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Identifying Changes in Selective Constraints: Host Shifts in Influenza

Asif U. Tamuri, Mario dos Reis, Alan J. Hay, Richard A. Goldstein, Christophe Fraser
<span title="2009-11-13">2009</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ch57atmlprauhhbqdf7x4ytejm" style="color: black;">PLoS Computational Biology</a> </i> &nbsp;
The method is of broad applicability to investigating changes in selective constraints when the timing of the changes is known.  ...  We identify 172 amino acid sites with strong support and 518 sites with moderate support of different selection constraints in human and avian viruses.  ...  Flanagan provided the Java optimisation library used in this work. Author Contributions Conceived and designed the experiments: MdR AJH RAG. Performed the experiments: AUT RAG.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1000564">doi:10.1371/journal.pcbi.1000564</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19911053">pmid:19911053</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2770840/">pmcid:PMC2770840</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7ydu5ot2eze5zcl7mflruwbi64">fatcat:7ydu5ot2eze5zcl7mflruwbi64</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171015131256/http://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000564&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/4c/28/4c28d4ea79647f2f1d5ff0977b6d8244d2bf5694.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1000564"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2770840" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Geometric constraints dominate the antigenic evolution of influenza H3N2 hemagglutinin [article]

Austin G Meyer, Claus O Wilke
<span title="2015-01-22">2015</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
In summary, proximity to the receptor-binding region, and not host immune bias, seems to be the primary determinant of H3 evolution.  ...  We have carried out a comprehensive analysis of the determinants of human influenza A H3 hemagglutinin evolution, considering three distinct predictors of evolutionary variation at individual sites: solvent  ...  Tamuri AU, dos Reis M, Hay AJ, Goldstein RA (2009) Identifying changes in selective 573 constraints: Host shifts in influenza. PLoS Comput Biol 5: e1000564. 574 18.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/014183">doi:10.1101/014183</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gfix72tz3nbljf4qyriycbcnxi">fatcat:gfix72tz3nbljf4qyriycbcnxi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190501210337/https://www.biorxiv.org/content/biorxiv/early/2015/04/09/014183.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/37/ac/37ac7f7071909c3d1c98ec76f7638faf6ff5575a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/014183"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Geometric Constraints Dominate the Antigenic Evolution of Influenza H3N2 Hemagglutinin

Austin G. Meyer, Claus O. Wilke, Jesse D Bloom
<span title="2015-05-28">2015</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/bcchuruegramvpr4vupdzp5jfm" style="color: black;">PLoS Pathogens</a> </i> &nbsp;
These results suggest that either the available epitope sites do not accurately represent the true influenza antigenic sites or that host immune bias may be less important for influenza evolution than  ...  Author Summary The influenza virus is one of the most rapidly evolving human viruses.  ...  aminoacid changes in the mature protein.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.ppat.1004940">doi:10.1371/journal.ppat.1004940</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26020774">pmid:26020774</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4447415/">pmcid:PMC4447415</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jypghngagneilfgt7qngxnmlu4">fatcat:jypghngagneilfgt7qngxnmlu4</a> </span>
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Constraints of Viral RNA Synthesis on Codon Usage of Negative-Strand RNA Virus

Ryan H. Gumpper, Weike Li, Ming Luo, Rebecca Ellis Dutch
<span title="2018-12-12">2018</span> <i title="American Society for Microbiology"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/w3gj5mynrnbtndalcc5jnhymym" style="color: black;">Journal of Virology</a> </i> &nbsp;
Our work suggests a paradigm shift that the interactions between the RNA genome and the nucleocapsid protein regulate the activity of vRdRp, which selects codon usage.  ...  The stability of the genomic RNA in the nucleocapsid appears to regulate its accessibility to the viral RNA polymerase, thus placing constraints on codon usage to balance viral RNA synthesis.  ...  ACKNOWLEDGMENTS We acknowledge Apurv Patel for assistance in cloning the various chimeric minigenomes. This work was funded in part by an NIH grant (R01 AI106307).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1128/jvi.01775-18">doi:10.1128/jvi.01775-18</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30541832">pmid:30541832</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6384081/">pmcid:PMC6384081</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/iuuydrff4rbyvkugxn36d5o2bm">fatcat:iuuydrff4rbyvkugxn36d5o2bm</a> </span>
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Simultaneously reconstructing viral cross-species transmission history and identifying the underlying constraints

N. R. Faria, M. A. Suchard, A. Rambaut, D. G. Streicker, P. Lemey
<span title="2013-02-04">2013</span> <i title="The Royal Society"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/p7stgfom7rbkheuw5cc6avanwu" style="color: black;">Philosophical Transactions of the Royal Society of London. Biological Sciences</a> </i> &nbsp;
[5] to use an operational definition of host shifts and CST: while inferred changes in host in the ancestral history between these lineages reflects host shifting, viral jumps between the dominant host  ...  The observation that host genetic distances represent important constraints for both CST spillover and host shifts is not a stand-alone finding.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1098/rstb.2012.0196">doi:10.1098/rstb.2012.0196</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23382420">pmid:23382420</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3678322/">pmcid:PMC3678322</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/l2votoaqozgc7l5dmkpuhnr3qu">fatcat:l2votoaqozgc7l5dmkpuhnr3qu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190227004121/http://pdfs.semanticscholar.org/79cc/90b294c1ed1ad84feabe65ae2865f537a35c.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/79/cc/79cc90b294c1ed1ad84feabe65ae2865f537a35c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1098/rstb.2012.0196"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3678322" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Evolutionary Constraints Shaping Streptococcus pyogenes –Host Interactions

Reid V. Wilkening, Michael J. Federle
<span title="">2017</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/bpz6fp6hmnevtfyr7aueihjx2i" style="color: black;">Trends in Microbiology</a> </i> &nbsp;
, the nasopharynx, and its ability to either live with its host in an asymptomatic lifestyle or as an agent of superficial infections.  ...  changes leading to pandemic strains.  ...  Acknowledgments Support for these efforts were provided by The American Heart Association Predoctoral fellowship 15PRE22710027 for RVW, the Burroughs Wellcome Fund Investigators in the Pathogenesis of  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.tim.2017.01.007">doi:10.1016/j.tim.2017.01.007</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28216292">pmid:28216292</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5474166/">pmcid:PMC5474166</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fy7px4yn4jfblfph55lz7djwjq">fatcat:fy7px4yn4jfblfph55lz7djwjq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200210010006/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5474166&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d9/a5/d9a51984b52ac28eb791b1c2d889ad211ad31148.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.tim.2017.01.007"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5474166" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Genome-wide transposon mutagenesis of paramyxoviruses reveals constraints on genomic plasticity

Satoshi Ikegame, Shannon M. Beaty, Christian Stevens, Sohui T. Won, Arnold Park, David Sachs, Patrick Hong, Benhur Lee, Patricia A. Thibault, Anice C. Lowen
<span title="2020-10-09">2020</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/bcchuruegramvpr4vupdzp5jfm" style="color: black;">PLoS Pathogens</a> </i> &nbsp;
disruptions; but the envelope glycoproteins were not, highlighting structural constraints that contribute to the restricted antigenic drift in paramyxoviruses.  ...  Nonetheless, when we applied our strategy to a fusion-defective Newcastle disease virus (Avulavirinae subfamily), we could select for F-revertants and other insertants in the 5' end of the genome.  ...  This is in contrast to the well-known propensity for antigenic drift of influenza virus, another negative-sense RNA virus, in response to various pressures including host populations' adaptive immune responses  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.ppat.1008877">doi:10.1371/journal.ppat.1008877</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33035269">pmid:33035269</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ljgqkbyjn5hkpj3wr3bb7p76ie">fatcat:ljgqkbyjn5hkpj3wr3bb7p76ie</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201122101316/https://journals.plos.org/plospathogens/article/file?id=10.1371%2Fjournal.ppat.1008877&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/5c/37/5c37ce34a8cf7ff283f6f4dfd1e38049142887d7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.ppat.1008877"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a>

Analysis of Dengue Virus Genetic Diversity during Human and Mosquito Infection Reveals Genetic Constraints

October M. Sessions, Andreas Wilm, Uma Sangumathi Kamaraj, Milly M. Choy, Angelia Chow, Yuwen Chong, Xin Mei Ong, Niranjan Nagarajan, Alex R. Cook, Eng Eong Ooi, Philip M. Armstrong
<span title="2015-09-01">2015</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/23nqq3odsjhmbi5tqavvcn7cfm" style="color: black;">PLoS Neglected Tropical Diseases</a> </i> &nbsp;
Importantly, we identified a region within the NS3 protein coding sequence that is refractory to mutation during human and mosquito infection.  ...  High-throughput sequencing of DENV-1 genome directly from twelve, paired dengue patients' sera and then passaging these sera into the two primary mosquito vectors showed consistent and distinct sequence changes  ...  To identify regions of constraint within the DENV1 genome, we aggregated all predicted single nucleotide variants (SNVs) to detect regions with (i) a local enrichment in intra-host SNV calls (mutational  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pntd.0004044">doi:10.1371/journal.pntd.0004044</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26327586">pmid:26327586</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4556638/">pmcid:PMC4556638</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vtspld54unbi7n77lauhhpbie4">fatcat:vtspld54unbi7n77lauhhpbie4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171015025845/http://journals.plos.org/plosntds/article/file?id=10.1371/journal.pntd.0004044&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/36/91/36913c2f47894afa1563ea2c74cca946c6871d0f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pntd.0004044"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4556638" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Subtype-specific structural constraints in the evolution of influenza A virus hemagglutinin genes

Alexander P. Gultyaev, Monique I. Spronken, Mathilde Richard, Eefje J. A. Schrauwen, René C. L. Olsthoorn, Ron A. M. Fouchier
<span title="">2016</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tnqhc2x2aneavcd3gx5h7mswhm" style="color: black;">Scientific Reports</a> </i> &nbsp;
Structural constraints were identified by analysis of covariations of nucleotides suggested to be paired by structure prediction algorithms.  ...  Existence of subtype-specific structured regions in the segments of the influenza A virus genome is apparently an important factor in virus evolution and reassortment of its genes.  ...  We thank Ramona Mögling and Miranda de Graaf for assistance in setup of plaque assay, and Minoushka Oduber for making some of the mutants.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/srep38892">doi:10.1038/srep38892</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27966593">pmid:27966593</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5155281/">pmcid:PMC5155281</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/inpfm3wmunbsldb2xycxdtadiy">fatcat:inpfm3wmunbsldb2xycxdtadiy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180720192129/https://openaccess.leidenuniv.nl/bitstream/handle/1887/46983/ScientificReports6%282016%2938892.pdf?sequence=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/4a/a9/4aa9a3df7eb64faa6b5a95bdb7864b78decd19dc.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/srep38892"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5155281" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Plasticity and constraints in development and evolution

Jason Hodin
<span title="2000-04-15">2000</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6jhel4ehgzafrcojwt6qwq6ocu" style="color: black;">Journal of Experimental Zoology</a> </i> &nbsp;
Parallelisms, on the other hand, may characterize developmental processes subject to constraints.  ...  The other main class of homoplasy, convergence, is superficial similarity in morphological structures in which the underlying ontogenetic mechanisms are distinct.  ...  Developmental constraints in practice So how can developmental constraints be positively identified?  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/(sici)1097-010x(20000415)288:1&lt;1::aid-jez1&gt;3.0.co;2-7">doi:10.1002/(sici)1097-010x(20000415)288:1&lt;1::aid-jez1&gt;3.0.co;2-7</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/10750048">pmid:10750048</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bcmuqeycaba5xmwcdnmpbroflu">fatcat:bcmuqeycaba5xmwcdnmpbroflu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808192426/https://web.stanford.edu/~seastar/pdf/Hodin2000.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f9/1c/f91c01af6ec0e07afa141829f8cf0c8c5dd96c8d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/(sici)1097-010x(20000415)288:1&lt;1::aid-jez1&gt;3.0.co;2-7"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

Plasticity and constraints in development and evolution

Jason Hodin
<span title="2000-04-15">2000</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6jhel4ehgzafrcojwt6qwq6ocu" style="color: black;">Journal of Experimental Zoology</a> </i> &nbsp;
Parallelisms, on the other hand, may characterize developmental processes subject to constraints.  ...  The other main class of homoplasy, convergence, is superficial similarity in morphological structures in which the underlying ontogenetic mechanisms are distinct.  ...  Developmental constraints in practice So how can developmental constraints be positively identified?  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/(sici)1097-010x(20000415)288:1&lt;1::aid-jez1&gt;3.3.co;2-z">doi:10.1002/(sici)1097-010x(20000415)288:1&lt;1::aid-jez1&gt;3.3.co;2-z</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/10750048">pmid:10750048</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/t2lnyrumyjdh7mfuw6iotxt3hu">fatcat:t2lnyrumyjdh7mfuw6iotxt3hu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808192426/https://web.stanford.edu/~seastar/pdf/Hodin2000.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f9/1c/f91c01af6ec0e07afa141829f8cf0c8c5dd96c8d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/(sici)1097-010x(20000415)288:1&lt;1::aid-jez1&gt;3.3.co;2-z"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

Genome-wide transposon mutagenesis of paramyxoviruses reveals constraints on genomic plasticity: implications for vaccine and gene therapy [article]

Satoshi Ikegame, Shannon M Beaty, Christian Stevens, Taylor Sohiu Won, Arnold Park, David Sachs, Patrick Hong, Patricia Allison Thibault, Benhur Lee
<span title="2020-03-31">2020</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
disruptions; but the envelope glycoproteins were not, highlighting structural constraints that contribute to the restricted antigenic drift in paramyxoviruses.  ...  Nonetheless, when we applied our strategy to a fusion-defective Newcastle disease virus (Avulavirinae subfamily), we could select for F-revertants and other insertants in the 5' end of the genome.  ...  This is in contrast to the well-known propensity for antigenic drift of 48 influenza virus, another negative-sense RNA virus, in response to various pressures including host 49 populations' adaptive immune  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.03.30.016493">doi:10.1101/2020.03.30.016493</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/o4weh73tijhnhj3qj6trx3nzky">fatcat:o4weh73tijhnhj3qj6trx3nzky</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200711222202/https://www.biorxiv.org/content/biorxiv/early/2020/06/13/2020.03.30.016493.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/95/c0/95c0dd980f702be302c28b5cf748d0045e710557.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.03.30.016493"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Charting the Host Adaptation of Influenza Viruses

M. dos Reis, A. U. Tamuri, A. J. Hay, R. A. Goldstein
<span title="2010-11-25">2010</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4bimmtjdczetrfmnc3ijbmwpoy" style="color: black;">Molecular biology and evolution</a> </i> &nbsp;
The 2009 pandemic virus seems to have undergone preadaptation to human-like selective constraints during its period of circulation in swine.  ...  Understanding which changes have contributed to the adaptation of the virus to the human host is essential in assessing the pandemic potential of current and future animal viruses.  ...  Materials and Methods Host Adaptation Measure In addition to identifying locations in influenza proteins where there is a change in selective constraints following a host shift from birds to humans,  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/molbev/msq317">doi:10.1093/molbev/msq317</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21109586">pmid:21109586</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3098510/">pmcid:PMC3098510</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/o4527zcdi5awfjnrdksmp6thm4">fatcat:o4527zcdi5awfjnrdksmp6thm4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190429171307/https://qmro.qmul.ac.uk/xmlui/bitstream/handle/123456789/14886/Dos%20Reis%20Charting%20the%20host%20adaptation%202010%20Published.pdf;jsessionid=24DD064AA7BD5B812C0FE34C59CE1006?sequence=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/3a/29/3a2982f50dfaba9d60ee92b3ec70ab4489139b92.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/molbev/msq317"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3098510" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server

Luciano A. Abriata, Christophe Bovigny, Matteo Dal Peraro
<span title="2016-06-17">2016</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Remarkably, metabolic costs of the amino acids pose strong constraints to variability at protein surfaces in nature but not in the laboratory.  ...  hitherto unknown constraints to variation in alignments, and (iii) point at different sources of variation among related experimental datasets or between experimental and alignment-based data.  ...  might be compensated by changes in constraints at others.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-016-1124-4">doi:10.1186/s12859-016-1124-4</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27315797">pmid:27315797</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4912743/">pmcid:PMC4912743</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xmqgho77ybbbnili4n34zjeioi">fatcat:xmqgho77ybbbnili4n34zjeioi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190312120122/https://core.ac.uk/download/pdf/81594287.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/41/ef/41efc0028de2e6957a585df509dc3be4d76f0492.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-016-1124-4"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4912743" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Correlation of fitness landscapes from three orthologous TIM barrels originates from sequence and structure constraints

Yvonne H. Chan, Sergey V. Venev, Konstantin B. Zeldovich, C. Robert Matthews
<span title="2017-03-06">2017</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/a4wan6l5o5dfzn767kyz7jqevi" style="color: black;">Nature Communications</a> </i> &nbsp;
Limits on evolution imposed by constraints on sequence and structure were explored using a model TIM barrel protein, indole-3-glycerol phosphate synthase (IGPS).  ...  landscapes can be translocated in sequence space.  ...  constraints we observed hold true in the natural environment.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/ncomms14614">doi:10.1038/ncomms14614</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28262665">pmid:28262665</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5343507/">pmcid:PMC5343507</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jeymkk2ezjb2lnuemdzlgeda6q">fatcat:jeymkk2ezjb2lnuemdzlgeda6q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190304015753/http://pdfs.semanticscholar.org/beec/7d76f3aec932e3b8ec4b2c4ee38b5a2919eb.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/be/ec/beec7d76f3aec932e3b8ec4b2c4ee38b5a2919eb.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/ncomms14614"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> nature.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5343507" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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