most of the cells are chasing the same narrow range of resources). The result of this increased competition is slower growth of the tumour compared with the initially diverse tumour cell population.\nThe mathematical models developed by the authors suggest that cancers that are growing exponetially are unlikely to respond to therapies targeting cell–cell interactions, whilst those that show increased coupling over time are likely to be more sensitive to such therapies. The authors emphasised that the therapeutic potential of the models has not been tested in clinical trials and are currently only theoretical; however, the findings could be useful in designing therapies that target functional coupling of cells to control tumor growth.\n","date":1576952287,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1576952287,"objectID":"437def8d5710d90f648f7f111a0cdb99","permalink":"http://InfrPopGen.github.io/blog/chatty/","publishdate":"2019-12-21T18:18:07Z","relpermalink":"/blog/chatty/","section":"blog","summary":"A [recent paper](https://www.pnas.org/content/116/6/1918) by Professor Paul K. Newton and his doctoral student Jeffrey West (both of University of Southern California), suggests that the natural competition between cells may be exploited to slow tumor growth---the study is another example of the potential of eco-evolutionary models in the design of cancer therapies (so called 'ecological therapies')","tags":["oncology","evolution","ecology","therapy"],"title":"Communicative Cancers Grow More Slowly","type":"blog"},{"authors":["S.W. Attwood"],"categories":["Research Advance","Pre-clinical"],"content":"    In blog post \u0026ldquo;An Eye for Nature\u0026rdquo; we looked at artificial retina solutions for degenerative conditions like AMD that are common cause of blindness in humans. As a follow up I would like to mention a 2019 paper which offers an amazingly simple potential treatment for such retinal damge.\nThe authors noted that, whilst the opsins, the protein part of light-sensitive receptors found in the rod and cone cells of the human retina, are normally embedded in the molecular complex of the G-protein-coupled-receptor signalling cascade that amplifies and moderates (through feedback loops) the signal from the photoreceptive pigments, these complexes are common to many kinds of cells not just rods and cones. They were also aware that although the rods and cones are lost in many retinal degenerative diseases, the main nerve cells of the retina, the retinal ganglion cells, are not lost and remain active albeit insensitive to light. Putting these two facts together led them to ask the question, if we put the genes coding for a retinal photoreceptor into retinal ganglion cells might the opsins automatically integrate into the ganglions\u0026rsquo; G-protein signalling complexes, without the need to somehow transplant the entire opsin-signalling complex? To address this they used an Adeno-Associated Virus (AAV) to carry the gene coding for green cone cell opsin into the genome of the retinal ganglion cells of blind mice. Although many neuroscientists would have said that this simple approach should not work, the experiment did in fact work. The blind mice were not only able to pass several of the tests used in humans to test eyesight (and were almost indistiguishable from normal mice in such tests), but their transformed ganglia even adjusted the photo-response according to the light level, turning the signal up in low light and down in bright light!\nAlthough the findings appear miraculous, there is some way to go before this technique can be used to treat people. Although the AAV used specifically infects retinal ganglion cells, and so can be precisely targeted, there are issues of insertional mutagenesis because the viral genome can insert itself into the cells\u0026rsquo; genomes at random positions (this can potentially cause cancer or loss of essential gene function—for more on this see this paper). The authors note that because the human eye contains thousands of times more ganglion cells than that of the mouse, much larger doses of AAV would be needed to treat a human. Nevertheless, AAV vectors have been FDA approved for use in human degenerative retinal conditions in cases where there is alternative treatment. The treatment might not be suitable for treatment of all retinal degenerative diseases because the retinal ganglion cells do not survive in all such conditions. In [retinitis pigmentosa](https://www.rnib.org.uk/eye-health/eye-conditions/retinitis-pigmentosa), the target disease of these authors, 30% to 75% of these cells survive relative to normal eyes (for details see this paper, whereas in wet AMD over half of the cells are lost. In dry AMD the approach is most promising as cell survival in this case is as good as in normal eyes (for more see this paper); however, we need to consider that these cells are also lost with ageing and the conditions to be treated are mostly those of old age. Nevertheless, the finding has great potential in the treatment of retinal degenerative disease.\n","date":1576951117,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1576951117,"objectID":"69e5e0dbb19da82cf9b9315c20ec22b5","permalink":"http://InfrPopGen.github.io/blog/3mice/","publishdate":"2019-12-21T17:58:37Z","relpermalink":"/blog/3mice/","section":"blog","summary":"A team led by Ehud Isacoff and John Flannery at University of California—Berkeley have found a surprisingly simple way to restore sight after retinal damage!","tags":["Regenerative Medicine"],"title":"Three Blind Mice See Again!","type":"blog"},{"authors":["S.W. Attwood"],"categories":["Research Advance","Pre-clinical"],"content":"    Retinal degenerative disorders, such as Age-Related Macular Degeneration (AMD), affect millions of people around the world. In the UK alone, AMD is the main cause of loss of sight, affecting over 600,000 people. In all of these disorders, the photoreceptor cells lining the retina at the back of the eye lose function, which leads to the loss of sight. Available treatments are at best capable of only slowing the degeneration in some individuals. The devastating impact of these disorders on human wellbeing and the lack of a cure have prompted researchers to seek radical solutions to the problem. The idea they came up with was to replace the damaged retina with an artificial one, and the development of such ‘bionic’ eyes has exploded into a wide range of devices and systems. The US Department of Energy even ran its own Artificial Retina Project leading to the first clinical trial Argus I in 2002 in which six patients received ‘bionic’ eye implants. By 2006, trials of the Argos II device had been carried out in 30 patients across Europe and the United States. By 2011 the device was approved for clinical use in Europe and by 2013 70 people had received these implants. Unfortunately, these retinal prosthetics use arrays of electrodes or photodiodes to convey small pulses of electricity to mimic the action of the lost retinal cells by stimulating the nerves of the retina; they are therefore limited by the density of photoreceptors and by the weight and bulk of the materials used. Consequently, these implants generate very low resolution images and are of benefit only to those with extensive sight loss.\nFortunately, a team at the University of Oxford’s Department of Chemistry, and led by Dphil student Vanessa Restrepo-Schild stepped in with an innovative solution to many of the problems faced by these ‘digital camera’ style implants. Restrepo-Schild realised that the scarring and inflammation caused by such devices, which limited their utility, could be avoided by building a retina out of biological materials―using only materials that occur naturally in the eye. Consequently she set about building a photosensitive array similar to that of the retina from materials normally used in cell culture. The resulting implant would be not only less inflammatory, but also more soft and flexible to mimic better the original retina. Vanessa Restrepo-Schild realised that the hydrogels normally used in the laboratory had the right strength and flexibility for the job, but the team developed their own tailored gel for the purpose.\nTo emulate the light response function of the retina, they developed what they called ‘synthetic cells’, which were produced by arranging water droplets on the hydrogel in a lipid-containing oil. A lipid bilayer then formed naturally around each droplet, creating a ‘synthetic cell’. The cells were made photosensitive by adding the light-driven proton pump, bacteriorhodopsin, to the water droplets. In addition to flexibility and compatibility, the tiny water droplets can achieve arrays with greater pixel density than the ‘digital camera’ style devices. The approach is particularly neat because, as Restrepo-Schild points out, their synthetic retina already speaks the same language as the underlying nerve cells, and so should generate electrical impulses exactly as the real retina would. The impulses, when passed to the brain, are likely to be interpreted more readily as natural sight. Restrepo-Schild’s next step is to create, in fact print on their lab’s bespoke 3D printer, a 3D version of the device and observe how it communicates with nerve cells in tissue culture. The team is confident that they will soon have a system able to not only recognise colours, but also shapes and patterns, prior to preclinical testing and then clinical trials.\nRestrepo-Schild cites her childhood fascination with the difference between the living and the machine as the source of her inspiration. She has long been pondering the idea of using parts of our own living bodies in devices that would not themselves be living, but would function as in vivo. We at Bang! are thankful that her childhood interests never faded, and rather proud that this potentially life changing research was done here, in Oxford.\nVanessa Restrepo-Schild is a student in the laboratory of Professor Hagan Bayley and their original research paper can be found here: www.nature.com/articles/srep46585.\n","date":1575992328,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1575992328,"objectID":"5cb4b36327b49326bd820a5b35dce2b1","permalink":"http://InfrPopGen.github.io/blog/eye4nature/","publishdate":"2019-12-10T15:38:48Z","relpermalink":"/blog/eye4nature/","section":"blog","summary":"This is a sligtly updated version of an article I wrote for _Bang!_ (TT17 issue):","tags":["Regenerative Medicine"],"title":"An Eye for Nature","type":"blog"},{"authors":null,"categories":null,"content":"Academic is designed to give technical content creators a seamless experience. You can focus on the content and Academic handles the rest.\nHighlight your code snippets, take notes on math classes, and draw diagrams from textual representation.\nOn this page, you'll find some examples of the types of technical content that can be rendered with Academic.\nExamples Code Academic supports a Markdown extension for highlighting code syntax. You can enable this feature by toggling the highlight option in your config/_default/params.toml file.\n```python import pandas as pd data = pd.read_csv(\"data.csv\") data.head() ``` renders as\nimport pandas as pd data = pd.read_csv(\u0026#34;data.csv\u0026#34;) data.head() Math Academic supports a Markdown extension for $\\LaTeX$ math. You can enable this feature by toggling the math option in your config/_default/params.toml file and adding markup: mmark to your page front matter.\nTo render inline or block math, wrap your LaTeX math with $$...$$.\nExample math block:\n$$\\gamma_{n} = \\frac{ \\left | \\left (\\mathbf x_{n} - \\mathbf x_{n-1} \\right )^T \\left [\\nabla F (\\mathbf x_{n}) - \\nabla F (\\mathbf x_{n-1}) \\right ] \\right |} {\\left \\|\\nabla F(\\mathbf{x}_{n}) - \\nabla F(\\mathbf{x}_{n-1}) \\right \\|^2}$$ renders as\n\\[\\gamma_{n} = \\frac{ \\left | \\left (\\mathbf x_{n} - \\mathbf x_{n-1} \\right )^T \\left [\\nabla F (\\mathbf x_{n}) - \\nabla F (\\mathbf x_{n-1}) \\right ] \\right |}{\\left \\|\\nabla F(\\mathbf{x}_{n}) - \\nabla F(\\mathbf{x}_{n-1}) \\right \\|^2}\\]\nExample inline math $$\\left \\|\\nabla F(\\mathbf{x}_{n}) - \\nabla F(\\mathbf{x}_{n-1}) \\right \\|^2$$ renders as \\(\\left \\|\\nabla F(\\mathbf{x}_{n}) - \\nabla F(\\mathbf{x}_{n-1}) \\right \\|^2\\) .\nExample multi-line math using the \\\\ math linebreak:\n$$f(k;p_0^*) = \\begin{cases} p_0^* \u0026amp; \\text{if }k=1, \\\\ 1-p_0^* \u0026amp; \\text {if }k=0.\\end{cases}$$ renders as\n\\[f(k;p_0^*) = \\begin{cases} p_0^* \u0026 \\text{if }k=1, \\\\ 1-p_0^* \u0026 \\text {if }k=0.\\end{cases}\\]\nDiagrams Academic supports a Markdown extension for diagrams. You can enable this feature by toggling the diagram option in your config/_default/params.toml file or by adding diagram: true to your page front matter.\nAn example flowchart:\n```mermaid graph TD; A--B; A--C; B--D; C--D; ``` renders as\ngraph TD; A--B; A--C; B--D; C--D; An example sequence diagram:\n```mermaid sequenceDiagram participant Alice participant Bob Alice-John: Hello John, how are you? loop Healthcheck John-John: Fight against hypochondria end Note right of John: Rational thoughts prevail... John--Alice: Great! John-Bob: How about you? Bob--John: Jolly good! ``` renders as\nsequenceDiagram participant Alice participant Bob Alice-John: Hello John, how are you? loop Healthcheck John-John: Fight against hypochondria end Note right of John: Rational thoughts prevail... John--Alice: Great! John-Bob: How about you? Bob--John: Jolly good! An example Gantt diagram:\n```mermaid gantt dateFormat YYYY-MM-DD section Section A task :a1, 2014-01-01, 30d Another task :after a1 , 20d section Another Task in sec :2014-01-12 , 12d another task : 24d ``` renders as\ngantt dateFormat YYYY-MM-DD section Section A task :a1, 2014-01-01, 30d Another task :after a1 , 20d section Another Task in sec :2014-01-12 , 12d another task : 24d Todo lists You can even write your todo lists in Academic too:\n- [x] Write math example - [x] Write diagram example - [ ] Do something else renders as\n Write math example Write diagram example Do something else  Tables Represent your data in tables:\n| First Header | Second Header | | ------------- | ------------- | | Content Cell | Content Cell | | Content Cell | Content Cell | renders as\n   First Header Second Header     Content Cell Content Cell   Content Cell Content Cell    Asides Academic supports a Markdown extension for asides, also referred to as notices or hints. By prefixing a paragraph with A\u0026gt;, it will render as an aside. You can enable this feature by adding markup: mmark to your page front matter, or alternatively using the Alert shortcode.\nA\u0026gt; A Markdown aside is useful for displaying notices, hints, or definitions to your readers. renders as\n A Markdown aside is useful for displaying notices, hints, or definitions to your readers.\n Did you find this page helpful? Consider sharing it 🙌 ","date":1562889600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1562889600,"objectID":"07e02bccc368a192a0c76c44918396c3","permalink":"http://InfrPopGen.github.io/post/writing-technical-content/","publishdate":"2019-07-12T00:00:00Z","relpermalink":"/post/writing-technical-content/","section":"post","summary":"Academic is designed to give technical content creators a seamless experience. You can focus on the content and Academic handles the rest.\nHighlight your code snippets, take notes on math classes, and draw diagrams from textual representation.\nOn this page, you'll find some examples of the types of technical content that can be rendered with Academic.\nExamples Code Academic supports a Markdown extension for highlighting code syntax. You can enable this feature by toggling the highlight option in your config/_default/params.","tags":null,"title":"Writing technical content in Academic","type":"post"},{"authors":["Stephen W. Attwood","Michael J. Edel"],"categories":null,"content":"","date":1551398400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1551398400,"objectID":"cdcfaaee2c40a46b94a103ce800a3d04","permalink":"http://InfrPopGen.github.io/publication/attwood-ips-cell-2019/","publishdate":"2019-12-07T17:32:03.399227Z","relpermalink":"/publication/attwood-ips-cell-2019/","section":"publication","summary":"The use of induced Pluripotent Stem Cells (iPSC) as a source of autologous tissues shows great promise in regenerative medicine. Nevertheless, several major challenges remain to be addressed before iPSC-derived cells can be used in therapy, and experience of their clinical use is extremely limited. In this review, the factors affecting the safe translation of iPSC to the clinic are considered, together with an account of efforts being made to overcome these issues. The review draws upon experiences with pluripotent stem-cell therapeutics, including clinical trials involving human embryonic stem cells and the widely transplanted mesenchymal stem cells. The discussion covers concerns relating to: (i) the reprogramming process; (ii) the detection and removal of incompletely differentiated and pluripotent cells from the resulting medicinal products; and (iii) genomic and epigenetic changes, and the evolutionary and selective processes occurring during culture expansion, associated with production of iPSC-therapeutics. In addition, (iv) methods for the practical culture-at-scale and standardization required for routine clinical use are considered. Finally, (v) the potential of iPSC in the treatment of human disease is evaluated in the light of what is known about the reprogramming process, the behavior of cells in culture, and the performance of iPSC in pre-clinical studies.","tags":["evolution","stem cell","stem cell therapy","safety","adverse event","clinical translation","genetic stability","pluripotent stem-cell","stem-cell research"],"title":"iPS-Cell Technology and the Problem of Genetic Instability—Can It Ever Be Safe for Clinical Use?","type":"publication"},{"authors":["Stephen Attwood"],"categories":[],"content":"from IPython.core.display import Image Image(\u0026#39;https://www.python.org/static/community_logos/python-logo-master-v3-TM-flattened.png\u0026#39;) print(\u0026#34;Welcome to Academic!\u0026#34;) Welcome to Academic!  Install Python and JupyterLab Install Anaconda which includes Python 3 and JupyterLab.\nAlternatively, install JupyterLab with pip3 install jupyterlab.\nCreate or upload a Jupyter notebook Run the following commands in your Terminal, substituting \u0026lt;MY-WEBSITE-FOLDER\u0026gt; and \u0026lt;SHORT-POST-TITLE\u0026gt; with the file path to your Academic website folder and a short title for your blog post (use hyphens instead of spaces), respectively:\nmkdir -p \u0026lt;MY-WEBSITE-FOLDER\u0026gt;/content/post/\u0026lt;SHORT-POST-TITLE\u0026gt;/ cd \u0026lt;MY-WEBSITE-FOLDER\u0026gt;/content/post/\u0026lt;SHORT-POST-TITLE\u0026gt;/ jupyter lab index.ipynb The jupyter command above will launch the JupyterLab editor, allowing us to add Academic metadata and write the content.\nEdit your post metadata The first cell of your Jupter notebook will contain your post metadata (front matter).\nIn Jupter, choose Markdown as the type of the first cell and wrap your Academic metadata in three dashes, indicating that it is YAML front matter:\n--- title: My post's title date: 2019-09-01 # Put any other Academic metadata here... --- Edit the metadata of your post, using the documentation as a guide to the available options.\nTo set a featured image, place an image named featured into your post's folder.\nFor other tips, such as using math, see the guide on writing content with Academic.\nConvert notebook to Markdown jupyter nbconvert index.ipynb --to markdown --NbConvertApp.output_files_dir=. Example This post was created with Jupyter. The orginal files can be found at https://github.com/gcushen/hugo-academic/tree/master/exampleSite/content/post/jupyter\n","date":1549324800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1567641600,"objectID":"6e929dc84ed3ef80467b02e64cd2ed64","permalink":"http://InfrPopGen.github.io/post/jupyter/","publishdate":"2019-02-05T00:00:00Z","relpermalink":"/post/jupyter/","section":"post","summary":"Learn how to blog in Academic using Jupyter notebooks","tags":[],"title":"Display Jupyter Notebooks with Academic","type":"post"},{"authors":[],"categories":[],"content":"Welcome to Slides Academic\n Features  Efficiently write slides in Markdown 3-in-1: Create, Present, and Publish your slides Supports speaker notes Mobile friendly slides   Controls  Next: Right Arrow or Space Previous: Left Arrow Start: Home Finish: End Overview: Esc Speaker notes: S Fullscreen: F Zoom: Alt + Click PDF Export: E   Code Highlighting Inline code: variable\nCode block:\nporridge = \u0026#34;blueberry\u0026#34; if porridge == \u0026#34;blueberry\u0026#34;: print(\u0026#34;Eating...\u0026#34;)  Math In-line math: $x + y = z$\nBlock math:\n$$ f\\left( x \\right) = ;\\frac{{2\\left( {x + 4} \\right)\\left( {x - 4} \\right)}}{{\\left( {x + 4} \\right)\\left( {x + 1} \\right)}} $$\n Fragments Make content appear incrementally\n{{% fragment %}} One {{% /fragment %}} {{% fragment %}} **Two** {{% /fragment %}} {{% fragment %}} Three {{% /fragment %}} Press Space to play!\nOne Two Three  A fragment can accept two optional parameters:\n class: use a custom style (requires definition in custom CSS) weight: sets the order in which a fragment appears   Speaker Notes Add speaker notes to your presentation\n{{% speaker_note %}} - Only the speaker can read these notes - Press `S` key to view {{% /speaker_note %}} Press the S key to view the speaker notes!\n Only the speaker can read these notes Press S key to view    Themes  black: Black background, white text, blue links (default) white: White background, black text, blue links league: Gray background, white text, blue links beige: Beige background, dark text, brown links sky: Blue background, thin dark text, blue links    night: Black background, thick white text, orange links serif: Cappuccino background, gray text, brown links simple: White background, black text, blue links solarized: Cream-colored background, dark green text, blue links   Custom Slide Customize the slide style and background\n{{\u0026lt; slide background-image=\u0026#34;/img/boards.jpg\u0026#34; \u0026gt;}} {{\u0026lt; slide background-color=\u0026#34;#0000FF\u0026#34; \u0026gt;}} {{\u0026lt; slide class=\u0026#34;my-style\u0026#34; \u0026gt;}}  Custom CSS Example Let's make headers navy colored.\nCreate assets/css/reveal_custom.css with:\n.reveal section h1, .reveal section h2, .reveal section h3 { color: navy; }  Questions? Ask\nDocumentation\n","date":1549324800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1549324800,"objectID":"0e6de1a61aa83269ff13324f3167c1a9","permalink":"http://InfrPopGen.github.io/slides/example/","publishdate":"2019-02-05T00:00:00Z","relpermalink":"/slides/example/","section":"slides","summary":"An introduction to using Academic's Slides feature.","tags":[],"title":"Slides","type":"slides"},{"authors":["Stephen W. Attwood","Liang Liu","Guan-Nan Huo"],"categories":null,"content":"","date":1546300800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1546300800,"objectID":"ae4781b61a8bad97806c1f223d116ea3","permalink":"http://InfrPopGen.github.io/publication/attwood-population-2019/","publishdate":"2019-12-07T17:32:03.398768Z","relpermalink":"/publication/attwood-population-2019/","section":"publication","summary":"Background Neotricula aperta is the snail-intermediate host of the parasitic blood-fluke Schistosoma mekongi which causes Mekong schistosomiasis in Cambodia and the Lao PDR. Despite numerous phylogenetic studies only one DNA-sequence based population-genetic study of N. aperta had been published, and the origin, structure and persistence of N. aperta were poorly understood. Consequently, a phylogenetic and population genetic study was performed, with addition of new data to pre-existing DNA-sequences for N. aperta from remote and inaccessible habitats, including one new taxon from Laos and 505 bp of additional DNA-sequence for all sampled taxa,. Principal findings Spatial Principal Component Analysis revealed the presence of significant spatial-genetic clustering. Genetic-distance-based clustering indicated four populations with near perfect match to a priori defined ecogeographical regions. Spring-dwelling taxa were found to form an ecological isolate relative to other N. aperta. The poor dispersal capabilities suggested by spatial-genetic analyses were confirmed by Bayesian inference of migration rates. Population divergence time estimation implied a mid-Miocene colonisation of the present range, with immediate and rapid radiation in each ecogeographical region. Estimated effective population sizes were large (120–310 thousand). Conclusions The strong spatial-genetic structure confirmed the poor dispersal capabilities of N. aperta—suggesting human-mediated reintroduction of disease to controlled areas as the primary reason for control failure. The isolation of the spring-dwelling taxa and ecogeographical structure suggests adaptation of sub-populations to different habitats; the epidemiological significance of this needs investigation. The large effective population sizes indicate that the high population densities observed in surveyed habitats are also present in inaccessible areas; affording great potential for recrudescence driven by animal-reservoir transmission in remote streams. Mid-Miocene colonisation implies heterochronous evolution of these snails and associated schistosomes and suggests against coevolution of snail and parasite. Heterochronicity favours ecological factors as shapers of host-parasite specificity and greater potential for escape from schistosomiasis control through host-switching.","tags":["Phylogenetic analysis","Phylogenetics","Phylogeography","Population genetics","Snails","Schistosoma","Cambodia","Rivers"],"title":"Population genetic structure and geographical variation in Neotricula aperta (Gastropoda: Pomatiopsidae), the snail intermediate host of Schistosoma mekongi (Digenea: Schistosomatidae)","type":"publication"},{"authors":["S.W. Attwood"],"categories":null,"content":"","date":1544623200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1544623200,"objectID":"2f16f30e7fc90581fe3852d38ffe9e1e","permalink":"http://InfrPopGen.github.io/talk/spatialpopgen/","publishdate":"2019-12-21T21:44:50Z","relpermalink":"/talk/spatialpopgen/","section":"talk","summary":"A demonstration of the application of spatial population genetics on a dataset beginning with PCA and...","tags":["Population Genetics","spatial analysis"],"title":"Hierarchical Strategy for Population Genetic Analysis","type":"talk"},{"authors":["S.W. Attwood"],"categories":null,"content":"","date":1500296400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1500296400,"objectID":"ac9cc4d30d3bf0780b16d00e0b3d76c4","permalink":"http://InfrPopGen.github.io/talk/biomphalaria/","publishdate":"2019-12-21T22:02:26Z","relpermalink":"/talk/biomphalaria/","section":"talk","summary":"The South American freshwater snail _Biomphalaria_ has been reorted from Guangdong Province in southern China. The introduction of snails...","tags":["Population Genetics","Molecular Systematics","Phylogenetics","invasive species","schistosmiasis"],"title":"An Update on Biomphalaria in China","type":"talk"},{"authors":null,"categories":null,"content":"","date":1461715200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1461715200,"objectID":"d1311ddf745551c9e117aa4bb7e28516","permalink":"http://InfrPopGen.github.io/project/external-project/","publishdate":"2016-04-27T00:00:00Z","relpermalink":"/project/external-project/","section":"project","summary":"An example of linking directly to an external project website using `external_link`.","tags":["Demo"],"title":"External Project","type":"project"},{"authors":null,"categories":null,"content":"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.\nNullam vel molestie justo. Curabitur vitae efficitur leo. In hac habitasse platea dictumst. Sed pulvinar mauris dui, eget varius purus congue ac. Nulla euismod, lorem vel elementum dapibus, nunc justo porta mi, sed tempus est est vel tellus. Nam et enim eleifend, laoreet sem sit amet, elementum sem. Morbi ut leo congue, maximus velit ut, finibus arcu. In et libero cursus, rutrum risus non, molestie leo. Nullam congue quam et volutpat malesuada. Sed risus tortor, pulvinar et dictum nec, sodales non mi. Phasellus lacinia commodo laoreet. Nam mollis, erat in feugiat consectetur, purus eros egestas tellus, in auctor urna odio at nibh. Mauris imperdiet nisi ac magna convallis, at rhoncus ligula cursus.\nCras aliquam rhoncus ipsum, in hendrerit nunc mattis vitae. Duis vitae efficitur metus, ac tempus leo. Cras nec fringilla lacus. Quisque sit amet risus at ipsum pharetra commodo. Sed aliquam mauris at consequat eleifend. Praesent porta, augue sed viverra bibendum, neque ante euismod ante, in vehicula justo lorem ac eros. Suspendisse augue libero, venenatis eget tincidunt ut, malesuada at lorem. Donec vitae bibendum arcu. Aenean maximus nulla non pretium iaculis. Quisque imperdiet, nulla in pulvinar aliquet, velit quam ultrices quam, sit amet fringilla leo sem vel nunc. Mauris in lacinia lacus.\nSuspendisse a tincidunt lacus. Curabitur at urna sagittis, dictum ante sit amet, euismod magna. Sed rutrum massa id tortor commodo, vitae elementum turpis tempus. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Aenean purus turpis, venenatis a ullamcorper nec, tincidunt et massa. Integer posuere quam rutrum arcu vehicula imperdiet. Mauris ullamcorper quam vitae purus congue, quis euismod magna eleifend. Vestibulum semper vel augue eget tincidunt. Fusce eget justo sodales, dapibus odio eu, ultrices lorem. Duis condimentum lorem id eros commodo, in facilisis mauris scelerisque. Morbi sed auctor leo. Nullam volutpat a lacus quis pharetra. Nulla congue rutrum magna a ornare.\nAliquam in turpis accumsan, malesuada nibh ut, hendrerit justo. Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus. Quisque sed erat nec justo posuere suscipit. Donec ut efficitur arcu, in malesuada neque. Nunc dignissim nisl massa, id vulputate nunc pretium nec. Quisque eget urna in risus suscipit ultricies. Pellentesque odio odio, tincidunt in eleifend sed, posuere a diam. Nam gravida nisl convallis semper elementum. Morbi vitae felis faucibus, vulputate orci placerat, aliquet nisi. Aliquam erat volutpat. Maecenas sagittis pulvinar purus, sed porta quam laoreet at.\n","date":1461715200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1461715200,"objectID":"8f66d660a9a2edc2d08e68cc30f701f7","permalink":"http://InfrPopGen.github.io/project/internal-project/","publishdate":"2016-04-27T00:00:00Z","relpermalink":"/project/internal-project/","section":"project","summary":"An example of using the in-built project page.","tags":["Deep Learning"],"title":"Internal Project","type":"project"},{"authors":["Stephen Attwood"],"categories":["Demo"],"content":"Create a free website with Academic using Markdown, Jupyter, or RStudio. Choose a beautiful color theme and build anything with the Page Builder - over 40 widgets, themes, and language packs included!\nCheck out the latest demo of what you'll get in less than 10 minutes, or view the showcase of personal, project, and business sites.\n 👉 Get Started 📚 View the documentation 💬 Ask a question on the forum 👥 Chat with the community 🐦 Twitter: @source_themes @GeorgeCushen #MadeWithAcademic 💡 Request a feature or report a bug ⬆️ Updating? View the Update Guide and Release Notes ❤ Support development of Academic:  ☕️ Donate a coffee 💵 Become a backer on Patreon 🖼️ Decorate your laptop or journal with an Academic sticker 👕 Wear the T-shirt 👩‍💻 Contribute       Academic is mobile first with a responsive design to ensure that your site looks stunning on every device.   Key features:\n Page builder - Create anything with widgets and elements Edit any type of content - Blog posts, publications, talks, slides, projects, and more! Create content in Markdown, Jupyter, or RStudio Plugin System - Fully customizable color and font themes Display Code and Math - Code highlighting and LaTeX math supported Integrations - Google Analytics, Disqus commenting, Maps, Contact Forms, and more! Beautiful Site - Simple and refreshing one page design Industry-Leading SEO - Help get your website found on search engines and social media Media Galleries - Display your images and videos with captions in a customizable gallery Mobile Friendly - Look amazing on every screen with a mobile friendly version of your site Multi-language - 15+ language packs including English, 中文, and Português Multi-user - Each author gets their own profile page Privacy Pack - Assists with GDPR Stand Out - Bring your site to life with animation, parallax backgrounds, and scroll effects One-Click Deployment - No servers. No databases. Only files.  Themes Academic comes with automatic day (light) and night (dark) mode built-in. Alternatively, visitors can choose their preferred mode - click the sun/moon icon in the top right of the Demo to see it in action! Day/night mode can also be disabled by the site admin in params.toml.\nChoose a stunning theme and font for your site. Themes are fully customizable.\nEcosystem  Academic Admin: An admin tool to import publications from BibTeX or import assets for an offline site Academic Scripts: Scripts to help migrate content to new versions of Academic  Install You can choose from one of the following four methods to install:\n one-click install using your web browser (recommended) install on your computer using Git with the Command Prompt/Terminal app install on your computer by downloading the ZIP files install on your computer with RStudio  Then personalize and deploy your new site.\nUpdating View the Update Guide.\nFeel free to star the project on Github to help keep track of updates.\nLicense Copyright 2016-present George Cushen.\nReleased under the MIT license.\n","date":1461110400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1555459200,"objectID":"279b9966ca9cf3121ce924dca452bb1c","permalink":"http://InfrPopGen.github.io/post/getting-started/","publishdate":"2016-04-20T00:00:00Z","relpermalink":"/post/getting-started/","section":"post","summary":"Create a beautifully simple website in under 10 minutes.","tags":["Academic"],"title":"Academic: the website builder for Hugo","type":"post"},{"authors":["Guan-Nan Huo","Liang Liu","Hong-Bin He","Stephen W. Attwood"],"categories":null,"content":"","date":1451606400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1451606400,"objectID":"049ef1cd159c4b691597c8d9eb385141","permalink":"http://InfrPopGen.github.io/publication/huo-investigation-2016/","publishdate":"2019-12-07T17:32:03.397974Z","relpermalink":"/publication/huo-investigation-2016/","section":"publication","summary":"Schistosoma japonicum remains a major challenge to human and animal health. Earlier microsatellite-based studies reported possible definitive-host-specific private alleles within S. japonicum, opening the possibility that different definitive hosts might harbour different parasite strains. Previous investigations have also detected near-identical multilocus genotypes in populations of adult worms - possibly the result of mutations occurring during the asexual (intramolluscan) phase of clonal expansion. Research has also revealed extensive deviations from Hardy-Weinberg Proportions (HWP) and conflicting results among studies. The present study was performed to examine some of the potential effects of infrapopulation structure on microsatellite-based studies of the transmission ecology of S. japonicum. Potential sources of bias considered included organotropic distribution of worms, non-random mating and corrections for clonal expansion.","tags":["population genetics","Schistosoma japonicum","Hardy-Weinberg","microsatellite","Genetic differentiation","Infrapopulation","Mating","Organotropic","Sampling bias"],"title":"An investigation into the potential effects of infrapopulation structure and other sources of sampling error, on population genetic studies of the transmission of Schistosoma japonicum (Trematoda: Digenea)","type":"publication"},{"authors":["S.W. Attwood"],"categories":null,"content":"","date":1442671200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1442671200,"objectID":"34223555cd12b890487093878ce42083","permalink":"http://InfrPopGen.github.io/talk/coevolution01/","publishdate":"2019-12-26T16:55:02Z","relpermalink":"/talk/coevolution01/","section":"talk","summary":"_Schistosoma japonicum_ causes major public health problems in China and the Philippines; this parasite, which is transmitted by...","tags":["Molecular Systematics","Co-evolution","Phylogenetics","Schistosomiasis"],"title":"Co-evolution in schistosomiasis","type":"talk"},{"authors":["Stephen W. Attwood","Motomu Ibaraki","Yasuhide Saitoh","Naoko Nihei","Daniel A. Janies"],"categories":null,"content":"","date":1435708800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1435708800,"objectID":"af422e53a9d97286df6b66e35cbc5248","permalink":"http://InfrPopGen.github.io/publication/attwood-comparative-2015/","publishdate":"2019-12-07T17:32:03.390589Z","relpermalink":"/publication/attwood-comparative-2015/","section":"publication","summary":"Author Summary Schistosomiasis is a disease caused by a parasitic worm transmitted to humans by certain species of freshwater snails. In spite of several decades of intensive coordinated control schistosomiasis still infects around 1 million people in China. In order to understand the potential for spread of the disease into new areas and new snail species, it is helpful to know if the snails and parasites in China are coevolved; this means that evolutionary divergence in one group (the snails) is matched by a corresponding divergence in the other (the parasites), which is what would be expected if the two groups are locked in an evolutionary arms race. DNA-sequence data were collected for snails and parasites from the same localities. The findings indicated that coevolution was unlikely to have occurred. The implications of this are that host-switching or acquisition is more likely than previously thought. Consequently, there is a greater potential for spread of the parasite into new areas. The role of mountain barriers in confining schistosomiasis to certain regions was highlighted; this is important in view of the current plans to breach these barriers by road and rail construction that will link China and Southeast Asia.","tags":null,"title":"Comparative Phylogenetic Studies on Schistosoma japonicum and Its Snail Intermediate Host Oncomelania hupensis: Origins, Dispersal and Coevolution","type":"publication"},{"authors":["S.W. Attwood"],"categories":null,"content":"","date":1430327815,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1430327815,"objectID":"d0bfb6f563dced94bc7a6bb8762f9568","permalink":"http://InfrPopGen.github.io/talk/phylogenies4cancer/","publishdate":"2019-12-26T17:22:44Z","relpermalink":"/talk/phylogenies4cancer/","section":"talk","summary":"Practical considerations are reviewed for the estimation of phylogenies in cancer research.","tags":["Cancer","Phylodynamics","Phylogenetics","Oncology","Molecular Systematics"],"title":"A practical guide to estimating phylogenies for cancer","type":"talk"},{"authors":["Stephen W. Attwood","Maud Cottet"],"categories":null,"content":"","date":1420070400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1420070400,"objectID":"6abe6c1382afddb13e5a504770fe5a17","permalink":"http://InfrPopGen.github.io/publication/attwood-malacological-2015/","publishdate":"2019-12-07T17:32:03.391019Z","relpermalink":"/publication/attwood-malacological-2015/","section":"publication","summary":"","tags":null,"title":"Malacological and parasitological surveys along the Xe Bangfai and its tributaries in Khammouane Province, Lao PDR","type":"publication"},{"authors":["S. W. Attwood"],"categories":null,"content":"","date":1420070400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1420070400,"objectID":"41aa17836d15d335db20fa15ba06b5b6","permalink":"http://InfrPopGen.github.io/publication/attwood-triculinae-2015/","publishdate":"2019-12-07T17:32:03.399025Z","relpermalink":"/publication/attwood-triculinae-2015/","section":"publication","summary":"","tags":null,"title":"The Triculinae: remarkable freshwater snail biodiversity - remarkably neglected","type":"publication"},{"authors":["Stephen W. Attwood","Guan-Nan Huo","Jian-Wen Qiu"],"categories":null,"content":"","date":1420070400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1420070400,"objectID":"f40ef334eff66a4286e9ff9b5b2325fe","permalink":"http://InfrPopGen.github.io/publication/attwood-update-2015/","publishdate":"2019-12-07T17:32:03.398173Z","relpermalink":"/publication/attwood-update-2015/","section":"publication","summary":"In 1973 planorbid snails then identified as Biomphalaria straminea were discovered in Hong Kong, China. It was assumed that these snails had been introduced to Hong Kong via the import of tropical fish by air from South America. In 2012 Biomphalaria were found for the first time in Guangdong Province, China. In view of the renewed interest in these invasive snails, a morphological and DNA-sequence based phylogenetic study was undertaken for seven populations of Biomphalaria snails collected in Guangdong. Morphologically and phylogenetically, five of the populations clustered more closely with Biomphalaria kuhniana than with B. straminea. Levels of genetic diversity among the populations were about half those of autochthonous populations in Brazil, the phylogenetic relationships did not correlate with a radiation from any one international port in China, and different lineages appeared associated with different ports. Consequently in explaining the current distribution of the snails, multiple colonization events, each establishing a new local snail population near to maritime international container ports, were considered more likely than the spread of snails from Hong Kong to China. The displacement of B. straminea by B. kuhniana in Guangdong is considered as an explanation for the habitat changes observed among the snails between Hong Kong in the 1980s and the present. The conclusions of the study are that any risk of Schistosoma mansoni transmission in China is more likely to come from parasite importation in the intramolluscan stage, than from transmission by migrant workers from South America or Africa. In addition, although likely to be rare, sporadic outbreaks of imported schistosomiasis (caused by invading infected snails) could be a threat to public health in the vicinity of International container ports (not only in Guangdong Province). Further work is called for to investigate further the presence of B. kuhniana and its potential interactions with B. straminea (the former is thought to be incompatible with S. mansoni), and the responses of Chinese Biomphalaria to potential competitors such as Thiaridae. The current expansion of container ports in Brazil and Venezuela, and the increase in trade with China, is likely to accentuate any current risk of imported schistosomiasis, and surveillance around ports in China, together with further research, are necessary.","tags":["China","Schistosomiasis","Gastropoda","Biomphalaria","invasive species","phylogenetic"],"title":"Update on the distribution and phylogenetics of Biomphalaria (Gastropoda: Planorbidae) populations in Guangdong Province, China","type":"publication"},{"authors":["S.W. Attwood"],"categories":null,"content":"","date":1415280600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1415280600,"objectID":"232ff491a5f23974bdc6cab337308e1e","permalink":"http://InfrPopGen.github.io/talk/cancerphylodynamics/","publishdate":"2019-12-26T17:33:47Z","relpermalink":"/talk/cancerphylodynamics/","section":"talk","summary":"The potential for harnessing population genetics and phylogenetics in the study of cancer is discussed, together with applications in the development of improved therapies.","tags":["Cancer","Oncology","Phylodynamics","Phylogenetics","Molecular Systematics"],"title":"Cancer Phylodynamics","type":"talk"},{"authors":["Liang Liu","Guan-Nan Huo","Hong-Bin He","Benjiang Zhou","Stephen W. Attwood"],"categories":null,"content":"","date":1388534400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1388534400,"objectID":"bf0db14cc5a222c1c64f849e527433c9","permalink":"http://InfrPopGen.github.io/publication/liu-phylogeny-2014/","publishdate":"2019-12-07T17:32:03.397595Z","relpermalink":"/publication/liu-phylogeny-2014/","section":"publication","summary":"The Pomatiopsidae are reported from northern India into southern China and Southeast Asia, with two sub-families, the Pomatiopsinae (which include freshwater, amphibious, terrestrial and marine species) and the freshwater Triculinae. Both include species acting as intermediate host for species of the blood-fluke Schistosoma which cause a public health problem in East Asia. Also, with around 120 species, triculine biodiversity exceeds that of any other endemic freshwater molluscan fauna. Nevertheless, the origins of the Pomatiopsidae, the factors driving such a diverse radiation and aspects of their co-evolution with Schistosoma are not fully understood. Many taxonomic questions remain; there are problems identifying medically relevant species. The predicted range is mostly unsurveyed and the true biodiversity of the family is underestimated. Consequently, the aim of the study was to collect DNA-sequence data for as many pomatiopsid taxa as possible, as a first step in providing a resource for identification of epidemiologically significant species (by non-malacologists), for use in resolving taxonomic confusion and for testing phylogeographical hypotheses. PMID: 24548800","tags":null,"title":"A phylogeny for the pomatiopsidae (Gastropoda: Rissooidea): a resource for taxonomic, parasitological and biodiversity studies","type":"publication"},{"authors":["Stephen W. Attwood","E. Suchart Upatham"],"categories":null,"content":"","date":1356998400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1356998400,"objectID":"20bda54634f343348dc4e9601ea2e64f","permalink":"http://InfrPopGen.github.io/publication/attwood-population-2013/","publishdate":"2019-12-07T17:32:03.397222Z","relpermalink":"/publication/attwood-population-2013/","section":"publication","summary":"PLOS Neglected Tropical Diseases is an open-access journal publishing peer-reviewed research on the worldś most neglected tropical diseases, such as elephantiasis, river blindness, leprosy, hookworm, schistosomiasis, and African sleeping sickness","tags":["infectious diseases","epidemiology","pathology","control","Public Health","medical","neglected tropical diseases","online science journal","open access","open-access","plos","plos journal","plos neglected tropical diseases","plos ntd","plos ntds","prevention","public library of science","public policy","scientific","treatment","tropical diseases"],"title":"A Population Growth Trend Analysis for Neotricula aperta, the Snail Intermediate Host of Schistosoma mekongi, after Construction of the Pak-Mun Dam","type":"publication"},{"authors":["Stephen W Attwood","E Suchart Upatham"],"categories":null,"content":"","date":1325376000,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1325376000,"objectID":"01cf304276ceb180af578e058efe947a","permalink":"http://InfrPopGen.github.io/publication/attwood-observations-2012/","publishdate":"2019-12-07T17:32:03.396842Z","relpermalink":"/publication/attwood-observations-2012/","section":"publication","summary":"BACKGROUND  The snail Neotricula aperta transmits Mekong schistosomiasis in southern Laos and Cambodia, with about 1.5 million people at risk of infection. Plans are under consideration for at least 12 hydroelectric power dams on the lower Mekong river and much controversy surrounds predictions of their environmental impacts. Unfortunately, there are almost no ecological data (such as long-term population trend studies) available for N. aperta which could be used in impact assessment. Predictions currently assume that the impacts will be the same as those observed in Africa (i.e., a worsening of the schistosomiasis problem); however, marked ecological differences between the snails involved suggest that region specific models are required. The present study was performed as an initial step in providing data, which could be useful in the planning of water resource development in the Mekong. Snail population density records were analyzed for populations close to, and far downstream of, the Nam Theun 2 (NT2) project in Laos in order to detect any changes that might be attributable to impoundment.   RESULTS  The population immediately downstream of NT2 and that sampled 400 km downstream in Thailand both showed a long-term trend of slow growth from 1992 to 2005; however, both populations showed a marked decline in density between 2005 and 2011. The decline in Thailand was to a value significantly lower than that predicted by a linear mixed model for the data, whilst the population density close to NT2 fell to undetectable levels in 2011 from densities of over 5000 m(-2) in 2005. The NT2 dam began operation in 2010.   CONCLUSIONS  The impact of the NT2 dam on N. aperta population density could be more complex than first thought and may reflect the strict ecological requirements of this snail. There was no indication that responses of N. aperta populations to dam construction are similar to those observed with Bulinus and Schistosoma haematobium in Africa, for example. In view of the present findings, more ecological data (in particular population density monitoring and surveillance for new habitats) are urgently required in order to understand properly the likely impacts of water resource development on Mekong schistosomiasis.","tags":null,"title":"Observations on Neotricula aperta (Gastropoda: Pomatiopsidae) population densities in Thailand and central Laos: implications for the spread of Mekong schistosomiasis","type":"publication"},{"authors":["Stephen W. Attwood"],"categories":null,"content":"","date":1325376000,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1325376000,"objectID":"68a91000733c5f281aebb1bedd7d03b9","permalink":"http://InfrPopGen.github.io/publication/attwood-public-2012/","publishdate":"2019-12-07T17:32:03.39631Z","relpermalink":"/publication/attwood-public-2012/","section":"publication","summary":"","tags":null,"title":"Public health: Use snail ecology to assess dam impact","type":"publication"},{"authors":["James V Conlan","Banchob Sripa","Stephen Attwood","Paul N Newton"],"categories":null,"content":"","date":1293840000,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1293840000,"objectID":"cc7b96f23dde46581a5a7d401bcc3d31","permalink":"http://InfrPopGen.github.io/publication/conlan-review-2011/","publishdate":"2019-12-07T17:32:03.396487Z","relpermalink":"/publication/conlan-review-2011/","section":"publication","summary":"Parasitic zoonoses are common and widely distributed in the Southeast Asian region. However, the interactions between parasites, hosts and vectors are influenced by environmental, socio-cultural and livestock production changes that impact on the distribution, prevalence and severity of disease. In this review we provide an update on new knowledge in the context of ongoing changes for the food-borne pig associated zoonoses Taenia solium and Trichinella spp., the food-borne trematodes Opisthorchis viverrini and Clonorchis sinensis, the water-borne trematodes Schistosoma spp., the vector-borne zoonotic protozoa Plasmodium knowlesi and Leishmania spp. and the soil-borne zoonotic hookworm Ancylostoma ceylanicum. These various changes need to be considered when assessing or developing regional control programs or devising new research initiatives in a changing SE Asia.","tags":null,"title":"A review of parasitic zoonoses in a changing Southeast Asia","type":"publication"},{"authors":["Stephen W Attwood"],"categories":null,"content":"","date":1262304000,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1262304000,"objectID":"6dd39e29599144f12ec56eefd85c13a0","permalink":"http://InfrPopGen.github.io/publication/attwood-studies-2010/","publishdate":"2019-12-07T17:32:03.396128Z","relpermalink":"/publication/attwood-studies-2010/","section":"publication","summary":"In this chapter a review of research published since 2000 on the biology of the snail intermediate hosts of trematode parasites of medical importance in Southeast Asia, and related taxa is presented. Recent taxonomic revisions of the first intermediate hosts of Paragonimus in the region are considered and an account of changes in current perspectives regarding the evolution of intermediate-host:parasite associations for both Paragonimus and Schistosoma is given. The latest phylogeographical hypotheses for Schistosoma, Paragonimus, Fasciola and Fasciolopsis are also reviewed and compared. Work performed in the region on the snail intermediate hosts of other less studied parasites, such as Opisthorchis/Clonorchis and haplorchids, is also described.","tags":null,"title":"Studies on the parasitology, phylogeography and the evolution of host-parasite interactions for the snail intermediate hosts of medically important trematode genera in Southeast Asia","type":"publication"},{"authors":["Liang Liu","Mohammed Mondal","Mohamed Idris","Hakim Lokman","PRV Jayanthe Rajapakse","Fadjar Satrija","Jose Diaz","E Suchart Upatham","Stephen Attwood"],"categories":null,"content":"","date":1262304000,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1262304000,"objectID":"168f03e28135bf1c69960925c754647f","permalink":"http://InfrPopGen.github.io/publication/liu-phylogeography-2010/","publishdate":"2019-12-07T17:32:03.395918Z","relpermalink":"/publication/liu-phylogeography-2010/","section":"publication","summary":"BACKGROUND:The freshwater snail Indoplanorbis exustus is found across India, Southeast Asia, central Asia (Afghanistan), Arabia and Africa. Indoplanorbis is of economic importance in that it is responsible for the transmission of several species of the genus Schistosoma which infect cattle and cause reduced livestock productivity. The snail is also of medical importance as a source of cercarial dermatitis among rural workers, particularly in India. In spite of its long history and wide geographical range, it is thought that Indoplanorbis includes only a single species. The aims of the present study were to date the radiation of Indoplanorbis across Asia so that the factors involved in its dispersal in the region could be tested, to reveal potential historical biogeographical events shaping the phylogeny of the snail, and to look for signs that I. exustus might be polyphyletic.RESULTS:The results indicated a radiation beginning in the late Miocene with a divergence of an ancestral bulinine lineage into Assam and peninsular India clades. A Southeast Asian clade diverged from the peninsular India clade late-Pliocene; this clade then radiated at a much more rapid pace to colonize all of the sampled range of Indoplanorbis in the mid-Pleistocene.CONCLUSIONS:The phylogenetic depth of divergences between the Indian clades and Southeast Asian clades, together with habitat and parasitological differences suggest that I. exustus may comprise more than one species. The timescale estimated for the radiation suggests that the dispersal to Arabia and to Southeast Asia was facilitated by palaeogeographical events and climate change, and did not require human involvement. Further samples from Afghanistan, Africa and western India are required to refine the phylogeographical hypothesis and to include the African Recent dispersal.","tags":null,"title":"The phylogeography of Indoplanorbis exustus (Gastropoda: Planorbidae) in Asia","type":"publication"},{"authors":["S.W. Attwood"],"categories":null,"content":"","date":1230768000,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1230768000,"objectID":"525548ba9b3a9064c7a1077927405ac1","permalink":"http://InfrPopGen.github.io/publication/attwood-mekong-2009/","publishdate":"2019-12-07T17:32:03.396676Z","relpermalink":"/publication/attwood-mekong-2009/","section":"publication","summary":"","tags":null,"title":"Mekong Schistosomiasis: Where Did It Come from and Where Is It Going?","type":"publication"},{"authors":["Zheng Xiang","Xinwen Chen","Lijun Yang","Yongshu He","Runsheng Jiang","Benjamin M. Rosenthal","Pengtao Luan","S.W. Attwood","Yangxian Zuo","Ya-ping Zhang","Zhaoqing Yang"],"categories":null,"content":"","date":1230768000,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1230768000,"objectID":"11bf3ddf3ffc9c41f3dd6ec7ec807536","permalink":"http://InfrPopGen.github.io/publication/xiang-non-invasive-2009/","publishdate":"2019-12-07T17:32:03.39571Z","relpermalink":"/publication/xiang-non-invasive-2009/","section":"publication","summary":"Because the excreted sporocysts and/or oocysts of various species of Sarcocystis may not be discriminated morphologically, we sought to validate a diagnostic technique based on variation in the 18S rDNA sequence. Oocysts and/or sporocysts from three taxa of Sarcocystis were collected from human, feline, and canine definitive hosts that had fed upon meats infected with the muscle cysts of Sarcocystis hominis, Sarcocystis fusiformis and a species of Sarcocystis from water buffalo that could not be distinguished from Sarcocystis cruzi. Using a new collection method employing filter paper, these excreted oocysts and sporocysts were subjected to DNA extraction, as were the corresponding muscle cysts. Methods employing PCR-RFLP and DNA sequencing of a partial 18S rDNA gene (ssrRNA) sequence were then used to successfully distinguish among the three taxa. The same, unique restriction digestion pattern characterizes the tissue cysts and oocysts and/or sporocysts of each parasite taxon. The technique makes possible amplification and identification of species specific gene sequences based on DNA extracted from as few as 7 excreted sporocysts (the equivalent of 3 and 1/2 oocysts) from freshly prepared material, or as few as 50 sporocysts from feces samples that had been stored in potassium dichromate (K2Cr2O7) for as long as 6 years. This represents the first report using molecular diagnostic procedures to diagnose oocysts of Sarcocystis in faecal samples, describing a valuable new tool for studying the epidemiology of various Sarcocystis species.","tags":["Diagnostics","18S rRNA","Faeces","Oocysts"],"title":"Non-invasive methods for identifying oocysts of Sarcocystis spp. from definitive hosts","type":"publication"},{"authors":["S. W Attwood","F. A Fatih","E. S Upatham"],"categories":null,"content":"","date":1199145600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1199145600,"objectID":"e66348dce76324ef3d0e7b6352729130","permalink":"http://InfrPopGen.github.io/publication/attwood-study-2008/","publishdate":"2019-12-07T17:32:03.395183Z","relpermalink":"/publication/attwood-study-2008/","section":"publication","summary":"","tags":null,"title":"A study of DNA-sequence variation among Schistosoma mekongi (Trematoda: Digenea) populations and related taxa; phylogeography and the current distribution of Asian schistosomiasis","type":"publication"},{"authors":["F. Guan","A. O Niu","S. W Attwood","Li YL","Zhang B.","Y. H Zhu"],"categories":null,"content":"","date":1199145600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1199145600,"objectID":"77f0ad6278891ddcd91003230efae21d","permalink":"http://InfrPopGen.github.io/publication/guan-molecular-2008/","publishdate":"2019-12-07T17:32:03.397043Z","relpermalink":"/publication/guan-molecular-2008/","section":"publication","summary":"","tags":null,"title":"Molecular phylogenetics of Triculine snails (Gastropoda: Pomatiopsidae) from southern China","type":"publication"},{"authors":["S. W Attwood","F. A Fatih","I. C Campbell","E. S Upatham"],"categories":null,"content":"","date":1199145600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1199145600,"objectID":"ce963c7cd6b9937ade2b8b4d734f01b5","permalink":"http://InfrPopGen.github.io/publication/attwood-distribution-2008/","publishdate":"2019-12-07T17:32:03.395004Z","relpermalink":"/publication/attwood-distribution-2008/","section":"publication","summary":"","tags":null,"title":"The distribution of Mekong schistosomiasis, past and future: preliminary indications from an analysis of genetic variation in the intermediate host","type":"publication"},{"authors":["S. W Attwood","F. A Fatih","M. M.H Mondal","M. A Alim","S. Fadjar","R. P.V.J Rajapakse","D. Rollinson"],"categories":null,"content":"","date":1167609600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1167609600,"objectID":"0fa4436ee5d7f058816c6a4f72209188","permalink":"http://InfrPopGen.github.io/publication/attwood-dna-2007/","publishdate":"2019-12-07T17:32:03.397795Z","relpermalink":"/publication/attwood-dna-2007/","section":"publication","summary":"","tags":null,"title":"A DNA sequence-based study of the Schistosoma indicum (Trematoda: Digenea) group: population phylogeny, taxonomy and historical biogeography","type":"publication"},{"authors":["Lian-Yong Chen","Ben-Jiang Zhou","Zhao-Qing Yang","Cui-Ying Li","S. W Attwood","Wen-Lin Wang","Lin Lei","Xiao-Dong Sun","Zai-Xing Zhang"],"categories":null,"content":"","date":1167609600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1167609600,"objectID":"8eb69efe52c68f1a2c9cf9ec5b5a61ea","permalink":"http://InfrPopGen.github.io/publication/chen-effects-2007/","publishdate":"2019-12-07T17:32:03.395522Z","relpermalink":"/publication/chen-effects-2007/","section":"publication","summary":"","tags":["taxonomy","Sarcocystis","Morphology","Cyst","Frozen storage","Ultrastructure"],"title":"Effects of frozen storage on the structure of sarcocysts in pig muscle and implications in taxonomic studies","type":"publication"},{"authors":["S. W Attwood","H. S Lokman","K. Y Ong"],"categories":null,"content":"","date":1104537600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1104537600,"objectID":"72569b9c1f70ed3a3d2b154eaaed4f20","permalink":"http://InfrPopGen.github.io/publication/attwood-robertsiella-2005/","publishdate":"2019-12-07T17:32:03.395355Z","relpermalink":"/publication/attwood-robertsiella-2005/","section":"publication","summary":"","tags":null,"title":"Robertsiella silvicola, a new species of triculine snail (Caenogastropoda: Pomatiopsidae) from peninsular Malaysia, intermediate host of Schistosoma malayensis (Trematoda: Digenea)","type":"publication"},{"authors":["S. W Attwood","E. S Upatham","Y. -P Zhang","Z. -Q Yang","V. R Southgate"],"categories":null,"content":"","date":1072915200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1072915200,"objectID":"f38fa0c0d35c9710cd983d0ab40f1e5e","permalink":"http://InfrPopGen.github.io/publication/attwood-dna-sequence-2004/","publishdate":"2019-12-07T17:32:03.398422Z","relpermalink":"/publication/attwood-dna-sequence-2004/","section":"publication","summary":"","tags":null,"title":"A DNA-sequence based phylogeny for triculine snails (Gastropoda: Pomatiopsidae: Triculinae), intermediate hosts for Schistosoma (Trematoda: Digenea): phylogeography and the origin of Neotricula","type":"publication"},{"authors":["S. W Attwood","I. Campbell","E. S Upatham","D. Rollinson"],"categories":null,"content":"","date":1072915200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1072915200,"objectID":"ddc7041587dd3f895922f497cc11f414","permalink":"http://InfrPopGen.github.io/publication/attwood-schistosomiasis-2004/","publishdate":"2019-12-07T17:32:03.394466Z","relpermalink":"/publication/attwood-schistosomiasis-2004/","section":"publication","summary":"","tags":null,"title":"Schistosomiasis in the Xe Kong river of Cambodia: the detection of Schistosoma mekongi in a natural population of snails and observations on intermediate host distribution","type":"publication"},{"authors":["S. W Attwood","D. S Brown","X. H Meng","V. R Southgate"],"categories":null,"content":"","date":1041379200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1041379200,"objectID":"daa94cc1f0600fd61f396cff1b12bd69","permalink":"http://InfrPopGen.github.io/publication/attwood-new-2003/","publishdate":"2019-12-07T17:32:03.394294Z","relpermalink":"/publication/attwood-new-2003/","section":"publication","summary":"","tags":null,"title":"A new species of Tricula (Pomatiopsidae: Triculinae) from Sichuan Province, PR China: intermediate host of Schistosoma sinensium","type":"publication"},{"authors":["S. W Attwood","S. Ambu","X. H Meng","E. S Upatham","F. -S Xu","V. R Southgate"],"categories":null,"content":"","date":1041379200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1041379200,"objectID":"b8f31ce536d503783d159223746047b7","permalink":"http://InfrPopGen.github.io/publication/attwood-phylogenetics-2003/","publishdate":"2019-12-07T17:32:03.394638Z","relpermalink":"/publication/attwood-phylogenetics-2003/","section":"publication","summary":"","tags":null,"title":"The phylogenetics of triculine snails (Rissooidea: Pomatiopsidae) from south-east Asia and southern China: historical biogeography and the transmission of human schistosomiasis","type":"publication"},{"authors":["A. E Lockyer","P. D Olson","P. Østergaard","D. Rollinson","D. A Johnston","S. W Attwood","V. R Southgate","P. Horak","S. D Snyder","T. H Le","T. Agatsuma","D. P McManus","A. C Carmichael","S. Naem","D. 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W Attwood","X. -W Chen","Y. -P Zhang"],"categories":null,"content":"","date":1009843200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1009843200,"objectID":"7d679099f454e8f3d6083aaf2dd9f868","permalink":"http://InfrPopGen.github.io/publication/li-pcr-based-2002/","publishdate":"2019-12-07T17:32:03.394114Z","relpermalink":"/publication/li-pcr-based-2002/","section":"publication","summary":"","tags":["parasitology","Sarcocystis"],"title":"A PCR-based analysis of Sarcocystis cruzi (Protozoa: Scarcocystidae) in Yunnan Province, PR China, reveals the water buffalo (Bubalus bubalis) as a natural intermediate host","type":"publication"},{"authors":["S. W Attwood","C. Panasoponkul","E. S Upatham","X. H Meng","V. 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