tag:blogger.com,1999:blog-65923004896436626632024-02-07T07:38:24.560-06:00SymbionticismA blog about microbes and symbiosisAnonymoushttp://www.blogger.com/profile/15985401261412486690noreply@blogger.comBlogger140125tag:blogger.com,1999:blog-6592300489643662663.post-88639547063577400432018-12-21T14:12:00.001-06:002019-03-22T01:31:59.955-05:00Two Postdoc Positions AvailableTwo postdoctoral positions are offered to join the <a href="http://lab.vanderbilt.edu/bordenstein/" target="_blank">Bordenstein Lab</a> in the Departments of Biological Sciences and Pathology, Microbiology and Immunology at Vanderbilt University in Nashville, TN. The candidates will join one of two projects. <br />
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<li>(Closed) The first project seeks applicants with interests and/or skill sets in <b>personalized medicine and multi-omic analyses</b> (genome, metabolome, metagenome, and metallome) to investigate the consequences of diet, ethnicity, and genetic variation on the human microbiome (<a href="https://doi.org/10.1371/journal.pbio.2006842" target="_blank">recent paper</a>). The candidate will join and have the opportunity to take a leading role in the fast growing, trans-institutional <a href="https://my.vanderbilt.edu/microbiome/" target="_blank">Vanderbilt Microbiome Initiative</a>. Strong computational expertise (data analysis, coding, and bioinformatics) will be important in this position. </li>
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<li>(Closed) The second project seeks applicants with interests and skill sets in <b>animal-microbe interactions</b>, evolution, endosymbiosis, phylosymbiosis, quantitative genetics, transcriptomes, fluorescent microscopy, or gene knockdowns/knockouts. The candidate will in part join a National Science Foundation <a href="https://nsf.gov/awardsearch/showAward?AWD_ID=1456778&HistoricalAwards=false" target="_blank">project</a> to study the genetic basis of symbioses between insects (Nasonia parasitoid wasps) and endosymbiotic bacteria (Wolbachia). The candidate will also participate in launching a second project (<a href="http://science.sciencemag.org/content/341/6146/667" target="_blank">related paper</a>) on the genetic basis of phylosymbiosis (host phylogenetic signal in the gut microbiome) and speciation. </li>
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More information about the lab, topics, and systems can be found at the lab website: <a href="http://lab.vanderbilt.edu/bordenstein/" target="_blank">lab.vanderbilt.edu/bordenstein/</a><br />
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Additional information and resources for postdocs at Vanderbilt can be found at the Office of <a href="https://gradschool.vanderbilt.edu/postdoctoral/about.php" target="_blank">Postdoctoral Affairs</a> and <a href="https://medschool.vanderbilt.edu/postdoc/" target="_blank">Postdoctoral Resources</a> pages. <br />
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If interested, please contact <a href="mailto:s.bordenstein@vanderbilt.edu" target="_blank">Seth Bordenstein</a> immediately with a single pdf including (i) earliest start date (ii) a full curriculum vitae noting at least three references (iii) a statement of intent, career goal, research experience, and areas of growth and (iv) two example publications or other writings.<br />
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Vanderbilt University campus is a National Arboretum located in the heart of Nashville, the capital of Tennessee, and known internationally as “Music City USA”. Nashville is also the home to Nashville Hot Chicken, professional sports teams, the Nashville Symphony, the Frist Center for the Visual Arts, and numerous activities for outdoor enthusiasts. Nashville, Tennessee is a wonderful place to live, work, and raise a family.Anonymoushttp://www.blogger.com/profile/15985401261412486690noreply@blogger.com0tag:blogger.com,1999:blog-6592300489643662663.post-76977486045533048632018-12-13T21:33:00.002-06:002018-12-13T21:37:04.958-06:00New publication on the ethnicity hypothesis for gut microbiome variation <span aria-hidden="false"><span class="ember-view" id="ember1322">Our latest research published at <a href="https://doi.org/10.1371/journal.pbio.2006842" target="_blank">PLOS Biology</a> last week answers the question of whether self-declared ethnicity significantly associates with the diversity of microbes in human gut microbiomes, particularly from individuals residing in the same country. Importantly, results are replicated across two datasets within the United States of America, and we identify 12 microbial taxa that consistently vary in abundance between ethnicities. Machine learning approaches were able to predict ethnicity from the gut microbiome data alone. Many of the 12 taxa also associate with human genotype variation, and some have been linked to gut health disparities. While the work remains to be replicated in larger datasets, this one is a small step towards potentially adding the microbiome into more personalized health and medicine approaches. The work was led by senior graduate student <a href="https://twitter.com/ABrooksy19" target="_blank">Andy Brooks</a> and was conducted in collaboration with the <a href="http://blekhmanlab.org/" target="_blank">Blekhman lab</a> at the University of Minnesota. </span></span><br />
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News: <a href="https://news.vanderbilt.edu/2018/12/04/ethnicity-proves-reliable-indicator-of-what-microbes-thrive-in-the-gut/">https://news.vanderbilt.edu/2018/12/04/ethnicity-proves-reliable-indicator-of-what-microbes-thrive-in-the-gut/</a><br />
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<br />Anonymoushttp://www.blogger.com/profile/15985401261412486690noreply@blogger.com0tag:blogger.com,1999:blog-6592300489643662663.post-49539897956710238692018-05-08T15:58:00.001-05:002018-05-09T10:43:03.652-05:00The Vanderbilt Microbiome Initiative website<div style="text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEimij1OnzUYmhzCaSXueKMmqXp0laXY7jAZ3oHx8OMHQIpDKN09mZTvharUPu4lDp-3_6RowIiNJCAqDQq3y8BX6sgsvTuuBRsYlGBcQWl1XyXFbDvPv75AIogNEa6ywwD233IALLbng7k0/s1600/Microbiome+Wordmark_horizontal_black.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="103" data-original-width="509" height="64" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEimij1OnzUYmhzCaSXueKMmqXp0laXY7jAZ3oHx8OMHQIpDKN09mZTvharUPu4lDp-3_6RowIiNJCAqDQq3y8BX6sgsvTuuBRsYlGBcQWl1XyXFbDvPv75AIogNEa6ywwD233IALLbng7k0/s320/Microbiome+Wordmark_horizontal_black.png" width="320" /></a> </div>
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The<b> <a href="https://my.vanderbilt.edu/microbiome/" target="_blank">Vanderbilt Microbiome Initiative (VMI)</a></b>, sponsored by the <span class="mentions-texteditor__highlight" data-id="urn:li:school:19443" data-mentionworkflowid="jexDTzJITbu9jO8225iOBQ==">Vanderbilt University</span> Trans-Institutional Programs, is very pleased to announce the launch of its new website. VMI aims to unify the community within and beyond the region, support innovative research, and engage in outreach and science education. <br />
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As the science of the microbiome matures, Vanderbilt
will lead basic, translational, and clinical research, build new devices and technologies, help communicate the research, evaluate new
developments, fund new projects, and train the next generation
of scientists, philosophers, lawyers, and educators in this discipline.</div>
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Check in for recent research and education developments, resources, awards, etc. Join us there!</div>
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<a href="https://my.vanderbilt.edu/microbiome/">https://my.vanderbilt.edu/microbiome/</a></div>
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Anonymoushttp://www.blogger.com/profile/15985401261412486690noreply@blogger.com0tag:blogger.com,1999:blog-6592300489643662663.post-8114728688035643902018-04-25T21:36:00.005-05:002018-04-25T21:46:09.690-05:00New paper on the phage genes that hijack animal reproduction <i>Wolbachia </i>are maternally transmitted bacteria that are estimated to infect millions of arthropod species worldwide. One of <i>Wolbachia</i>'s greatest weapons is the ability to poison sperm and
nullify that poison in eggs, all of which enable the bacteria to spread
like wildfire in arthropods and to control mosquitoes. Indeed, the World Health Organization recently recommended pilot deployment of <i>Wolbachia</i>-infected mosquitoes to curb viral transmission to humans. Turns out that
under the hood of this cunning phenomena called cytoplasmic
incompatibility is a simple genetic basis: two phage genes poison the sperm
and one of those same genes ensures the infected eggs live. Ergo, the
'Two-by-One' model of cytoplasmic incompatibility by talented graduate student <a href="https://dylanshropshireblog.wordpress.com/" target="_blank">Dylan Shropshire</a>, former undergraduate and technician Danny On, and two current undergraduates Helen Zhou and <a href="https://twitter.com/emilymlayton" target="_blank">Emily Layton</a>. See below for a link to the paper, VU news story, and graphical summary. <br />
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Paper: <a href="http://www.pnas.org/content/early/2018/04/19/1800650115">http://www.pnas.org/content/early/20y18/04/19/1800650115</a><br />
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Vanderbilt Research: <a href="https://news.vanderbilt.edu/2018/04/23/unraveling-genetic-mystery-next-step-in-zika-and-dengue-fight/">https://news.vanderbilt.edu/2018/04/23/unraveling-genetic-mystery-next-step-in-zika-and-dengue-fight/</a><br />
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Graphical Summary:<br />
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<br />Anonymoushttp://www.blogger.com/profile/15985401261412486690noreply@blogger.com0tag:blogger.com,1999:blog-6592300489643662663.post-343080857452389792018-01-12T16:09:00.000-06:002018-03-04T12:06:32.411-06:00Postdoctoral position in functional genetics of animal-microbe symbioses<div style="text-align: left;">
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<span style="color: purple;"><span style="font-family: Arial, Helvetica, sans-serif;"><span style="font-size: large;"><i>(Note: Position is no longer available; applicants with independent funding are welcome)</i></span></span></span><br />
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<span style="font-size: large;">A postdoctoral position is available in the Bordenstein laboratory (<a href="http://bordensteinlab.vanderbilt.edu/">bordensteinlab.vanderbilt.edu</a>) to functionally characterize endosymbiont-host interactions in <i>Drosophila</i>. This project will dissect the <b>number and types of <i>Drosophila</i> genes and functional pathways that are manipulated by bacteria in the genus <i>Wolbachia</i></b>. The candidate will develop methods and apply multiple technologies to dissect how the bacteria modify fly embryonic development and induce lethality at the molecular, genetic, and/or biochemical levels. As <i>Wolbachia</i> are increasingly relevant to vector control efforts to curb arbovirus transmission, translational aspects of this work include development of transgenic strategies for vector and pest control.</span></div>
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<span style="font-size: large;">Applicants soon to acquire their Ph.D. or with previous postgraduate experience are welcome. Applicants should have a demonstrated ability to work both independently and collaboratively, possess excellent oral and written communication skills, and have a record of productivity as evidenced by publication history. <b>Successful candidates will have some of the following skills:<span class="Apple-converted-space"> </span></b>proteomics, transcriptomics, functional genetics, computational biology, <i>Drosophila</i> and <i>Wolbachia<span class="Apple-converted-space"> </span></i>rearing, fluorescent microscopy, molecular evolution, and molecular biology of phages. </span></div>
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<span style="font-size: large;">Vanderbilt University campus is a National Arboretum located in the heart of Nashville, the capital of Tennessee. Known internationally as Music City USA, Nashville is also the home to professional sports teams, the Nashville Symphony, the Frist Center for the Visual Arts, and numerous activities for outdoor enthusiasts. Nashville, Tennessee is a wonderful place to live, work, and raise a family and has been named one of the 15 best U.S. cities for work and family and one of the 25 cities most likely to have the country's highest job growth over the coming five years. Major industries include tourism, printing and publishing, technology manufacturing, music production, higher education, finance, insurance, automobile production and health care management.</span></div>
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<span style="font-size: large;"><b>To apply, please send a single pdf<span class="Apple-converted-space"> </span></b>including a cover letter stating career interests, research strengths, areas to develop, earliest start date, curriculum vitae, an example publication, and contact information for three or more references to s.bordenstein@vanderbilt.edu. </span><br />
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<span style="font-size: large;">The position is available now and renewable up to two years contingent upon satisfactory performance. Salary is commensurate with experience and includes a comprehensive benefits package. Review of applications will begin immediately and continue until the position is filled.</span></div>
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Anonymoushttp://www.blogger.com/profile/15985401261412486690noreply@blogger.com0tag:blogger.com,1999:blog-6592300489643662663.post-67168171170779292182017-08-23T22:18:00.000-05:002017-08-23T22:18:30.752-05:00Tenure-track job, Assistant Professor in Microbiome, Vanderbilt University, Nashville, TN, USA<div class="" style="-moz-text-size-adjust: auto; -webkit-text-stroke-width: 0px; color: black; font-family: Helvetica; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;">
<span style="font-size: small;">We are hiring a microbiome professor this year as part of Vanderbilt’s growing investment in the microbial sciences. If you know anyone on the market who cuts across basic and translational endeavors in the microbiome, please share this ad with them and beyond. It’s an awesome opportunity. </span></div>
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<span style="font-size: small;">Vanderbilt University is a private, internationally renowned research
university located in vibrant Nashville, Tennessee. Its 10 distinct
schools share a single cohesive campus that nurtures interdisciplinary
activities. With a metro population of approximately 1.5 million people, Nashville
has been named one of the 15 best U.S. cities for work and family and one of the 25 cities most likely to have the
country's highest job growth over the coming five years. Major
industries include tourism, printing and publishing, technology
manufacturing, music production, higher education, finance, insurance,
automobile production and health care management..</span></div>
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<span style="font-size: small;"><b><span style="font-family: Arial;">TENURE TRACK ASSISTANT PROFESSOR - MICROBIOME<br />
DEPARTMENT OF BIOLOGICAL SCIENCES, VANDERBILT UNIVERSITY</span><span style="font-family: Arial; text-transform: uppercase;"> </span></b></span></div>
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<span style="font-size: small;"><b><span style="font-family: Arial; text-transform: uppercase;">Vanderbilt Institute for Infection,
Immunology and Inflammation</span></b></span></div>
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<span style="font-size: small;"><span style="font-family: Arial;">Vanderbilt University’s Department of Biological Sciences
and the Vanderbilt Institute for Infection, Immunology and Inflammation invite
applications for a tenure-track, faculty position in host-microbiome
interactions at the Assistant Professor rank. </span><span style="font-family: Arial;">The
individual will be expected to develop her or his own independent laboratory
research program and contribute to</span><span style="font-family: Arial;"> departmental strengths in evolution, chemical biology,
neuroscience, and cell and molecular biology
(https://as.vanderbilt.edu/biosci/)</span><span style="font-family: Arial;">. </span><span style="font-family: Arial;">The faculty member will play an integral
role within the new trans-institutional Vanderbilt Microbiome Initiative and may
benefit from collaborations with internationally recognized programs including the
Vanderbilt Genetics Institute, the Vanderbilt Institute of Chemical Biology, or
the Vanderbilt Institute for Global Health. The selection criteria are
excellence in research and the ability to teach undergraduate and graduate
students with a high level of effectiveness. Applicants should submit a letter
of interest, full curriculum vitae, statement of current and future research interests,
and statement of teaching philosophy and competency directly to </span><a href="https://apply.interfolio.com/43974"><span style="font-family: Arial;">https://apply.interfolio.com/43974</span></a><span style="font-family: Arial;">.<span>
</span>Applicants will arrange for four letters of recommendation to be sent to
the same address. Completed applications must be received no later than October
27, 2017. Vanderbilt University has a strong institutional commitment to
recruiting and retaining an academically and culturally diverse community of
faculty. Minorities, women, individuals with disabilities, and members of other
underrepresented groups, in particular, are encouraged to apply. Vanderbilt is
an Equal Opportunity/ Affirmative Action employer. Vanderbilt University is </span><span style="color: #262626; font-family: Arial;">a National Arboretum located
in the heart of Nashville, TN</span><span style="font-family: Arial;"> and consistently ranks in the top 15 US Best Colleges. </span></span></div>
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</span>Anonymoushttp://www.blogger.com/profile/15985401261412486690noreply@blogger.com0tag:blogger.com,1999:blog-6592300489643662663.post-13756624027840861932017-03-23T18:14:00.000-05:002017-03-23T18:14:12.040-05:00Two recent papers from the lab focus on functions of host-associated microbiomes and endosymbionts: Just sharing the lab's two recent papers that examine how microbial communities and specific bacterial endosmbionts (<i>Wolbachia</i>) function in their hosts. <br />
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1. Prophage WO genes recapitulate and enhance <em>Wolbachia</em>-induced cytoplasmic incompatibility. <a href="http://www.nature.com/nature/journal/vaop/ncurrent/full/nature21391.html" target="_new">Nature</a>. Lepage, D.*, J.A. Metcalf*, S.R. Bordenstein, J. On, J. Perlmutter, J.D. Shropshire, E. Layton, J. Beckmann, and S.R. Bordenstein (*Co-first authors) Select coverage:
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<ul>
<li><a href="https://news.vanderbilt.edu/2017/02/27/new-tool-for-combating-mosquito-borne-disease-insect-parasite-genes/" target="_new">Vanderbilt Research News</a> 2/27/17</li>
<li><a href="http://www.nature.com/nature/journal/vaop/ncurrent/full/nature21509.html?WT.feed_name=subjects_genetics" target="_new">Nature News and Views</a> 2/27/17</li>
<li><a href="http://www.the-scientist.com/?articles.view/articleNo/48647/title/How-Bacteria-Interfere-with-Insect-Reproduction/" target="_new">The Scientist</a> 2/28/17</li>
</ul>
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Major point: Two genes, <i>cifA</i> and <i>cifB</i>, in the eukaryotic association module of prophage WO (<a href="http://www.nature.com/articles/ncomms13155" target="_blank">related paper</a> from the lab) enable <i>Wolbachia </i>to cause cytoplasmic incompatibility</div>
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Description: The genus <i>Wolbachia</i> is an archetype of maternally inherited
intracellular bacteria that infect the germline of numerous invertebrate
species worldwide. They can selfishly alter arthropod sex ratios and
reproductive strategies to increase the proportion of the infected
matriline in the population. The most common reproductive manipulation
is cytoplasmic incompatibility, which results in embryonic lethality in
crosses between infected males and uninfected females. Females infected
with the same <i>Wolbachia</i> strain rescue this lethality. Despite more than 40 years of research and relevance to symbiont-induced speciation, as well as control of arbovirus vectors and agricultural pests,
the bacterial genes underlying cytoplasmic incompatibility remain
unknown. Here we use comparative and transgenic approaches to
demonstrate that two differentially transcribed, co-diverging genes in
the eukaryotic association module of prophage WO from <i>Wolbachia</i> strain <i>w</i>Mel recapitulate and enhance cytoplasmic incompatibility. Dual expression in transgenic, uninfected males of <i>Drosophila melanogaster</i>
crossed to uninfected females causes embryonic lethality. Each gene
additively augments embryonic lethality in crosses between infected
males and uninfected females. Lethality associates with embryonic
defects that parallel those of wild-type cytoplasmic incompatibility and
is notably rescued by <i>w</i>Mel-infected embryos in all cases. The discovery of cytoplasmic incompatibility factor genes <i>cifA</i> and <i>cifB</i> pioneers genetic studies of prophage WO-induced reproductive manipulations and informs the continuing use of <i>Wolbachia</i> to control dengue and Zika virus transmission to humans.</div>
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<span class="title style12">2. </span>Phylosymbiosis: Relationships and functional effects of microbial communities across host evolutionary history <em></em><a href="http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2000225&utm_content=bufferf704d&utm_medium=social&utm_source=twitter.com&utm_campaign=buffer" target="_new">PLOS Biology</a> (open access) By Brooks AW*,
Kohl KD*,
Brucker RM*,
van Opstal EJ,
Bordenstein SR
(Co-first authors)
Select coverage:</div>
<ul>
<li><a href="http://collections.plos.org/open-highlights-holobiont" target="_new">PLOS Biology Open Highlight:</a> Evolving as a Holobiont</li>
<li><a href="http://www.the-scientist.com/?articles.view/articleNo/47619/title/Animal-Microbiomes-Are-Unique-and-Beneficial/" target="_new">The Scientist</a></li>
</ul>
Major point: Host-associated microbial communities can be specific and beneficial to their hosts, even among closely-related host species.<br />
<br />
Description: Studies on the assembly and function of host-microbiota symbioses are
inherently complicated by the diverse effects of diet, age, sex, host
genetics, and endosymbionts. Central to unraveling one effect from the
other is an experimental framework that reduces confounders. Using
common rearing conditions across four animal groups (deer mice, flies,
mosquitoes, and wasps) that span recent host speciation events to more
distantly related host genera, this study tests whether microbial
community assembly is generally random with respect to host relatedness
or "phylosymbiotic," in which the phylogeny of the host group is
congruent with ecological relationships of their microbial communities.
Across all four animal groups and one external dataset of great apes, we
demonstrate
phylosymbiosis to varying degrees in each group. Moreover, consistent
with selection on host–microbiota or holobiont interactions driving phylosymbiosis,
transplanting interspecific microbial communities in mice significantly
decreased their ability to digest food. Similarly, wasps that received
transplants of microbial communities from different wasp species had
lower survival than those given their own microbiota. Overall, this
experimental and statistical framework shows how microbial community
assembly and functionality across related species can be linked to
animal evolution, health, and survival. Anonymoushttp://www.blogger.com/profile/15985401261412486690noreply@blogger.com0tag:blogger.com,1999:blog-6592300489643662663.post-50905583960417780762017-01-24T19:33:00.004-06:002017-01-24T19:34:30.760-06:00The Most Important Blog Post - Scientist March on WashingtonEverybody has a reason to march. This is the most important post of this blog. Tune in. <br />
<br />
Source: <a href="http://www.scientistsmarchonwashington.com/">http://www.scientistsmarchonwashington.com/</a><br />
<br />
<h3 class="post-title entry-title" itemprop="name">
<a href="http://www.scientistsmarchonwashington.com/2017/01/what-is-scientists-march-on-washington.html">What is the Scientists' March on Washington</a>
</h3>
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<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="color: black; font-family: "arial"; font-size: 14.6667px; font-weight: 700; vertical-align: baseline; white-space: pre-wrap;">UPDATE: 4:00 1-24-16 : Since 10am today, over 50 people have volunteered to help make this event a reality! We're going to get back to everyone and try to make sure that everyone's time is put to the best use possible. A single google hangout looks unfeasible if volunteers keep coming in at this rate until Saturday, so we're working ways to break into working groups. Stay tuned!</span><br />
<span style="color: black; font-family: "arial"; font-size: 14.6667px; font-weight: 700; vertical-align: baseline; white-space: pre-wrap;"><br /></span>
<span style="color: black; font-family: "arial"; font-size: 14.6667px; font-weight: 700; vertical-align: baseline; white-space: pre-wrap;">Twitter: <a href="https://twitter.com/ScienceMarchDC" target="_blank">@ScienceMarchDC</a></span><br />
<span style="color: black; font-family: "arial"; font-size: 14.6667px; font-weight: 700; vertical-align: baseline; white-space: pre-wrap;">Facebook: <a href="https://www.facebook.com/groups/1862739727343189/">https://www.facebook.com/groups/1862739727343189/</a></span><br />
<span style="color: black; font-family: "arial"; font-size: 14.6667px; font-weight: 700; vertical-align: baseline; white-space: pre-wrap;">Reddit: /r/scientistsmarch</span><br />
<span style="color: black; font-family: "arial"; font-size: 14.6667px; font-weight: 700; vertical-align: baseline; white-space: pre-wrap;">Get <a href="http://eepurl.com/cyUV7T">Email Updates</a></span><br />
<span style="color: black; font-family: "arial"; font-size: 14.6667px; font-weight: 700; vertical-align: baseline; white-space: pre-wrap;">To help: <a href="https://goo.gl/forms/zAdY02dBEz3Ykii42">https://goo.gl/forms/zAdY02dBEz3Ykii42</a></span><br />
<span style="font-family: "arial";"><span style="font-size: 14.6667px; white-space: pre-wrap;"><b>Contact: <a href="mailto:scientistsmarchonwashington@gmail.com">scientistsmarchonwashington@gmail.com</a></b></span></span><br />
<span style="color: black; font-family: "arial"; font-size: 14.6667px; font-weight: 700; vertical-align: baseline; white-space: pre-wrap;"><br /></span>
<span style="color: black; font-family: "arial"; font-size: 14.6667px; font-weight: 700; vertical-align: baseline; white-space: pre-wrap;">We accept the following as provisionally true:</span></div>
<span id="docs-internal-guid-34ef2ecc-c319-1ffe-cc14-6ef367daef15" style="font-weight: normal;"><br /></span>
<br />
<ul style="margin-bottom: 0pt; margin-top: 0pt;">
<li dir="ltr" style="font-family: arial; font-size: 14.6667px; list-style-type: disc; vertical-align: baseline;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="color: black; font-family: "arial"; font-size: 14.6667px; vertical-align: baseline; white-space: pre-wrap;">The Earth is becoming warmer due to human action. </span></div>
</li>
<li dir="ltr" style="font-family: arial; font-size: 14.6667px; list-style-type: disc; vertical-align: baseline;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="color: black; font-family: "arial"; font-size: 14.6667px; vertical-align: baseline; white-space: pre-wrap;">The diversity of life arose by evolution.</span></div>
</li>
<li dir="ltr" style="font-family: arial; font-size: 14.6667px; list-style-type: disc; vertical-align: baseline;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="color: black; font-family: "arial"; font-size: 14.6667px; vertical-align: baseline; white-space: pre-wrap;">An American government that ignores science to pursue ideological agendas threatens not only the environment of which humans are a part, but America itself.</span></div>
</li>
<li dir="ltr" style="font-family: arial; font-size: 14.6667px; list-style-type: disc; vertical-align: baseline;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="color: black; font-family: "arial"; font-size: 14.6667px; vertical-align: baseline; white-space: pre-wrap;">Scientific research in the United States is underfunded.</span></div>
</li>
<li dir="ltr" style="font-family: arial; font-size: 14.6667px; list-style-type: disc; vertical-align: baseline;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="color: black; font-family: "arial"; font-size: 14.6667px; vertical-align: baseline; white-space: pre-wrap;">Politicians who devalue expertise risk making decisions that do not reflect reality.</span></div>
</li>
</ul>
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<span style="color: black; font-family: "arial"; font-size: 14.6667px; font-weight: 700; vertical-align: baseline; white-space: pre-wrap;">Who can participate:</span></div>
<span style="font-weight: normal;"><br /></span>
<br />
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="color: black; font-family: "arial"; font-size: 14.6667px; vertical-align: baseline; white-space: pre-wrap;"><span class="Apple-tab-span" style="white-space: pre;"> </span></span><span style="color: black; font-family: "arial"; font-size: 14.6667px; vertical-align: baseline; white-space: pre-wrap;">Science is a methodology and a way of thinking. Anyone who uses and values these tools for understanding the world, not just professional scientists, may participate. </span></div>
<span style="font-weight: normal;"><br /></span>
<br />
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="color: black; font-family: "arial"; font-size: 14.6667px; font-weight: 700; vertical-align: baseline; white-space: pre-wrap;">How can I help?</span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="color: black; font-family: "arial"; font-size: 14.6667px; vertical-align: baseline; white-space: pre-wrap;"><span class="Apple-tab-span" style="white-space: pre;"> </span></span><span style="color: black; font-family: "arial"; font-size: 14.6667px; vertical-align: baseline; white-space: pre-wrap;">We are still in the very early stages of organizing this event. We need all the help we can get, especially from people with expertise in the following areas:</span></div>
<span style="font-weight: normal;"><br /></span>
<br />
<ul style="margin-bottom: 0pt; margin-top: 0pt;">
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<span style="color: black; font-family: "arial"; font-size: 14.6667px; vertical-align: baseline; white-space: pre-wrap;">Web Design</span></div>
</li>
<li dir="ltr" style="font-family: arial; font-size: 14.6667px; list-style-type: disc; vertical-align: baseline;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="color: black; font-family: "arial"; font-size: 14.6667px; vertical-align: baseline; white-space: pre-wrap;">Logo/Graphic design</span></div>
</li>
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<span style="color: black; font-family: "arial"; font-size: 14.6667px; vertical-align: baseline; white-space: pre-wrap;">Law, incorporation of a not-for-profit</span></div>
</li>
<li dir="ltr" style="font-family: arial; font-size: 14.6667px; list-style-type: disc; vertical-align: baseline;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="color: black; font-family: "arial"; font-size: 14.6667px; vertical-align: baseline; white-space: pre-wrap;">Fundraising</span></div>
</li>
<li dir="ltr" style="font-family: arial; font-size: 14.6667px; list-style-type: disc; vertical-align: baseline;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="color: black; font-family: "arial"; font-size: 14.6667px; vertical-align: baseline; white-space: pre-wrap;">Public relations and media relations</span></div>
</li>
<li dir="ltr" style="font-family: arial; font-size: 14.6667px; list-style-type: disc; vertical-align: baseline;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="color: black; font-family: "arial"; font-size: 14.6667px; vertical-align: baseline; white-space: pre-wrap;">Social media management</span></div>
</li>
<li dir="ltr" style="font-family: arial; font-size: 14.6667px; list-style-type: disc; vertical-align: baseline;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="color: black; font-family: "arial"; font-size: 14.6667px; vertical-align: baseline; white-space: pre-wrap;">Organizing large events</span></div>
</li>
<li dir="ltr" style="font-family: arial; font-size: 14.6667px; list-style-type: disc; vertical-align: baseline;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="color: black; font-family: "arial"; font-size: 14.6667px; vertical-align: baseline; white-space: pre-wrap;">Acquiring permits in DC</span></div>
</li>
<li dir="ltr" style="font-family: arial; font-size: 14.6667px; list-style-type: disc; vertical-align: baseline;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="color: black; font-family: "arial"; font-size: 14.6667px; vertical-align: baseline; white-space: pre-wrap;">Contacts with possible speakers</span></div>
</li>
</ul>
<span style="font-weight: normal;"><br /></span>
<br />
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="color: black; font-family: "arial"; font-size: 14.6667px; vertical-align: baseline; white-space: pre-wrap;">You don’t need to be a professional scientist to participate. Just fill out this google form: https://goo.gl/forms/zAdY02dBEz3Ykii42</span><span style="color: black; font-family: "arial"; font-size: 14.6667px; vertical-align: baseline; white-space: pre-wrap;"> and please let us know how you can help. </span></div>
<span style="font-weight: normal;"><br /></span>
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<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="color: black; font-family: "arial"; font-size: 14.6667px; font-weight: 700; vertical-align: baseline; white-space: pre-wrap;">How can I donate?</span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="color: black; font-family: "arial"; font-size: 14.6667px; vertical-align: baseline; white-space: pre-wrap;"><span class="Apple-tab-span" style="white-space: pre;"> </span></span><span style="color: black; font-family: "arial"; font-size: 14.6667px; vertical-align: baseline; white-space: pre-wrap;">You can’t yet. We’re working on figuring out a legal framework that will allow you to donate.</span></div>
<span style="font-weight: normal;"><br /></span>
<br />
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="color: black; font-family: "arial"; font-size: 14.6667px; font-weight: 700; vertical-align: baseline; white-space: pre-wrap;">When will it be?</span></div>
<span style="font-weight: normal;"><br /></span>
<br />
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-indent: 36pt;">
<span style="color: black; font-family: "arial"; font-size: 14.6667px; vertical-align: baseline; white-space: pre-wrap;">We’re still in the very earliest stages. The date will be announced as soon as it is available. </span></div>
<span style="font-weight: normal;"><br /></span>
<br />
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="color: black; font-family: "arial"; font-size: 14.6667px; font-weight: 700; vertical-align: baseline; white-space: pre-wrap;">Isn’t science apolitical?</span></div>
<br />
<span style="color: black; font-family: "arial"; font-size: 14.6667px; vertical-align: baseline; white-space: pre-wrap;"> Yes. Scientists, however are not. The march is non-partisan, however it is intended to have </span><br />
<span style="color: black; font-family: "arial"; font-size: 14.6667px; vertical-align: baseline; white-space: pre-wrap;"> an impact on policy makers</span>Anonymoushttp://www.blogger.com/profile/15985401261412486690noreply@blogger.com0tag:blogger.com,1999:blog-6592300489643662663.post-71748674784649107862016-10-31T12:02:00.000-05:002016-10-31T12:02:56.491-05:00Guest Blog Post on Holobiont Theory by Jonathan Klassen and Sarah Kopac
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Recently, <a href="https://twitter.com/SarahMicrobio" target="_blank">Sarah Kopac</a> and <a href="http://jonathanklassenlab.com/" target="_blank">Jonathan Klassen</a> described a new
model to understand the evolution of host-microbe symbioses in their paper “<a href="http://journal.frontiersin.org/article/10.3389/fmicb.2016.01647/full" target="_blank">Can They Make It on Their Own? Hosts, Microbes, and the Holobiont Niche</a>”.
In this model, hosts and microbes can change the shape of their respective
niches, and thereby the context in which selection can act. This permits a test of holobiont theory by identifying instances where an organism’s
phenotype depends on its symbiotic partners. Jonathan answered the following
questions, incorporating feedback from Sarah. Be sure to read all the way through.</div>
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<img alt="SMK" class="ProfileAvatar-image " height="200" src="https://pbs.twimg.com/profile_images/713076631259058176/Fxj06Pgj_400x400.jpg" width="200" /> <img alt="Jonathan Klassen" class="ProfileAvatar-image " height="200" src="https://pbs.twimg.com/profile_images/3646045844/592d1e7e3213d41bfa24aa3e75c27aa7_400x400.jpeg" width="200" /> </div>
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<span style="font-size: large;"><b><span>1.<span style="font-family: "Times New Roman"; font-feature-settings: normal; font-kerning: auto; font-language-override: normal; font-size-adjust: none; font-stretch: normal; font-style: normal; font-synthesis: weight style; font-variant: normal; font-weight: normal; line-height: normal;"> </span></span></b><b>What motivated the theory reported in
the paper? </b></span></div>
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<a href="https://www.blogger.com/null" name="_gjdgxs"></a>It feels a bit murky now, but looking
back I think there were three main motivations. First, we were quite struck by
how host-microbe relationships can be thought of as a community ecology
problem, i.e., where and how do interspecific relationships form and what is
their outcome? So because much of the holobiont/hologenome literature has
started from a population-genetics perspective (e.g., <a href="http://journal.frontiersin.org/article/10.3389/fmicb.2014.00046/full"><span style="color: #0563c1;">http://journal.frontiersin.org/article/10.3389/fmicb.2014.00046/full</span></a>),
we thought that drawing from a different intellectual tradition might be a way
to get beyond current sticking points in the field's discussion. Another interesting aspect of the community ecology
perspective is that it defines the context in which selection <b style="mso-bidi-font-weight: normal;">might</b> act, leaving whether or not
selection <b style="mso-bidi-font-weight: normal;">does</b> act as a separate
question. I think that it is too common to assume selection without rigorously
testing against alternative hypotheses, e.g., drift or dispersal limitation, to
our detriment. Second, we wanted to strongly highlight how any selection that
did occur likely impacted hosts and microbes differently, e.g., because
microbes have shorter lifespans and higher population sizes and dispersal rates
than their hosts (<a href="http://doi.wiley.com/10.1002/bies.201500074"><span style="color: #0563c1;">http://doi.wiley.com/10.1002/bies.201500074</span></a>).
Third, one major take-away from my years of reading the lovely Dynamic Ecology
blog (<a href="https://dynamicecology.wordpress.com/"><span style="color: #0563c1;">https://dynamicecology.wordpress.com/</span></a>)
is that mathematical models have a rigor and testability that verbal models
cannot match, and thereby overcome the potential for verbal models to become
misconstrued. Expressing our ideas mathematically so that they would be
unambiguously testable therefore became an important goal.</div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormalCxSpMiddle" style="margin-left: 0.5in; text-indent: -0.25in;">
<span style="font-size: large;"><b><span>2.<span style="font-family: "Times New Roman"; font-feature-settings: normal; font-kerning: auto; font-language-override: normal; font-size-adjust: none; font-stretch: normal; font-style: normal; font-synthesis: weight style; font-variant: normal; font-weight: normal; line-height: normal;"> </span></span></b><b>How did you come up with the title?</b></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
Truthfully, this was a revision suggested by one of the
reviewers. (And they were right - thanks!) Sarah came up with this version, and
I think it’s great because it really captures the key question of our model: do
host-microbe interactions matter for the evolution of either partner? I think
the answer is that it depends on the context, i.e., does the interaction change
the shape of either partner’s niche in a way that changes how selection might
act? I also love how (in my mind at least) there’s a U2 reference - <a href="https://www.youtube.com/watch?v=CuDqHtAR6L8"><span style="color: #0563c1;">https://www.youtube.com/watch?v=CuDqHtAR6L8</span></a>.
I’ve long been a fan. </div>
<div class="MsoNormal">
<br /></div>
<span style="font-size: large;">
</span><div class="MsoNormalCxSpMiddle" style="margin-left: 0.5in; text-indent: -0.25in;">
<span style="font-size: large;"><b><span>3.<span style="font-family: "Times New Roman"; font-feature-settings: normal; font-kerning: auto; font-language-override: normal; font-size-adjust: none; font-stretch: normal; font-style: normal; font-synthesis: weight style; font-variant: normal; font-weight: normal; line-height: normal;"> </span></span></b><b>When and how did you two come together and
agree on this paper? Were there varied opinions about how to approach the
problem?</b></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
We agreed on the central idea of explaining holobionts in
terms of niche theory early on, and so were unified on that front. There was a
bit of divide and conquer after that, with Sarah focusing more on the examples
of different niche shifts and I focusing more on the models themselves. <span style="mso-fareast-font-family: Arial;">Then we came back together and made sure that
the examples we saw in the literature could be explained using our models.</span>
I found it very helpful to get someone else’s view of the literature –
accurately synthesizing everything that’s out there alone would have been a
massive challenge. </div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormalCxSpMiddle" style="margin-left: 0.5in; text-indent: -0.25in;">
<span style="font-size: large;"><span>4.<span style="font-family: "Times New Roman"; font-feature-settings: normal; font-kerning: auto; font-language-override: normal; font-size-adjust: none; font-stretch: normal; font-style: normal; font-synthesis: weight style; font-variant: normal; font-weight: normal; line-height: normal;">
</span></span><b>What are the
most salient findings?</b></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
I think that it is striking how our models are agnostic
towards any particular mechanism of host-microbe interaction. For example, a
similar shift in a host’s niche could be result from that host selecting
microbes with a particular trait from the environment each generation, or it
could be due to tight host-microbe co-evolution and vertical transmission. The
important thing is that in either case the interaction changes the shape of a
host’s niche in a way that selection might act upon. Both partners are
therefore needed to completely describe host evolution. I am also struck by how
our models accommodate the full diversity of symbiotic relationships, including
the various forms of conflict that change the shape of a host’s niche but in a
different way than mutualism. Finally, it seems that the symbiosis community
has already been at least implicitly thinking in terms of our model because it
was easy to find studies that had already tested it by changing one parameter
at a time, e.g., by swapping microbiomes between constant host genotypes and
vice versa. Hopefully our work can guide future experiments that continue to
explicitly test these ideas.</div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormalCxSpMiddle" style="margin-left: 0.5in; text-indent: -0.25in;">
<span style="font-size: large;"><span>5.<span style="font-family: "Times New Roman"; font-feature-settings: normal; font-kerning: auto; font-language-override: normal; font-size-adjust: none; font-stretch: normal; font-style: normal; font-synthesis: weight style; font-variant: normal; font-weight: normal; line-height: normal;">
</span></span><b>What are the
most crucial questions moving forward in your mind? What do you want
to do next? </b></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
Perhaps one problem with our model is that precisely
defining the shape of an organism’s niche is fiendishly difficult, mostly
because there are a potentially infinite number of niche axes to consider. I
think it will be interesting to understand how many of these are actually
needed to come up with an accurate niche description. For example, to what
extent to do microbe-microbe interactions need to be considered to describe how
microbes alter a host’s niche? I also think it will be critical to learn more
about microbes in non-host environments so that we can determine if hosts
modify the niches of their microbial symbionts outside of obvious cases like
intracellular mutualists and pathogens. Lastly and as described above, I think
it will be crucial to explicitly test whether any host-microbe interaction
phenotype actually arises due to selection, e.g., vs drift or dispersal
limitation. </div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormalCxSpMiddle" style="margin-left: 0.5in; text-indent: -0.25in;">
<span style="font-size: large;"><span>6.<span style="font-family: "Times New Roman"; font-feature-settings: normal; font-kerning: auto; font-language-override: normal; font-size-adjust: none; font-stretch: normal; font-style: normal; font-synthesis: weight style; font-variant: normal; font-weight: normal; line-height: normal;">
</span></span><b>Anything else
you want to add?</b></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
Thanks to our colleagues in the symbiosis field for being so
collegial, even in disagreement! I look forward to increasing the rigor of our
studies, and to a deeper understanding of how ecology and evolution both shape
host-microbe relationships.</div>
<div class="MsoNormal">
<br /></div>
Anonymoushttp://www.blogger.com/profile/15985401261412486690noreply@blogger.com0tag:blogger.com,1999:blog-6592300489643662663.post-17202849136101592016-10-19T21:29:00.000-05:002016-10-20T15:36:25.212-05:00My Talk and Interview on Microbes and Speciation from Germany I returned last month from Kiel University for the <a href="http://www.dzg-meeting.de/">109th German Zoological Society Meeting</a>. A Zoological Society Meeting alone is impressive these days, not to mention its 109 year history. <a href="http://www.bosch.zoologie.uni-kiel.de/">Thomas Bosch</a> invited me out for the keynote lecture. Thomas has been at the forefront of advancing a better appreciation of the natural world, namely the intricate interactions between a simple model system of the non-senescent cnidarian Hydra and its microbial community. Hydra represent an early key transition in the evolution of animals and therefore are critical to studying the origins of developmental mechanisms. Thomas is a <a href="https://www.cifar.ca/profiles/thomas-bosch/">CIFAR fellow</a> and directs the <a href="http://www.metaorganism-research.com/">Metaorganisms Collaborative Research Center</a>, which is a beacon for systems biology thinking about the animal-microbiome assemblage. <br />
<div>
<br /></div>
<div>
Anyway, I presented our long-term studies on the role of bacteria in reproductive isolation and the origin of species. I presented old and new work, most recently by <a href="https://twitter.com/ABrooksy19">@ABrooksy19</a>, <a href="https://twitter.com/KevinDKohl">@KevinDKohl</a>, <a href="https://twitter.com/liveinsymbiosis">@liveinsymbiosis</a> and <a href="https://twitter.com/teddy1387">@teddy1387</a> on phylosymbiosis across various animals. This work is currently in press. Here's the <a href="https://www.youtube.com/watch?v=pXAjxScxLU4">talk</a> and <a href="https://www.youtube.com/watch?v=C0ItCG3hTs0">interview</a> that the Collaborative Research Center clearly put a lot of work into - many thanks to the team. <br />
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Anonymoushttp://www.blogger.com/profile/15985401261412486690noreply@blogger.com0tag:blogger.com,1999:blog-6592300489643662663.post-36383620261985116882016-10-15T10:05:00.000-05:002016-10-18T08:58:30.156-05:00Phage WO: Guest Blog Post by Sarah Bordenstein<style>
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The latest craze over phage WO, the bacterial virus that
infects <i style="mso-bidi-font-style: normal;">Wolbachia</i>, has been both
exciting and overwhelming. The press is great at communicating the science in a digestible
format, but it can sometimes become sensationalized and misleading. When one
press release builds upon the hype of a previous release, the end result is
much like the game of telephone. As an author of “<a href="http://www.nature.com/articles/ncomms13155">Eukaryotic association module in phage
WO genomes from </a><i style="mso-bidi-font-style: normal;"><a href="http://www.nature.com/articles/ncomms13155">Wolbachia</a></i>”, I want to
make sure that the science in the public's eye is not over-represented and that we are providing a
realistic view of the data.
</div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
Let’s first talk about what the paper <i style="mso-bidi-font-style: normal;">is not</i>, though headlines have claimed otherwise. </div>
<div class="MsoListParagraphCxSpFirst" style="mso-list: l0 level1 lfo1; text-indent: -.25in;">
<span style="font-family: "symbol"; mso-bidi-font-family: Symbol; mso-fareast-font-family: Symbol;"><span style="mso-list: Ignore;">·<span style="font: 7.0pt "Times New Roman";">
</span></span></span><b style="mso-bidi-font-weight: normal;">Phage WO
does not encode the entire black widow venom (latrotoxin) gene.</b> In fact, as
we present in the paper, it contains DNA that is similar to just the C-terminal
domain. This particular region of the gene is associated with the protoxin that
is hypothesized to be involved in lysis of the spider’s secretion cells. </div>
<div class="MsoListParagraphCxSpLast" style="mso-list: l0 level1 lfo1; text-indent: -.25in;">
<span style="font-family: "symbol"; mso-bidi-font-family: Symbol; mso-fareast-font-family: Symbol;"><span style="mso-list: Ignore;">·<span style="font: 7.0pt "Times New Roman";">
</span></span></span><b style="mso-bidi-font-weight: normal;">The phage
did not necessarily “steal” the DNA from the spider.</b> Yes, viruses hijack
DNA from their hosts and this has been shown in both bacterial viruses and
animal viruses. Viruses are incredible, rapidly evolving entities. Due to the
level of divergence between the sequences in this particular study, the genetic
transfer, if it did happen, occurred long, long ago. We can’t definitively say
if the spider transferred to phage or phage to spider, but in our opinion both
would be equally exciting. The current data leans towards spider to virus,
possibly via a yet-to-be-discovered intermediary (see the paper for more
discussion). We also can’t definitively say that it was even a legitimate transfer
event. It could have been the result of convergent evolution. This is when
different organisms independently evolve similar traits. Given the fact that
widow spiders are often infected with <i style="mso-bidi-font-style: normal;">Wolbachia</i>,
and <i style="mso-bidi-font-style: normal;">Wolbachia</i> are often infected with
phage WO, there is an ecological niche that would provide opportunity for
genetic transfer. Plus, we present other examples in the paper that support genetic
transfer from animal to virus. Beyond that, many other research groups have
reported the transfer of DNA between <i style="mso-bidi-font-style: normal;">Wolbachia</i>
and their animal hosts, so the transfer between the phages and the animal is
not a huge stretch. </div>
<div class="MsoNormal">
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With that said, this is what the paper <i style="mso-bidi-font-style: normal;">is</i>:</div>
<div class="MsoListParagraphCxSpFirst" style="mso-list: l0 level1 lfo1; text-indent: -.25in;">
<span style="font-family: "symbol"; mso-bidi-font-family: Symbol; mso-fareast-font-family: Symbol;"><span style="mso-list: Ignore;">·<span style="font: 7.0pt "Times New Roman";">
</span></span></span>To our knowledge, <b style="mso-bidi-font-weight: normal;">this is the first report of animal-like DNA found in a bacterial virus</b>.
Is this a completely absurd, mind-blowing discovery? Not really. Bacterial
viruses are known to exchange DNA with their bacterial hosts and animal viruses
with animals. However, we don’t really know much about how viruses of bacteria
might interact with animals. This field is really in its infancy.</div>
<div class="MsoListParagraphCxSpMiddle" style="mso-list: l0 level1 lfo1; text-indent: -.25in;">
<span style="font-family: "symbol"; mso-bidi-font-family: Symbol; mso-fareast-font-family: Symbol;"><span style="mso-list: Ignore;">·<span style="font: 7.0pt "Times New Roman";">
</span></span></span><b style="mso-bidi-font-weight: normal;">Phage WO
harbors a eukaryotic association module. </b>About half of WO’s genome is
devoted to structural genes (such as capsid, tail, baseplate) and other common
phage elements. However, it also devotes a large percentage of its genome to
unique genes that putatively encode functions relevant to animal interaction. Like
some other viruses, phage WO appears to take different chunks of DNA from
different sources and mix and match the chunks to create unique genes. What do
these genes do? Do they retain the same functions as they did in the original
donor? These are all still mysteries to be solved; so many questions left to be
answered! I can tell you that some of the genes in the eukaryotic association
module quickly grabbed our attention and we look forward to expanding the story
of phage WO and <i style="mso-bidi-font-style: normal;">Wolbachia</i> in the
months to come. Stay tuned…</div>
<div class="MsoListParagraphCxSpMiddle" style="mso-list: l0 level1 lfo1; text-indent: -.25in;">
<span style="font-family: "symbol"; mso-bidi-font-family: Symbol; mso-fareast-font-family: Symbol;"><span style="mso-list: Ignore;">·<span style="font: 7.0pt "Times New Roman";">
</span></span></span><b style="mso-bidi-font-weight: normal;">Phage WO
integrates into the <i style="mso-bidi-font-style: normal;">Wolbachia</i> genome
via specific attachment (<i style="mso-bidi-font-style: normal;">att</i>) sites.</b>
Why does this matter? <i style="mso-bidi-font-style: normal;">Wolbachia</i> is an
obligate intracellular endosymbiont. That means, it is dependent on its animal
host for survival and cannot be cultured outside of the animal cell (as you
would with standard free-living microbes such as <i style="mso-bidi-font-style: normal;">E. coli</i>). This makes it very hard for scientists to test functions
of specific genes and fully understand its biology. We are particularly
interested in <i style="mso-bidi-font-style: normal;">Wolbachia</i> because it
infects over 40% of all arthropods as well as some nematodes of human health
relevance and crustaceans. The identification of WO’s <i style="mso-bidi-font-style: normal;">att</i> sites offers a potential method of accessing the <i style="mso-bidi-font-style: normal;">Wolbachia</i> chromosome in order to unlock
its secrets. Using the phage may or may not work, but it’s the best chance we
have to-date.<span style="mso-spacerun: yes;"> </span></div>
<div class="MsoListParagraphCxSpLast">
<span style="mso-spacerun: yes;"> </span></div>
<div class="MsoNormal">
On a personal note, I want to thank journalists such as Ed
Yong (The Atlantic - <a href="http://www.theatlantic.com/science/archive/2016/10/the-virus-with-spider-dna/503585/">link</a>) and Jacqueline Howard (CNN - <a href="http://www.cnn.com/2016/10/18/health/virus-black-widow-spider/index.html">link</a>) for directly reaching out to
us, the scientists, and making sure that they understood the complexity of the
system rather than simply promoting catchy phrases. When it comes to science,
words matter. I agree that this is a fun system to explore, but I hope that the
science can stand on its own without adding falsehoods and making incorrect
conclusions. </div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
Please don’t hesitate to reach out to scientists (including
me) if you have questions about our research and possibly don’t believe or
understand what you read in the news. We are honored to share this journey with
you and are particularly delighted to hear from the next generation of
researchers. Viruses are incredibly fascinating and, in my opinion, phage WO
tops the charts. We are just beginning to explore the landscape of viruses
infecting intracellular bacteria and I can’t wait to see what comes next.</div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<br /></div>
Anonymoushttp://www.blogger.com/profile/15985401261412486690noreply@blogger.com0tag:blogger.com,1999:blog-6592300489643662663.post-39631136360854149412016-07-11T20:40:00.000-05:002016-07-11T20:40:42.269-05:00Important Announcement: International Conference on Holobionts<div class="page" title="Page 1">
Over the last few years, the terms holobiont and hologenome have received heightened attention, leading to a high-water mark of the 1st dedicated conference on the topic next year at the Paris Natural History Museum (see below). The meeting will be an important event for the community in order to set goals and achieve unity, understanding, and needs for the future. I think it will also be an opportunity to resolve misuses of the terms and associated concepts (Getting the Hologenome Concept Right, <a href="http://msystems.asm.org/content/1/2/e00028-16">mSystems</a>). Many factors have played a part in raising the profile of these terms and concepts including our work and others. Due to an existing heavy travel schedule, work-life balance, and teaching, I declined the invitation to speak at this conference and recommended several young scientists. I heartily endorse this conference and encourage keeping a close eye on developments that come from it. While it is the 1st conference dedicated to the topic, many other conference symposiums and workshops on the topic are brewing or have already taken place. There will hopefully be a 2nd International Conference on Holobionts in the future. </div>
<div class="page" title="Page 1">
<br />
<div class="layoutArea">
<div class="column">
<span style="font-family: "calibri"; font-size: 18.000000pt;">International Conference on Holobionts,<br />
Paris (Natural History National Museum), April 19-21, 2017
</span><br />
<span style="font-family: "calibri"; font-size: 18.000000pt;"><br /></span>
<span style="font-family: "calibri"; font-size: 12.000000pt;">It is becoming increasingly clear that the development, nutrition, physiology and
health of most organisms are influenced by the complex microbial communities they host,
hereby shaping their ecology and evolution. Biology is indeed undergoing a paradigm shift,
where individual phenotypes are seen as a result of the combined expression of the host and
associated microbe genomes, leading to the popularization of the <u>holobiont concept (the
host and its microbiota) and the hologenome (the collective genomes of a holobiont)</u>.
Ecological and technical advances, especially in next generation sequencing technologies,
have greatly contributed to this conceptual shift, thereby revealing the diversity and roles of
the microbes hosted by diverse organisms, from people and plants, to sponges and insects.
The scientific community has now recognized that the host organisms cannot be studied
without taking resident microbiomes into account, making holobiont research imperative
across numerous fields of the life and medical sciences.
</span><br />
<span style="font-family: "calibri"; font-size: 12.000000pt;"><br /></span>
<span style="font-family: "calibri"; font-size: 12.000000pt;">The objective of the </span><span style="font-family: "calibri"; font-size: 12.000000pt; font-weight: 700;">International Conference on Holobionts, Paris 2017 </span><span style="font-family: "calibri"; font-size: 12.000000pt;">is to, for the
first time, bring scientists together who are interested in holobiont systems and their study.
This conference will highlight major advances in defining the key roles of host-borne
microbiota in the ecology and evolution of higher organisms and the potential implications
for human health, food production and ecosystem functioning. In addition, the conference
will offer a platform for debate related to the definition, assembly and evolution of
holobionts. By bringing a range of holobiont researchers together, the </span><span style="font-family: "calibri"; font-size: 12.000000pt; font-weight: 700;">International
Conference on Holobionts </span><span style="font-family: "calibri"; font-size: 12.000000pt;">seeks to help consolidate the field, facilitate exchange of
knowledge across systems and approaches and stimulate further developments in this
emerging discipline.
</span><br />
<span style="font-family: "calibri"; font-size: 12.000000pt;"><br /></span>
<span style="font-family: "calibri"; font-size: 12.000000pt; font-weight: 700;">Scientific program
</span><br />
<span style="font-family: "calibri"; font-size: 12.000000pt;">This conference will address the following topics:
</span><br />
<ol style="list-style-type: decimal;">
<li style="font-family: 'Calibri'; font-size: 12.000000pt;">
<span style="font-family: "calibri"; font-size: 12.000000pt;">Holobionts and evolution
</span><br />
</li>
<li style="font-family: 'Calibri'; font-size: 12.000000pt;">
<span style="font-family: "calibri"; font-size: 12.000000pt;">Emerging approaches to holobiont research
</span><br />
</li>
<li style="font-family: 'Calibri'; font-size: 12.000000pt;">
<span style="font-family: "calibri"; font-size: 12.000000pt;">Microbiota and host health
</span><br />
</li>
<li style="font-family: 'Calibri'; font-size: 12.000000pt;">
<span style="font-family: "calibri"; font-size: 12.000000pt;">Mechanisms for holobiont assembly
</span><br />
</li>
<li style="font-family: 'Calibri'; font-size: 12.000000pt;">
<span style="font-family: "calibri"; font-size: 12.000000pt;">Metabolic interactions between host and microbiota
</span><br />
</li>
</ol>
<span style="font-family: "calibri"; font-size: 12.000000pt;">For each topic, we encourage oral and poster communications on holobiont systems from
different perspectives including theoretical, empirical, fundamental and applied researches.
</span><br />
<span style="font-family: "calibri"; font-size: 12.000000pt;"><br /></span>
<span style="font-family: "calibri"; font-size: 12.000000pt; font-weight: 700;">Provisional list of invited speakers:<br />
Joël Doré </span><span style="font-family: "calibri"; font-size: 12.000000pt;">(INRA Jouy, France)<br />
</span><span style="font-family: "calibri"; font-size: 12.000000pt; font-weight: 700;">Ute Hentschel </span><span style="font-family: "calibri"; font-size: 12.000000pt;">(Helmholtz Centre for Ocean Research, Kiel, Germany)</span></div>
</div>
</div>
<div class="page" title="Page 2">
<div class="layoutArea">
<div class="column">
<span style="font-family: "calibri"; font-size: 12.000000pt; font-weight: 700;">Thierry Heulin </span><span style="font-family: "calibri"; font-size: 12.000000pt;">(CEA Cadarache, France), </span><span style="font-family: "calibri"; font-size: 12.000000pt; font-weight: 700;">confirmed<br />
Nancy Moran </span><span style="font-family: "calibri"; font-size: 12.000000pt;">(University of Texas, Austin, Texas, USA), </span><span style="font-family: "calibri"; font-size: 12.000000pt; font-weight: 700;">confirmed </span><br />
<span style="font-family: "calibri"; font-size: 12.000000pt; font-weight: 700;">Jeroen Raes </span><span style="font-family: "calibri"; font-size: 12.000000pt;">(Vrije Universiteit, Brussel, Belgium), </span><span style="font-family: "calibri"; font-size: 12.000000pt; font-weight: 700;">confirmed<br />
Eugene Rosenberg </span><span style="font-family: "calibri"; font-size: 12.000000pt;">(Tel Aviv University, Israel), </span><span style="font-family: "calibri"; font-size: 12.000000pt; font-weight: 700;">confirmed<br />
Paul Schulze-Lefert </span><span style="font-family: "calibri"; font-size: 12.000000pt;">(Max Planck Institute Koln, Germany), </span><span style="font-family: "calibri"; font-size: 12.000000pt; font-weight: 700;">confirmed </span><br />
<span style="font-family: "calibri"; font-size: 12.000000pt; font-weight: 700;">K</span><span style="font-family: "calibri"; font-size: 12pt; font-weight: 700;">evin Theis </span><span style="font-family: "calibri"; font-size: 12pt;">(Wayne State University, Detroit, Michigan)</span><br />
<span style="font-family: "calibri"; font-size: 12.000000pt;"><br /></span>
<span style="font-family: "calibri"; font-size: 12.000000pt; font-weight: 700;">Practical aspects
</span><br />
<span style="font-family: "calibri"; font-size: 12.000000pt;">This conference will last 2.5 days, from April 19</span><span style="font-family: "calibri"; font-size: 8.000000pt; vertical-align: 6.000000pt;">th </span><span style="font-family: "calibri"; font-size: 12.000000pt;">2 p.m. to from April 21</span><span style="font-family: "calibri"; font-size: 8.000000pt; vertical-align: 6.000000pt;">st </span><span style="font-family: "calibri"; font-size: 12.000000pt;">4 p.m. It will take
place right in the center of Paris, in the heart of “Quartier Latin” in the prestigious Grand
Amphithéâtre of the Natural History National Museum (</span><span style="color: rgb(0.000000% , 0.000000% , 100.000000%); font-family: "calibri"; font-size: 12.000000pt;"><a href="https://www.mnhn.fr/fr">https://www.mnhn.fr/fr</a></span><span style="font-family: "calibri"; font-size: 12.000000pt;">). </span><span style="font-family: "calibri"; font-size: 12.000000pt; font-weight: 700;">Note that
for space constraints, we won’t be able to take more than 300 registrations</span><span style="font-family: "calibri"; font-size: 12.000000pt;">. Registrations
will open by November 15, 2016 and be closed by January 30, 2017. A dedicated website for
registration and practical information is under construction at
</span><span style="color: rgb(0.000000% , 0.000000% , 100.000000%); font-family: "calibri"; font-size: 12.000000pt;"><a href="https://symposium.inra.fr/holobiont-paris2017">https://symposium.inra.fr/holobiont-paris2017</a></span><span style="font-family: "calibri"; font-size: 12.000000pt;">.
</span><br />
<span style="font-family: "calibri"; font-size: 12.000000pt;"><br /></span>
<span style="font-family: "calibri"; font-size: 12.000000pt; font-weight: 700;">Organizing institutions:
</span><br />
<span style="font-family: "calibri"; font-size: 12.000000pt;">CNRS (Centre National de la Recherche Scientifique), INRA (Institut National de la Recherche
Agronomique), MNHN (Museum National d’Histoire Naturelle). This conference is a joint
initiative of the Groupe de Recherche en Génomique Environnementale (GDR GE) and the
INRA Métaprogramme Méta-omiques et écosystèmes microbiens (MEM).
</span><br />
<span style="font-family: "calibri"; font-size: 12.000000pt;"><br /></span>
<span style="font-family: "calibri"; font-size: 12.000000pt; font-weight: 700;">Members of the Scientific Committee:
</span><br />
<span style="font-family: "calibri"; font-size: 12.000000pt;">Bourguet-Kondracki Marie-Lise (CNRS, MNHN Paris), Bourtzis Kostas (FAO/IAEA, Vienna,
Austria), Buée Marc (INRA Nancy, France), Faure Denis (CNRS Orsay, France), Heulin Thierry
(CNRS Marseille, France), Joly Dominique (CNRS Paris, France), Kowalchuk George (Utrecht
University, The Netherlands), Marchesi Julian (Imperial College, UK), Médigue Claudine
(CNRS Genoscope Evry, France), Mougel Christophe (INRA Rennes, France), Selosse Marc-
André (MNHN Paris), Simon Jean-Christophe (INRA Rennes, France), Vandenkoornhuyse
Philippe, (University Rennes 1, France) </span></div>
</div>
</div>
Anonymoushttp://www.blogger.com/profile/15985401261412486690noreply@blogger.com0tag:blogger.com,1999:blog-6592300489643662663.post-72303787683743754872016-06-26T05:01:00.004-05:002016-06-26T05:01:52.553-05:00Science & SciLifeLab Prize for Recent Ph.D.'s in Biology<a href="http://www.sciencemag.org/prizes/scilifelab/rules">Announcement</a> for a young scientist award: <br />
<br />
<div class="view-science-prizes-block">
<div>
<header class="article__header">
<h1 class="article__headline">
Science & SciLifeLab Prize for Young Scientists</h1>
</header>
<div class="prize-details">
<div class="prize-details__core">
<article class="media media--var ">
<div class="media__body">
This Prize was created to recognize that global economic health is
dependent upon a vibrant research community and we need to encourage
our best and brightest to continue in their chosen fields of research.
<br />
</div>
</article>
</div>
<ul class="prize-details__links">
<li><a href="http://www.sciencemag.org/prizes/SciLifeLab">About</a></li>
<li><a href="http://www.sciencemag.org/node/834063">How to Enter</a></li>
<li><a href="http://www.sciencemag.org/prizes/SciLifeLab/2015">Current Winners</a></li>
<li><a href="http://www.sciencemag.org/prizes/SciLifeLab/past-winners">Past Winners</a></li>
</ul>
</div>
</div>
</div>
<div class="article__body">
<span>The Prize is awarded annually to one young scientist for
outstanding life science research for which he/she was awarded a
doctoral degree in the previous two years. The topic of the entrant's
thesis research must be in one of the following categories: <strong>Cell and Molecular Biology</strong>, <strong>Genomics and Proteomics</strong>, <strong>Ecology and Environment</strong>, <strong>Translational Medicine</strong>.
Eligible entrants must have been awarded their doctoral degree in 2014
or 2015, and the subject of their thesis should match one of the Subject
Tracks below. The winners from each category will compete for the grand
prize.</span><br />
Prize money: US$30,000 for the grand prize winner, US$10,000 for each of the category winners.<br />
Publication: The grand prize winning essay will be published in <em>Science</em> and essays from the each of the category winners will be published online.<br />
Application deadline: <strong>August 1, 2016</strong><br />
<h2>
Rules of Eligibility</h2>
<ul>
<li>Entrants for the 2016 prize must have been awarded their Ph.D.
between January 1 2014 and December 31 2015. As a rule, we will only
accept submissions once within this time period.</li>
<li>The research described in the entrant’s thesis must fall within one of the following categories (Subject Tracks):
<ul>
<li><strong>Cell and Molecular Biology</strong>: research in this
category will include cellular and molecular processes at levels ranging
from single molecule to single cell to tissue and organ systems,</li>
<li><strong>Genomics and Proteomics</strong>: research in this category
focuses on analyses of gene- and protein-related events, at the scale of
gene or protein networks to the complete set of genes or proteins in an
organism,</li>
<li><strong>Ecology and Environment</strong>: research in this category
encompasses interactions between organisms and their environment, and
how these processes are influenced by human activity,</li>
<li><strong>Translational Medicine</strong>: research in this category
builds on in vitro or animal model studies of biological processes to
develop potential therapies or medical procedures.</li>
</ul>
</li>
<li>The prize will only recognize work that was performed while the entrant was a graduate student.</li>
<li>The prize will be awarded without regard to sex, race, or nationality.</li>
<li>Employees of SciLifeLab, <em>Science</em>/AAAS, and collaborators in the management or sponsorship of this Prize and their relatives are not eligible to compete.</li>
</ul>
<h2>
<strong>Procedures for Entry</strong></h2>
The entrant must submit the following items:<br />
<ul>
<li><a href="http://scilifelab.secure-platform.com/a/solicitations/home/3">A completed Entry Form</a>.</li>
<li>An essay, written by the entrant, describing the thesis work and its
implications for research in the selected Subject Track. The essay must
not exceed 1,000 words in length and may include one figure or table.</li>
<li>A one-page reference letter from your advisor or a member of your
thesis committee. The letter should include an assessment of the
applicant and comment on the significance of the applicant’s research.</li>
<li>The abstract of the thesis (not to exceed four double-spaced typed pages).</li>
<li>A list of the following:
<ul>
<li>Full citations of all published or in press papers on the research described in the essay;</li>
<li>Academic and professional awards and honors that the entrant has received; and</li>
<li>Relevant professional experience.</li>
</ul>
</li>
</ul>
The Entry Form and additional submission materials must be submitted electronically through our prize management system <a href="http://scilifelab.secure-platform.com/a/solicitations/home/3">here</a>.<br />
Below is a timeline for the prize selection process. You will be
contacted only if there are additional materials or information needed.<br />
August/September: Compilation and Review of Submissions<br />
October/November: Selection of Prize Winner<br />
December: Announcement of Prize Winner & Awards Ceremony in Stockholm<br />
<h2>
Deadline for Entries</h2>
<strong>August 1, 2016</strong><br />
<h2>
Judging Procedures</h2>
First, <em>Science</em> editors will screen the essays and select
three finalists from each Subject Track. Next, a committee of scientists
chaired by the Editor-in-Chief of <em>Science</em> will select a winner
for each Subject Track. The four winners will then compete for the
grand prize. The grand prize winner and three category winners will be
decided by October. <em>Science</em> will control both the evaluation process and the announcement of the winners.<br />
<h2>
Questions/Inquiries:</h2>
<a href="mailto:BoyalifeSciencePrize@aaas.org" style="background-color: transparent; box-sizing: inherit; color: grey; font-weight: bold; outline: 0px; text-decoration: none;">S</a><a href="mailto:ciLifeLabPrize@aaas.org">ciLifeLabPrize@aaas.org</a><br />
</div>
Anonymoushttp://www.blogger.com/profile/15985401261412486690noreply@blogger.com0tag:blogger.com,1999:blog-6592300489643662663.post-67238462102468774122016-05-18T19:36:00.002-05:002016-05-18T19:36:22.695-05:00Job Ad: Program Fellow in Symbiosis at Gordon and Betty Moore Foundation<table id="gnewtonJobDescription"><tbody>
<tr><td id="gnewtonJobDescriptionText"><div>
<div>
<b>Program Fellow, Science</b></div>
<div>
The Gordon and Betty Moore Foundation’s science program supports
exceptional scientists, invests in new technologies, and brings together
new scientific partnerships. We believe in the inherent value of
science and the sense of awe that discovery inspires. We believe that
unleashing the potential of inquiry and exploration not only leads to
scientific progress, but can also deliver important societal benefits.
We take risks and look for opportunities to transform or create entire
fields.</div>
<div>
</div>
<div>
To complement activities in the <a href="https://www.moore.org/initiative-strategy-detail?initiativeId=marine-microbiology-initiative" target="_blank">Marine Microbiology Initiative</a>
(MMI) and other current science program grantmaking, <b>we seek a program
fellow to explore opportunities for further foundation impact in the
realm of symbiosis</b>. Here, we refer to symbiosis as the interactions
between microbes (bacteria, archaea, and protists) and animals, plants,
fungi, and other microbes. We also consider the role of viruses in these
relationships. We consider symbiosis broadly in terms of habitat
(terrestrial and marine), degree of interdependence (transient,
obligatory, endosymbiotic, and that which results in organelle
evolution), and time (ancient to modern).</div>
<div>
</div>
<div>
<b>The Position</b></div>
<div>
The fellow will synthesize information regarding the state of
symbiosis research and related fields in the U.S. and abroad. The fellow
may also work on related topics that link with MMI and other current
symbiosis grantmaking at the foundation.</div>
<div>
</div>
<div>
The fellow will report to the MMI program director, and will work
with MMI team members, colleagues in the science program, and across the
foundation as needed. This role requires a highly developed ability to
collaborate. Experience with or an ability to rapidly learn academic,
government, and private funder structures and cultures is paramount.</div>
<div>
</div>
<div>
The Program Fellow role has a term of 12 months, with the
possibility of renewal for up to 12 additional months. Those with a
relevant advanced graduate degree—as well as researchers considering a
sabbatical—are welcome to apply.</div>
<div>
</div>
<div>
<b>Key Responsibilities</b></div>
<div>
The fellow will:</div>
<ul>
<li>Collaboratively explore opportunities within the realm of
symbiosis, working with the MMI program director, MMI staff, and others.</li>
<li>Synthesize and present written and spoken communications of
findings to internal foundation audiences; discuss and debate findings
using the foundation strategic lenses.</li>
<li>Establish connections with relevant external communities and efforts, as appropriate.</li>
<li>Depending on needs, may develop and conduct workshops and other in-person forums.</li>
</ul>
<div>
<b>Experience and Education</b></div>
<div>
The ideal candidate will possess:</div>
<ul>
<li>A Ph.D. in a relevant field (required).</li>
<li>Postdoctoral experience in a relevant field and/or other science-related post-graduate experience (required).</li>
<li>Demonstrated interest, initiative, and track record in the broad
area of symbiosis and evolution of organismal interactions that includes
microbes.</li>
<li>A track record of collaborative multidisciplinary work.</li>
<li>Experience working constructively within a team of diverse expertise, experience, and perspective.</li>
</ul>
<div>
<b>Competencies</b></div>
<div>
The ideal candidate will also have:</div>
<ul>
<li>Exceptional communication skills (speaking, writing, and listening).</li>
<li>A flexible, creative and positive approach to problem solving in a
highly collaborative team environment; comfort with ambiguity.</li>
<li>An ability to view the big picture and long-term goals while keeping in mind tactical short-term ramifications.</li>
<li>Experience with contributing to and/or coordinating large, multi-stakeholder projects and events.</li>
</ul>
<div>
<b>Attributes</b></div>
<div>
The ideal candidate will demonstrate the following attributes that
describe how we at the Foundation strive to do our work with each other
and our partners.</div>
<ul>
<li>Committed to Excellence</li>
<li>Passionate</li>
<li>Collegial</li>
<li>Open and Honest</li>
<li>Humble and Self-Aware</li>
</ul>
<div>
<b>Compensation and Benefits</b></div>
<div>
Compensation includes a competitive base salary and an excellent package of health, retirement savings and other benefits.</div>
<div>
</div>
<div>
<b>Application Process</b></div>
<div>
Applicants must be legally authorized to work in the United States.
Pursuant to the San Francisco Fair Chance Ordinance, we will consider
for employment qualified applicants with criminal histories in a manner
consistent with the requirements of the ordinance.</div>
<div>
</div>
<div>
The Gordon and Betty Moore Foundation is an equal opportunity employer. All correspondence will remain confidential.</div>
</div>
<br />
</td>
</tr>
<tr>
<td>
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Anonymoushttp://www.blogger.com/profile/15985401261412486690noreply@blogger.com0tag:blogger.com,1999:blog-6592300489643662663.post-43380803966937750182016-03-24T16:34:00.004-05:002016-03-25T09:32:52.251-05:00Guest Blog Post on Citizen Science: What Academic Scientists Can Do More OfThe front lines of science education and expanding scientific literacy are not in the ivory towers of universities, but in pre-college science education at all levels. <a href="http://discover.mbl.edu/">Discover the Microbes Within! The Wolbachia Project</a> has put many of us in contact with some of the most inspirational people we know - educators that love science, work hard, and want to bring that love to countless middle and high school students, and sometimes younger levels. Since 2007, the Wolbachia Project has been <span style="font-family: inherit;">working with Carolyn Wilczynski. I first met Carolyn at a Wolbachia Project workshop held at Cornell University during th<span style="font-family: inherit;">at </span>summer<span style="font-family: inherit;">, and a couple of days ago<span style="font-family: inherit;">, </span></span>I received this message from <span style="font-family: inherit;">her</span>. It struck a chord with me, and perhaps it will do the same for you. She has agreed to let me post the message as she wants it to go: "as far and as wide as possible! There are kids out there who LOVE science. I hear them say it and I see it in their actions. They need scientists to inspire and encourage them. A little goes a long way. Truly."</span><br />
<br />
Friends, <br />
<br />
This school year, I started up a science club, hoping to encourage students to pursue a study of something - anything related to science or science inquiry. A small grant from our district alumni foundation helped to fund the endeavor and I was able to buy supplies, pay entrance fees, get kids to/fro the fairs, and buy t-shirs and food. We all learned a lot. I took 10 kids to the local science fair and 8 advanced to the regional fair. 2 will now advance to the state-level and who knows beyond that! Not too bad for a novice!<br />
<br />
Perhaps because of my own bias towards organismal biology, most of the projects were biology based and most included some manner of organismal biology. From Madagascar hissing cockroaches detecting pesticides in produce to humans yawning to evolutionary relationships of fish species using protein gel electrophoresis. The projects were varied. The work to get there was insanely time consuming (which is why you haven’t heard much from me lately!). <b>One thing I’ve learned is that while science depends on peer review and feedback, not so with science fairs.</b> It took a personal request to the local fair coordinator to reach out to a judge to provide feedback to a student. That feedback resulted in a “highest honor” placement and a top award at the regional fair. Kids are quick learners! I hope that my suggestion to provide feedback to all students at the local science fair next year is taken to heart. <br />
<br />
The other lesson learned is that the majority of judges at science fairs are engineers and the sponsors are engineering organizations. I realize that it’s a sample size of 2, but I reach out to all of you to volunteer to be a judge at a local, regional or state science fair. Volunteer to speak at a science fair - again, the bias is towards engineers, The mindset of an engineer vs scientist is a bit different, though admittedly there is a lot of overlap. <b>Some of my students who did projects on organismal biology left yesterday’s fair discouraged. One boy kept asking me what he’d done wrong. I had no good answer for him</b>. His project was good, scientifically sound and completely appropriate for a science fair. Yet he came away with only a certificate of participation. One girl was asked by an engineer judge, why she provided water in her cockroach enclosures, since they might cause the produce to get moldy faster. Nice suggestion, except that even roaches need to drink water. The cleverness of her study was lost on trying to solve the problem of mold: scientist vs engineer. <br />
<br />
Lastly, <b>if you are members of professional societies and have any ability to do so, I would encourage sponsoring an award</b>. While monetary awards are always appreciated by the fair sponsors and the kids (even as little as $25 goes a long way to say “way to go”), certificates or books also make good awards. The local geological society in our area provided a fossil specimen. Who wouldn’t love a rock as a prize? Students know in advance who the sponsors are and the projects coming to the fair reflect that. So again, basic science is left in the dust. These young people, whether or not they become scientists, will at the least become voters in the future. Science fairs give them a good appreciation for what scientists do and may pay dividends in support of science in the future. <br />
<br />
The New York State Science Congress is June 4th in Buffalo (http://www.stanys.org/students.html), if you can find a way to support basic science in some way at this fair, I encourage you to do so. Or perhaps forward this to friends and colleagues who live nearer to Buffalo. Or if you can reach out to ESA, ABS, BSA, or whatever professional organization that you belong to, it would support science in those fields. <br />
<br />
Thanks for reading my soapbox speech! <br />
<br />
CarolynAnonymoushttp://www.blogger.com/profile/15985401261412486690noreply@blogger.com0tag:blogger.com,1999:blog-6592300489643662663.post-26849458256872785082016-02-04T09:24:00.003-06:002016-08-19T21:49:14.086-05:00Overdue community effort on getting the hologenome concept right<h1 class="highwire-cite-title" id="page-title" style="-webkit-font-smoothing: antialiased; border: 0px; line-height: 20pt; margin: 0px 0px 20px; outline: 0px; padding: 16px 0px 0px; vertical-align: baseline;">
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<span style="color: #101010; font-family: "helvetica neue"; font-size: 14pt;"><span style="font-weight: normal;">More
and more, it is becoming clear that the population biology processes affecting
animal and plant phenotypes interface with ecosystems science and the ecology
of host-associated microbiomes. Indeed, the so-called individual animal or
plant is increasingly appreciated as a "holobiont" comprised of the
host plus all of its associated microbes. Resultantly, all genomes of the
holobiont have been termed the “hologenome”. These terms and associated
concepts are relatively new and liable to misinterpretation. Our new </span><span style="color: black;"><span style="font-weight: normal;"><span style="color: #420178;">preprint at bioRxiv</span></span></span> <span style="font-weight: normal;">/ <b><a href="http://msystems.asm.org/content/1/2/e00028-16">manuscript published at mSystems</a></b> is a community effort to
pull various biologists and philosophers together around a definitive set of
arguments that accurately reflect the original literature. </span></span><span style="font-family: "helvetica neue"; font-size: 14pt; font-weight: normal;">As the largest collection of authors to date in this
area, spanning fifteen junior and senior investigators in the life sciences and
philosophy, we think this article will encourage productive discussion to
stimulate new ideas and understanding on holobionts and hologenomes that
consider the link between phenotype and genotype. I hope you check out the short piece. Feedback is most welcome!</span></div>
</h1>
<h2>
<span style="font-size: small;"><a href="http://msystems.asm.org/content/1/2/e00028-16">Getting the hologenome concept right: An eco-evolutionary framework for hosts and their microbiomes</a></span></h2>
<div>
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<div class="highwire-article-citation highwire-citation-type-highwire-article" data-apath="/biorxiv/early/2016/02/02/038596.atom" data-node-nid="10398" data-pisa-master="biorxiv;038596" data-pisa="biorxiv;038596v1" id="node10398" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">
<div class="highwire-cite highwire-cite-highwire-article highwire-citation-biorxiv-article-top clearfix has-author-tooltip" style="-webkit-font-smoothing: antialiased; border: 0px; font-family: inherit; font-size: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline; zoom: 1;">
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<span class="highwire-citation-authors" style="border: 0px; font-family: inherit; font-size: 11pt; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><span class="highwire-citation-author first article-author-popup-processed has-tooltip" data-delta="0" rel="#hw-article-author-popups-node10398 .author-tooltip-0" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;" title=""><span class="nlm-given-names" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Kevin R</span> <span class="nlm-surname" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Theis</span></span>, <span class="highwire-citation-author article-author-popup-processed has-tooltip" data-delta="1" rel="#hw-article-author-popups-node10398 .author-tooltip-1" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;" title=""><span class="nlm-given-names" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Nolwenn M. </span><span class="nlm-surname" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Dheilly</span></span>, <span class="highwire-citation-author article-author-popup-processed has-tooltip" data-delta="2" rel="#hw-article-author-popups-node10398 .author-tooltip-2" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><span class="nlm-given-names" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Jonathan L.</span> <span class="nlm-surname" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Klassen</span></span>, <span class="highwire-citation-author article-author-popup-processed has-tooltip" data-delta="3" rel="#hw-article-author-popups-node10398 .author-tooltip-3" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;" title=""><span class="nlm-given-names" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Robert M.</span> <span class="nlm-surname" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Brucker</span></span>, <span class="highwire-citation-author article-author-popup-processed has-tooltip" data-delta="4" rel="#hw-article-author-popups-node10398 .author-tooltip-4" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><span class="nlm-given-names" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">John F.</span> <span class="nlm-surname" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Baines</span></span>, <span class="highwire-citation-author article-author-popup-processed has-tooltip" data-delta="5" rel="#hw-article-author-popups-node10398 .author-tooltip-5" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;" title=""><span class="nlm-given-names" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Thomas C.G.</span><span class="nlm-surname" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Bosch</span></span>, <span class="highwire-citation-author article-author-popup-processed has-tooltip" data-delta="6" rel="#hw-article-author-popups-node10398 .author-tooltip-6" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;" title=""><span class="nlm-given-names" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">John F.</span> <span class="nlm-surname" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Cryan</span></span>, <span class="highwire-citation-author article-author-popup-processed has-tooltip" data-delta="7" rel="#hw-article-author-popups-node10398 .author-tooltip-7" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;" title=""><span class="nlm-given-names" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Scott F.</span> <span class="nlm-surname" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Gilbert</span></span>, <span class="highwire-citation-author article-author-popup-processed has-tooltip" data-delta="8" rel="#hw-article-author-popups-node10398 .author-tooltip-8" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><span class="nlm-given-names" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Charles J.</span> <span class="nlm-surname" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Goodnight</span></span>, <span class="highwire-citation-author article-author-popup-processed has-tooltip" data-delta="9" rel="#hw-article-author-popups-node10398 .author-tooltip-9" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><span class="nlm-given-names" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Elisabeth A.</span> <span class="nlm-surname" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Lloyd</span></span>, <span class="highwire-citation-author article-author-popup-processed has-tooltip" data-delta="10" rel="#hw-article-author-popups-node10398 .author-tooltip-10" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><span class="nlm-given-names" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Jan</span> <span class="nlm-surname" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Sapp</span></span>, <span class="highwire-citation-author article-author-popup-processed has-tooltip" data-delta="11" rel="#hw-article-author-popups-node10398 .author-tooltip-11" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;" title=""><span class="nlm-given-names" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Philippe</span><span class="nlm-surname" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Vandenkoornhuyse</span></span>, <span class="highwire-citation-author article-author-popup-processed has-tooltip" data-delta="12" rel="#hw-article-author-popups-node10398 .author-tooltip-12" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;" title=""><span class="nlm-given-names" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Ilana</span> <span class="nlm-surname" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Zilber-Rosenberg</span></span>, <span class="highwire-citation-author article-author-popup-processed has-tooltip" data-delta="13" rel="#hw-article-author-popups-node10398 .author-tooltip-13" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><span class="nlm-given-names" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Eugene</span> <span class="nlm-surname" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Rosenberg</span></span>, <span class="highwire-citation-author article-author-popup-processed has-tooltip" data-delta="14" rel="#hw-article-author-popups-node10398 .author-tooltip-14" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;" title=""><span class="nlm-given-names" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Seth R.</span> <span class="nlm-surname" style="border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Bordenstein</span></span></span></div>
<div class="highwire-cite-metadata" style="-webkit-font-smoothing: antialiased; border: 0px; color: #333333; font-family: inherit; font-size: 0.82rem; font-style: inherit; font-variant: inherit; line-height: 1.25; margin: 5px 0px 0px; outline: 0px; padding: 0px; vertical-align: baseline;">
<span class="highwire-cite-metadata-doi highwire-cite-metadata" style="border: 0px; font-family: inherit; font-size: 11pt; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><span class="label" style="border: 0px; font-family: inherit; font-size: 11pt; font-style: inherit; font-variant: inherit; font-weight: bold; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">doi:</span> http://dx.doi.org/10.1101/038596 </span></div>
<div class="highwire-cite-metadata" style="-webkit-font-smoothing: antialiased; border: 0px; color: #333333; font-family: inherit; font-size: 0.82rem; font-style: inherit; font-variant: inherit; line-height: 1.25; margin: 5px 0px 0px; outline: 0px; padding: 0px; vertical-align: baseline;">
<span class="highwire-cite-metadata-doi highwire-cite-metadata" style="border: 0px; font-family: inherit; font-size: 11pt; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><br /></span></div>
<div class="highwire-cite-metadata" style="-webkit-font-smoothing: antialiased; border: 0px; color: #333333; font-family: inherit; font-size: 0.82rem; font-style: inherit; font-variant: inherit; line-height: 1.25; margin: 5px 0px 0px; outline: 0px; padding: 0px; vertical-align: baseline;">
<span class="highwire-cite-metadata-doi highwire-cite-metadata" style="border: 0px; font-family: inherit; font-size: 11pt; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">
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<span class="highwire-cite-metadata-doi highwire-cite-metadata" style="border: 0px; font-family: inherit; font-size: 11pt; font-style: inherit; font-variant: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><span style="color: #131313; font-family: "helvetica neue"; font-size: 14.0pt;">Given the recently
appreciated complexity of symbioses among hosts and their microbes, significant
rethinking in biology is occurring today. Scientists and philosophers are
asking questions at new biological levels of hierarchical organization - What
is a holobiont and hologenome? When should this vocabulary and associated
concepts apply? Are these points of view a null hypothesis for host-microbe
systems or limited to a certain spectrum of symbiotic interactions such as
host-microbial coevolution? Legitimate questions, advancements and revisions
are warranted at this nascent stage of the field. However, a productive and
meaningful discourse can only commence when skeptics and proponents alike use
the same definitions and constructs. For instance, critiquing the hologenome
concept is not synonymous with critiquing coevolution, and arguing that an
entity is not necessarily the primary unit of selection is not synonymous with
arguing that it is not a unit of selection in general. Here, we succinctly
deconstruct and clarify these recent misconceptions. Holobionts (hosts and
their microbes) and hologenomes (all genomes of the holobiont) are multipartite
entities that result from ecological, evolutionary and genetic processes. They
are not restricted to one special process but constitute a wider vocabulary and
framework for host biology in light of the microbiome. We invite the community
to consider these new perspectives in biology.<o:p></o:p></span></span></div>
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Anonymoushttp://www.blogger.com/profile/15985401261412486690noreply@blogger.com0tag:blogger.com,1999:blog-6592300489643662663.post-10899604782024151002015-12-08T13:53:00.001-06:002015-12-30T10:38:12.639-06:00Horizontal gene transfer from two bacterial genomes into one animal nucleusFor the past two weeks, the science of horizontal gene transfer (exchange of DNA between unrelated organisms such as between microbes and animals) has been a source of scholarly debate, specifically for the case of tardigrades (see <a href="http://www.theatlantic.com/science/archive/2015/12/rival-scientists-kill-recent-discovery-about-invincible-animals/418755/">Atlantic article</a>). Our latest lab <a href="https://peerj.com/articles/1479/">publication</a> in PeerJ (an affordable, transparent, and open access journal) by first author <a href="https://twitter.com/DNAdiva87">@DNAdiva87</a> will not cause such a ruckus. Based on DNA sequencing, analysis, and importantly staining of the bacterial inserts in the animal genome, we show for the first time transfer of hundreds of genes from two different <i>Wolbachia</i> bacteria into one host grasshopper genome. Graphical and text abstract are enclosed below. It is also, as of today, featured at the top of the PeerJ journal site.<br />
<br />
This work could not have been done without the talents of a great scientist like Lisa and our colleagues in Spain. They and the work were featured in a podcast for "<a href="http://www.microbeworld.org/podcasts/this-week-in-microbiology/archives/2042-twim-117-finding-the-comammox">This Week in Microbiology</a>" on 12.17.15. You can check it out here from time 40:48 - 54:25.<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiYuIFtyDirusBWR9BrEsiu48mq9mCVsgheoKIs2IBgyDFHCebUF6DCeqdrIWeEns5i1VOi3cB9FgCySpyFAJGneAi9sPR4ames0-zCrN0UFGBqN8LB1CPP9i_5BcYd5hGMY1UX8zM7U8Jg/s1600/peerj-1479-graphical-abstract.jpg" imageanchor="1"><img border="0" height="640" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiYuIFtyDirusBWR9BrEsiu48mq9mCVsgheoKIs2IBgyDFHCebUF6DCeqdrIWeEns5i1VOi3cB9FgCySpyFAJGneAi9sPR4ames0-zCrN0UFGBqN8LB1CPP9i_5BcYd5hGMY1UX8zM7U8Jg/s640/peerj-1479-graphical-abstract.jpg" width="480" /></a><br />
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<div class="abstract" itemprop="description" style="color: #333333; font-family: 'Helvetica Neue', Helvetica, Arial, sans-serif; font-size: 16px; line-height: 24px;">
<div style="-webkit-font-smoothing: antialiased; font-size: 18px; line-height: 1.5; margin-bottom: 1.3em; text-rendering: optimizelegibility; word-wrap: break-word;">
Hybrid zones and the consequences of hybridization have contributed greatly to our understanding of evolutionary processes. Hybrid zones also provide valuable insight into the dynamics of symbiosis since each subspecies or species brings its unique microbial symbionts, including germline bacteria such as <i>Wolbachia</i>, to the hybrid zone. Here, we investigate a natural hybrid zone of two subspecies of the meadow grasshopper <i>Chorthippus parallelus</i> in the Pyrenees Mountains. We set out to test whether co-infections of B and F <i>Wolbachia</i> in hybrid grasshoppers enabled horizontal transfer of phage WO, similar to the numerous examples of phage WO transfer between A and B <i>Wolbachia</i> co-infections. While we found no evidence for transfer between the divergent co-infections, we discovered horizontal transfer of at least three phage WO haplotypes to the grasshopper genome. Subsequent genome sequencing of uninfected grasshoppers uncovered the first evidence for two discrete <i>Wolbachia</i>supergroups (B and F) contributing at least 448 kb and 144 kb of DNA, respectively, into the host nuclear genome. Fluorescent <i>in situ</i> hybridization verified the presence of <i>Wolbachia</i> DNA in <i>C. parallelus</i> chromosomes and revealed that some inserts are subspecies-specific while others are present in both subspecies. We discuss our findings in light of symbiont dynamics in an animal hybrid zone.</div>
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<div class="alert alert-info self-citation" style="background-color: #dcf1fc; border-bottom-left-radius: 2px; border-bottom-right-radius: 2px; border-top-left-radius: 2px; border-top-right-radius: 2px; border: 0px; color: #3a87ad; font-family: 'Helvetica Neue', Helvetica, Arial, sans-serif; font-size: 16px; line-height: 24px; margin-bottom: 20px; margin-top: 20px; padding: 8px 35px 8px 14px; text-shadow: rgba(255, 255, 255, 0.498039) 0px 1px 0px;">
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Cite this as</div>
<span class="self-citation-authors">Funkhouser-Jones LJ, Sehnert SR, Martínez-Rodríguez P, Toribio-Fernández R, Pita M, Bella JL, Bordenstein SR.</span> (<span class="self-citation-year">2015</span>) <span class="self-citation-title"><i>Wolbachia</i> co-infection in a hybrid zone: discovery of horizontal gene transfers from two <i>Wolbachia</i> supergroups into an animal genome</span>. <span itemprop="isPartOf" itemscope="itemscope" itemtype="http://schema.org/PublicationVolume"><span class="self-citation-journal" itemprop="isPartOf" itemscope="itemscope" itemtype="http://schema.org/Periodical" style="font-style: italic;"><span itemprop="name">PeerJ</span></span> <span class="self-citation-volume" itemprop="volumeNumber">3</span></span>:<span class="self-citation-elocation" itemprop="pageStart">e1479</span> <a href="https://doi.org/10.7717/peerj.1479" itemprop="url" style="color: #2a85e8; text-decoration: none;">https://doi.org/10.7717/peerj.1479</a></div>
Anonymoushttp://www.blogger.com/profile/15985401261412486690noreply@blogger.com0tag:blogger.com,1999:blog-6592300489643662663.post-88892853582469759722015-12-06T06:46:00.000-06:002016-08-19T21:50:34.680-05:00Getting the Hologenome Concept RightRelated publication: <a href="http://msystems.asm.org/content/1/2/e00028-16"><b>Getting the hologenome concept right: an eco-evolutionary framework for hosts and their microbiomes (2016)</b> </a><br />
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What is the target of natural selection in animals and plants? From a phenotypic perspective, selection sees trait variation that influences who passes on offspring and who does not. Given this rather obvious tenet, selection at the individual level is effectively selection on the holobiont - the community of microrganisms and its host. Consequently, variation in the collective genomes of the holobiont - i.e, the hologenome - yields variation in phenotypes upon which evolution can act. This hologenome concept of evolution distinguishes itself by placing emphasis on the vast symbiotic complexity and transmission routes inherent in holobiont animals and plants. As we emphasized in a recent <a href="http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002226">perspective</a>, it is also true that just as large parts of the nuclear genome can evolve neutrally or be in conflict, so too can large parts the hologenome.<br />
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Yesterday, I read a skeptical <a href="http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002311">essay</a> on the hologenome concept by Nancy Moran and Daniel Sloan. I have several thoughts on it. In short, it was great to see the attention on the topic, as all opinions and analyses are welcome at this nascent stage of the framework. Raising the profile of this area was precisely the intent of a <a href="http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002226">recent publication</a> with <a href="https://kevinrtheis.wordpress.com/">Kevin Theis</a>, in which we clarified the history and use of the terms, revised the hologenome concept to include new perspectives such as neutrality, and laid a foundation for hypothesis-driven research and theoretical analyses for the field. This article subsequently calls for some of the same, which is great, but it is unnecessarily narrow and divisive at times. I briefly lay out the misconceptions about the article.<br />
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From the start in paragraph 2, it wasn't clear if M&S read our publication in detail. They attribute the origin of the word "holobiont" to Mindell (1992) but we showed that it was first used by Lynn Margulis in 1991. I had the pleasure of corresponding with Mindell prior to our publication, and he humbly tipped us off to the false credit. As we state...<br />
<blockquote class="tr_bq">
<span style="background-color: white; color: #333333; font-family: "arial"; line-height: 18px;">The term "holobiont" traces back to Lynn Margulis and refers to symbiotic associations throughout a significant portion of an organism's lifetime, with the prefix holo- derived from the Greek word </span><i style="box-sizing: border-box; color: #333333; font-family: arial; line-height: 18px;">holos</i><span style="background-color: white; color: #333333; font-family: "arial"; line-height: 18px;">, meaning whole or entire. Amid the flourishing of host microbiome studies, holobiont is now generally used to mean every macrobe and its numerous microbial associates [</span><a class="ref-tip" href="http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002226#pbio.1002226.ref019" style="box-sizing: border-box; color: #3c63af; font-family: arial; line-height: 18px; text-decoration: none;">19</a><span style="background-color: white; color: #333333; font-family: "arial"; line-height: 18px;">,</span><a class="ref-tip" href="http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002226#pbio.1002226.ref022" style="box-sizing: border-box; color: #3c63af; font-family: arial; line-height: 18px; text-decoration: none;">22</a><span style="background-color: white; color: #333333; font-family: "arial"; line-height: 18px;">]</span></blockquote>
Second, M&S read our article well enough to extract some quotes, which I fully stand by. But they seem to be skeptical while at the same time they do not elaborate on the justifications spelled out in the paper. Take the example of thinking about host-microbe interactions as interspecific epistasis, similar to gene-gene interactions in the same genome. This is just scaling well accepted population genetic epistasis to community genetic epistasis and it has been done by many eco-evolutionary biologists. As we discuss in our essay, theory shows that there is an intellectual continuum between epistasis in the same genome and interspecific epistasis between different genomes, even for symbionts that are horizontally transmitted. This is not controversial or problematic. What is up for experimentation is the degree to which the epistasis comes and goes versus persist for selection to operate on it. The challenges are interestingly the same for both genetic epistasis in the same genome and intergenomic epistasis. There is nothing out of the ordinary here.<br />
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Third, I heartily agree with M&S that coevolution has run amok in the microbiome field (without any evidence) and has been applied incorrectly in most cases. Glad to see this getting more attention. It is precisely why I came up with the word "phylosymbiosis" in 2012-2013 because it does not confer coevolution or codiversification apriori to the observed pattern of microbial community relationships recapitulating host phylogenetics. It does, however, provide evidence for community selection in controlled studies of the microbiota where microbes are assembled in a deterministic manner that parallels host genetic relationships. Controlled studies of Nasonia wasps and Hydra best show this pattern. I also like their Figure 1 on phylosymbiosis and think that it could be improved as both models could be operating at the same time. Some microbes could be strictly evolving in synchrony with hosts by vertical transmission while other microbes may be horizontally transmitted.<br />
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Fourth, the essay ignores that hologenomic models fully accommodate mutualism and parasitism. It is a misconception that it does not. Just as selfish genes are part of the nuclear genome, pathogens are part of the hologenome. See Principle 8 of our <a href="http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002226">essay</a>.<br />
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<ol class="simple" style="background-color: #efefef; box-sizing: border-box; color: #333333; font-family: arial; font-size: 0.8125rem; line-height: 1.125rem; list-style: none; margin: 0px 0px 0.8125rem 1.25rem; padding: 0px 0px 0px 1.25rem;">
<li style="box-sizing: border-box; font-size: 0.8125rem; line-height: 1.125rem; margin: 0px 0px 9px; padding: 0px;">VIII. The hologenome is shaped by selection and neutrality<ul class="bulleted" style="box-sizing: border-box; font-family: inherit; font-size: 0.8125rem; line-height: 1.125rem; list-style-position: outside; list-style-type: none; margin: 0px 0px 0px 1.25rem; padding: 0px;">
<li style="box-sizing: border-box; font-size: 0.8125rem; line-height: 1.125rem; margin: 0px 0px 0.5625rem; padding: 0px 0px 0px 1.25rem; position: relative;">Natural selection can work to remove deleterious nuclear mutations or microbes while spreading advantageous nuclear mutations or microbes; in the absence of selection, the neutral spread of hologenomic variation through populations is an inherently stochastic process.</li>
<li style="box-sizing: border-box; font-size: 0.8125rem; line-height: 1.125rem; margin: 0px 0px 0.5625rem; padding: 0px 0px 0px 1.25rem; position: relative;">Mixed ecological models of stochastic and deterministic community assembly likely reflect natural systems, and partitioning the microbiota into stochastic versus deterministic subunits will be an important future goal of the field.</li>
</ul>
</li>
</ol>
Fifth, the hologenome concept fits squarely into multi-level selection theory. Most would agree that it is not correct to say that it is the only unit of selection, but it is equally not correct to say that the concept fails as a whole if there are others level of selection operating. Many levels are operating simultaneously. Moreover, for phenotypic selection, the key point is that nearly all individual selection is holobiont-level selection given the pervasive affects of the microbiota on host biology. The genetic response to selection is what's clearly more challenging to unravel and whether this occurs at a holobiont-level or not is indeed an experimental question worthy of future attention that people are working on.<br />
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<ol class="simple" style="background-color: #efefef; box-sizing: border-box; color: #333333; font-family: arial; font-size: 0.8125rem; line-height: 1.125rem; list-style: none; margin: 0px 0px 0.8125rem 1.25rem; padding: 0px 0px 0px 1.25rem;">
<li style="box-sizing: border-box; font-size: 0.8125rem; line-height: 1.125rem; margin: 0px 0px 9px; padding: 0px;">VII. The hologenome concept fits squarely into genetics and accommodates multilevel selection theory<ul class="bulleted" style="box-sizing: border-box; font-family: inherit; font-size: 0.8125rem; line-height: 1.125rem; list-style-position: outside; list-style-type: none; margin: 0px 0px 0px 1.25rem; padding: 0px;">
<li style="box-sizing: border-box; font-size: 0.8125rem; line-height: 1.125rem; margin: 0px 0px 0.5625rem; padding: 0px 0px 0px 1.25rem; position: relative;">Multilevel selection theory asserts that selection operates across multiple levels of genetic variation with phenotypic effects, from genes to hologenomes and beyond.</li>
<li style="box-sizing: border-box; font-size: 0.8125rem; line-height: 1.125rem; margin: 0px 0px 0.5625rem; padding: 0px 0px 0px 1.25rem; position: relative;">Holobionts are exclusive to hosts and their associated microbiota; different holobionts, such as a pollinator and a flower, interact with each other under standard ecological principles.</li>
</ul>
</li>
</ol>
Sixth, the paper frequently plays both sides of the debate. Obligate endosymbionts and organelles are presented as hologenomic entities, but then the paper at times claims hologenomic evolution could be relatively insignificant or rare. These statements are contradictory.<br />
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The paper's abstract concludes that "Although selection at the level of the symbiotic community, or hologenome, occurs in some cases, it should not be accepted as the null hypothesis for explaining features of host-symbiont associations". This opinion is largely based on the inaccurate pretense that scientists are claiming holobiont-level selection without evidence or that holobionts are a kumbaya conglomerate. Neither is true. It is easy to oversimplify any concept to death if one wants to. Yet as Einstein once noted "Everything should be made as simple as possible but not simpler".<br />
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<br />Anonymoushttp://www.blogger.com/profile/15985401261412486690noreply@blogger.com1tag:blogger.com,1999:blog-6592300489643662663.post-36195998159442702622015-11-24T16:18:00.000-06:002015-11-25T08:15:32.131-06:00Q&A on Holobionts and Hologenomes<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: right; margin-left: 1em; text-align: right;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhan1jOj_Pi0XMNIzcWZBCtMU3Y8Rk0O7l0UHBu-anxP3PIODK3ZFkUyBm434T8cx4dKcB4G0EgPRLFrl_LTCtYb6H0k4CrExaajr4pC5ZAya7BT-sAFWqvOVOilXIoRj_3UTIr_JIk9aEt/s1600/figure+1.v2.jpg" imageanchor="1" style="clear: right; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" height="195" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhan1jOj_Pi0XMNIzcWZBCtMU3Y8Rk0O7l0UHBu-anxP3PIODK3ZFkUyBm434T8cx4dKcB4G0EgPRLFrl_LTCtYb6H0k4CrExaajr4pC5ZAya7BT-sAFWqvOVOilXIoRj_3UTIr_JIk9aEt/s320/figure+1.v2.jpg" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Image from Brucker and Bordenstein, 2013, Zoology</td></tr>
</tbody></table>
<span style="font-family: "helvetica"; font-size: 18px;">In September, a few friends on twitter entered into a lively discussion on holobionts and hologenomes that was subsequently borne out in a series of Q&A emails. Below, we summarize this discourse - whose goal was to flesh out some of the nuances and foundations of the holobiont and hologenome terms (<a href="http://symbionticism.blogspot.com/2015/06/what-are-holobionts-and-hologenomes.html">related blog post</a> - What are holobionts and hologenomes?) and concepts. <a href="http://www.baltruslab.com/">David Baltrus</a> poses queries to Seth Bordenstein and <a href="https://kevinrtheis.wordpress.com/">Kevin Theis</a>. What follows is very informal, but useful for the three of us and perhaps our colleagues. We all hope it is helpful from the various angles that one may look at this stimulated area. </span><br />
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<span style="font-family: "arial"; font-size: 12.0pt; line-height: 200%;">Q1: The first point that I think
still needs clarifying after the hologenome article and the perspective piece
in Science is what the point of promoting “the hologenome” actually is. I’m
probably just too close...but to me it’s not a controversial idea that microbes
matter for evolution/ecology of macro-organisms.<br />
<br />
A1 (SB): There’s two ways to answer this question. First, I think that this is
an uncertain argument as one could raise that same question for virtually any
term. Why do we need the term “metagenome” if we knew there were previously
microbial genomes in soil, or why do we need the term "selfish gene” if we
already knew there were transposons, etc. We could stop there, but I think
these terms clearly have uses now that one would not question. Indeed, the
selfish gene debate early on is very similar to the holobiont and hologenome
terms; moreover I think it goes deeper than just this. We’re not just using
words willy nilly :) There hasn’t been a good singular term yet to describe the
entity of the multispecies organism and their genomes. In fact, we argue its
been quite the opposite as we describe in principle 2 (<a href="http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002226">link to paper</a>): <o:p></o:p></span></div>
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<div class="MsoNormalCxSpMiddle" style="line-height: 200%; margin-bottom: 10.0pt; margin-left: .5in; margin-right: .5in; margin-top: 0in; mso-add-space: auto;">
<span style="font-family: "arial"; font-size: 12.0pt; line-height: 200%;">“<i style="mso-bidi-font-style: normal;">There appears to be a considerable number of
misplaced characterizations and colloquialisms used to refer to host-microbiota
symbioses, and these misnomers can potentially act as impasses to new advances</i>”.
<o:p></o:p></span></div>
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<div class="MsoNormalCxSpMiddle" style="line-height: 200%;">
<span style="font-family: "arial"; font-size: 12.0pt; line-height: 200%;">We need to chuck out all the
superorganism and organ system colloquialisms for good reasons. Moreover, the holobionts
and hologenomes properly emphasize the diverse and complex array of symbionts
and their genomes in one host species. In contrast to binary symbioses, the
multispecies consortia are relatively new and universal features of macrobes
that emerged within the last decade for many biologists. That’s what the terms
best capture in a timely fashion. See Gordon, Knowlton, Reman, Rohwer, Youle
for similar arguments (<a href="http://www.microbemagazine.org/index.php?option=com_content&view=article&id=6300:superorganisms-and-holobionts&Itemid=1464">link</a>).
<span style="mso-spacerun: yes;"> </span><br style="mso-special-character: line-break;" />
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<span style="font-family: "arial"; font-size: 12.0pt; line-height: 200%;">A1 (KRT): Yes, it is readily
accepted that microbes matter for the evolution/ecology of macro-organisms, but
importantly the hologenome concept goes beyond this observation in a very
substantive way. Specifically, it posits that the host and its microbiota are a
potential primary unit of selection. It is this component of the concept, along
with the emphasis on the diversity of the symbiotic communities to be
considered, as SB already noted, that requires the use of new terminology. All macro-organisms
are populated by microbes, these associations are often not random but rather
are replicated across macro-organismal generations and are reflective of their
phylogeny, and these associations also often profoundly affect the phenotypes
of what we typically think of as individual macro-organisms. As we note in the
paper:<o:p></o:p></span></div>
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<div class="MsoNormalCxSpMiddle" style="line-height: 200%; margin-bottom: 10.0pt; margin-left: .5in; margin-right: .5in; margin-top: 0in; mso-add-space: auto;">
<span style="font-family: "arial"; font-size: 12.0pt; line-height: 200%;">“</span><i style="mso-bidi-font-style: normal;"><span style="font-family: "arial"; font-size: 12.0pt; line-height: 200%; mso-fareast-font-family: "MS Mincho"; mso-fareast-language: JA;">the debatable and testable issue of the hologenome is whether nuclear genes
and microbes are coinherited to a degree that evolution can operate on their
interaction</span></i><span style="font-family: "arial"; font-size: 12.0pt; line-height: 200%; mso-fareast-font-family: "MS Mincho"; mso-fareast-language: JA;">.” </span><span style="font-family: "arial"; font-size: 12.0pt; line-height: 200%;"><o:p></o:p></span></div>
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<span style="font-family: "arial"; font-size: 12.0pt; line-height: 200%;"><br />
Q2: In light of my own point #1 above, almost all of the PLoS principles paper
is couched in terms of microbial “symbionts”. While I gather that you are using
the broad term “symbionts” here which includes pathogens, it seems to me that
all the points that the piece brings up can be flipped and looked at from the
point of view of pathogens as well. I don’t think any of this is controversial
if it’s couched in terms of microbial pathogens, especially long term chronic
ones. HIV can be environmentally acquired or vertically inherited and certainly
causes changes in human phenotypes/evolution/ecology. These phenotypic changes
(i.e. loss of T cells) can appear to “reboot” some aspects of Lamarck’s ideas
just as much as beneficial microbes, only in this case the acquired phenotype
is disease. Do pathogenic infections count for rebooting Lamarckian principles
if they are inherited across generations? Seems like it's the same story, but
you guys put the Larmarckian thing in there to be a bit provocative, which is completely
understandable, it just kind of sticks out to me. I don’t think that you see a
distinction between beneficial and pathogenic microbes, but I think at least
some of the ideas mentioned have been pretty thoroughly worked out for
pathogens (speciation for <a href="http://rstb.royalsocietypublishing.org/content/365/1543/1139.full.pdf+html">one</a>).
If anything, I might argue that pathogens have more power to coevolve with
humans than beneficial microbes because of stronger selection pressures on both
ends (handwaving over a lot of assumptions).<br />
<br />
A2 (SB): I'm trying to follow the logic here, as it seems you are playing both
sides of the Q/A. First, you are right in that we have always used symbionts in
our publications to refer to all types of associations. And we do not subscribe
to overselling one phenotype for another. Quite the contrary, we write that <o:p></o:p></span></div>
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<div class="MsoNormalCxSpMiddle" style="line-height: 200%; margin-bottom: 10.0pt; margin-left: .5in; margin-right: .5in; margin-top: 0in; mso-add-space: auto;">
<span style="font-family: "arial"; font-size: 12.0pt; line-height: 200%;">”<i style="mso-bidi-font-style: normal;">In the microbiome, selection favors the
spread of beneficial microbes involved in nutrition, defense, or reproduction,
while pathogenic microbes are either purged by holobiont selection or the
pathogens deploy adaptations</i>….” <o:p></o:p></span></div>
<div class="MsoNormalCxSpMiddle" style="line-height: 200%;">
<br /></div>
<div class="MsoNormalCxSpMiddle" style="line-height: 200%;">
<span style="font-family: "arial"; font-size: 12.0pt; line-height: 200%;">Second, there is the issue of
Lamarck. You agree with Lamarckian aspects of pathogens, but then questions if
using Lamarck in the paper is too provocative. Mmmm…can’t have it both ways :)
Our goal is to get the science right in its most accurate way, not be
provocative in a purposeful sense. If that accuracy or view of science happens
to be taken as provocative, that might say something more about where the
community is now, than our intent per se. Indeed, Margaret McFall-Ngai once
told similar stories for some of her perspectives on the immune system’s role
in regulating beneficial microbes. The immunologists were initially up in arms.
Finally and to your last point, it is the very fact that many aspects of
symbioses have been worked out that we can reason the holobiont and hologenome
concepts are the best model to explain the complexity of the systems in a
comprehensive light. I think Kevin and I both agree also that its’ not perfect.
It needs to be made better with more concepts, theory, and experimentation that
is the stated intent of the essay.<o:p></o:p></span></div>
<div class="MsoNormalCxSpMiddle" style="line-height: 200%;">
<br /></div>
<div class="MsoNormalCxSpMiddle" style="line-height: 200%;">
<span style="font-family: "arial"; font-size: 12.0pt; line-height: 200%;">A2 (KRT): <span style="mso-spacerun: yes;"> </span>We do employ “symbiont” broadly, referring to
resident microbes: beneficial, pathogenic, or otherwise. The hologenome concept
accommodates each of these interaction types. Lamarckian evolution is simply heritability
of acquired characteristics. If acquired symbionts have fitness consequences
and are thereafter heritable, they are consistent with Lamarckian evolution. I
do not see that as provocative. It should, however, be noted that although we
present the argument for a Lamarckian element to the hologenome concept, the
Rosenbergs (and many others) of course originally did so (<a href="http://www.ncbi.nlm.nih.gov/pubmed/19573132">link</a>). <o:p></o:p></span></div>
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<div class="MsoNormalCxSpMiddle" style="line-height: 200%;">
<span style="font-family: "arial"; font-size: 12.0pt; line-height: 200%;">In general, strength of selection
may be greater on pathogenic interactions as you suggest, but it can be
substantial on beneficial interactions as well. The Rosenbergs’ coral example
comes readily to mind (<a href="http://www.nature.com/nrmicro/journal/v5/n5/full/nrmicro1635.html">link</a></span><span style="font-family: "arial"; font-size: 12.0pt; line-height: 200%;">). Regardless, this
is not consequential to the validation or refutation of the hologenome concept
as again it accommodates all interaction types. Lastly, I concur with SB, the
hologenome concept is not perfect, and in the essay we discuss where future
efforts should be focused, but it is the most comprehensive evolutionary
framework we currently have for discussing and investigating the ecological and
evolutionary complexities of host-microbial systems.<br />
<br />
Q3: We have a pretty good vocabulary for ideas like co-evolution, multi-level
selection, phenotypic plasticity. What makes the hologenome different enough to
warrant special mention in light of a lot of previous theory and literature? If
it’s combination of all these things, all of these ideas must inherently
incorporate each other in nature anyway, no?<br />
<br />
A3 (SB): I think A1 mostly applies here too, but let me know if I'm missing
something. Most importantly, we haven’t had a word/singular framework that
captures the fact that all of these evolutionary and ecological processes are
happening at once across the complexity of the holobiont. We’ve traditionally
seen host-microbe interactions as interactions between individual host and
individual microbe. The holobiont and holgoenome concepts instead place
emphasis on the complex systems biology of the whole system driving evolution.
For many phenotypes (and as Charles Goodnight initially put in an email to me),
so-called "individual selection" will actually be selection on the
community, with many players affecting the selection, and that is what we as a
community haven’t appreciated enough.<o:p></o:p></span></div>
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<br /></div>
<div class="MsoNormalCxSpMiddle" style="line-height: 200%;">
<span style="font-family: "arial"; font-size: 12.0pt; line-height: 200%;">A3 (KRT): Nice explanation SB. I will
only add that, for me at least, the holobiont concept is a redefining of that
which constitutes an individual animal or plant. This new construct, or unit,
requires a name and a clear definition. That definition is itself ‘evolving,’
hopefully catalyzed to some degree by our essay.<br />
<br />
Q4a: You say that the hologenome is “not complex” and point out that they are
really only referring to microbes (see microbiome in Title).<br />
<br />
A4a (SB): Mmmm, you’re taking words out of context here. We actually state the
opposite:<o:p></o:p></span></div>
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<br /></div>
<div class="MsoNormalCxSpMiddle" style="line-height: 200%; margin-bottom: 10.0pt; margin-left: .5in; margin-right: .5in; margin-top: 0in; mso-add-space: auto;">
<span style="font-family: "arial"; font-size: 12.0pt; line-height: 200%;">“<i style="mso-bidi-font-style: normal;">The holobiont and hologenome concepts
upgrade this conventional vision to encompass the vast ecological and genomic
COMPLEXITY of a host and its total microbiota</i>” <o:p></o:p></span></div>
<div class="MsoNormalCxSpMiddle" style="line-height: 200%;">
<br /></div>
<div class="MsoNormalCxSpMiddle" style="line-height: 200%;">
<span style="font-family: "arial"; font-size: 12.0pt; line-height: 200%;">And the particular quote excised
above was from the following paragraph: <o:p></o:p></span></div>
<div class="MsoNormalCxSpMiddle" style="line-height: 200%;">
<br /></div>
<div class="MsoNormalCxSpMiddle" style="line-height: 200%; margin-bottom: 10.0pt; margin-left: .5in; margin-right: .5in; margin-top: 0in; mso-add-space: auto;">
<span style="font-family: "arial"; font-size: 12.0pt; line-height: 200%;">“<i style="mso-bidi-font-style: normal;">For instance, do the genomes of an insect
pollinator and flower constitute a hologenome? The ANSWER HERE IS NOT COMPLEX.
Holobionts and their hologenomes are exclusive to the hosts and their
associated microbiota. Different holobionts, such as the aforementioned
pollinator and flower, clearly interact, but these interactions are not new to
biology, as they form the basis for all past and present ecological
investigations. They are simply holobionts themselves interacting with each
other</i>."<o:p></o:p></span></div>
<div class="MsoNormalCxSpMiddle" style="line-height: 200%; margin-left: -4.5pt; mso-add-space: auto;">
<span style="font-family: "arial"; font-size: 12.0pt; line-height: 200%;"><br />
Q4b: My read of this has always been that I don’t know why microbes should be
viewed any differently than macrobes that have close associations with humans.
The presence of worms can affect distributions of gut microbes across animal
life. Macrobes can have just as much an effect on human evolution as microbes.
Why the distinction? Is there a distinction? Is it because that
humans/etc...are hosts for microbes? Humans are hosts for worms and mites over
the course of their whole lives too. Worms and mites can show patterns of
vertical inheritance just like microbes. Why are worms and mites “holobionts
themselves interacting with one another”? Microbes inside of the microbiome
interact within one another, and can be hosts to other microbes and viruses
(see <i style="mso-bidi-font-style: normal;">Bdellovibrio</i> and prophage), why
isn’t each microbe itself a holobiont? <head briefly explodes>. There has
to be a distinction somewhere along the way, and I’m still not getting it even
after multiple discussions and reading the PLoS paper. Maybe I’m just prone to
thinking everything in Biology is complex and worry too much about the
specifics? Even so, there has to be a simple demarcation point going forward
that delineates what the hologenome is.<br />
<br />
A4b (SB): A4a applies here in addition to the salient difference that while
worms live in and outside humans, the worm and human can live without
themselves, but neither can live without their microbiomes. This is a key point
for why the holobiont and hologenome stop at the host and its associated
microbes. We as a community just haven’t appreciated this aspect enough and
there’s far more science to delve into because of it.<o:p></o:p></span></div>
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<br /></div>
<div class="MsoNormalCxSpMiddle" style="line-height: 200%;">
<span style="font-family: "arial"; font-size: 12.0pt; line-height: 200%;">A4b (KRT): I agree with SB’s broader
sentiment here, and will add that the hologenome concept explains (or seeks to
explain) the evolution of animals and plants, organisms (i.e. holobionts) whose
phenotypes are <u>necessarily</u> products of interactions between their own
genomes and those of their symbiotic microbes. The concept does not explain the
evolution of microbes. <br />
<br />
Q5: What about microbes that are completely neutral to the hologenome? Are
these incorporated into the concept (I assume they are)? I’m coining the term
“junk microbes” here for these very special cases so that we can have all the
fun of the ENCODE folks about arguing what percentage of the hologenome is
composed of junk microbes. If you include “junk” microbes into the discussion,
then the hologenome includes cases where selection doesn’t act. Therefore, the
hologenome idea would include post-reproductive stages of hosts as well, where
(hand waving about grandmother’s nurturing effects on evolution aside) the
hologenome doesn’t matter for evolution and is just there in the present time
for the host. The microbes will of course still evolve with each other. Maybe
one prediction is bacterial cheaters arising in older hosts? Just fuel for
discussion, another added layer to think about whether selection is
implicit in the concept of the hologenome (I don't think it is).<o:p></o:p></span></div>
<div class="MsoNormalCxSpMiddle" style="line-height: 200%;">
<span style="font-family: "arial"; font-size: 12.0pt; line-height: 200%;"><br />
A5 (SB): Are we really on Q5? Wow :) To your first point, principle VIII and
III is all about neutrality and selection in the hologenome. I think we’re on
the same page here. And this is an important point of the essay as the original
holobiont and hologenome concepts did not distinguish between neutral and
selected microbes.<br style="mso-special-character: line-break;" />
<!--[if !supportLineBreakNewLine]--><br style="mso-special-character: line-break;" />
<!--[endif]--><o:p></o:p></span></div>
<div class="MsoNormalCxSpMiddle" style="line-height: 200%;">
<span style="font-family: "arial"; font-size: 12.0pt; line-height: 200%;">A5 (KRT): Ah, see the “Microbiome
Mutiny Hypothesis” (</span><span class="pseudotab3"><span lang="EN-GB" style="color: #474848; font-family: "arial"; font-size: 12.0pt; line-height: 200%; mso-ansi-language: EN-GB;"><a href="http://www.biologydirect.com/content/10/1/3">link</a></span></span><span style="font-family: "arial"; font-size: 12.0pt; line-height: 200%;">).<o:p></o:p></span></div>
<div class="MsoNormalCxSpMiddle" style="line-height: 200%;">
<span style="font-family: "arial"; font-size: 12.0pt; line-height: 200%;"><br />
Q6: “Antibiotic or axenic experiments in speciation studies must be routine”.
This doesn’t make sense to me, even though I understand exactly where the data
is coming from and why you say it. Speciation has never occurred in the absence
of microbes in any eukaryote. Taking the microbes away is a completely
unrealistic environment and wouldn’t ever happen under natural conditions. I’d
be on board with saying microbe swaps are necessary for speciation studies, but
to me the axenic experiments don’t tell you anything about speciation <i style="mso-bidi-font-style: normal;">in naturo</i> because it’s artificial.<br />
<br />
A6 (SB): Would you believe that you disagree with Jerry Coyne too, as he stated
the same thing in his Nature review article in 1992! The axenic experiments
will importantly tell the relative fraction of reproductive isolation
phenotypes that are microbe dependent, something that is assumed by most
speciation geneticists to be rare if you were to poll them. So, its a starting
point to get us a “symbiotic heritability” if you will for the effects of
symbionts vs. host genes on reproductive isolation traits. The microbe swapping
is certainly a good next step, but the former is where we lack the most data
right now and the easiest to do for wide-ranging systems.<br />
<br />
Q7: Phylosymbiosis...Again, I completely get the concept in the broad sense,
but this is another place the absolutely needs to be fleshed out. Different
branches in the phylogeny should have their own microbiome signals. Where do
you draw the line? Microbiomes can easily differ within a species. Microbiomes
can easily differ within one individual within one species over time, sometimes
in really random ways…….My further guess is that, like most coevolution
studies, it’s going to be hard to distinguish between co-evolution and (for
lack of a better term) shared environments. Humans/chimps have largely
divergent microbiomes, enough to see phylosymbiotic signals. I’m not sure that
the same could be said for different species of lemurs on Madagascar because
they all fill different niches. Correlations make things messy.<br />
<br />
A7 (SB): The question of “where do you draw the line” of microbiome divergence
between species for within species is both an experimental question that we’re
trying to answer right now and an intellectual question that scales just as well
to good old fashion genes. The blurriness in transition from within to between
species variation is evidence for evolutionary change over time rather than
problematic. Phylosymbiosis is really only best done under “controlled” studies
that avoid confounding issues of diet, gender, age, etc. That is why the
Nasonia and Hydra studies stand out in my mind. We’ve got more data on other
systems as well now. And its important to note here that phylosymbiosis does
not equal coevolution. I think we've been pretty clear about this since its
inception. I actually came up with the word phylosymbiosis precisely because
the concordance between the host phylogeny and microbiome communities does not
necessarily mean coevolution.<span style="mso-spacerun: yes;"> </span><span style="mso-spacerun: yes;"> </span><o:p></o:p></span></div>
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<div class="MsoNormalCxSpMiddle" style="line-height: 200%;">
<span style="font-family: "arial"; font-size: 12.0pt; line-height: 200%;">A7 (KRT): As the field biologist, or
at least once upon a time field biologist, I will suggest that, while I agree
with everything SB wrote, broad phylosymbiotic investigations in the wild have
merit in that they reveal the extent of microbiota/microbiome variation among
hosts in natural systems (descriptive data that are needed), and, if no host phylogenetic
signal in symbiotic microbial community composition or structure is evident
(while taking into account other host characteristics like diet, sex, etc.),
then it strongly suggests that these host-microbial associations are not as
pronounced and persistent as the holobiont and hologenome concepts posit.<br />
<br />
Q8: I’m “in like” with the analogy to mitochondria and microbiomes, I’m
not in love with it. You can lose some of your microbes and still be
functional, you can’t lose your mitochondria and still be a functional human. I
think there is a fundamental difference, given phenotypic redundancy in the
microbiome. Always willing to be proven otherwise:)<br />
<br />
A8 (SB): Right…it's a gradient of dependency. I take the fact that certain
microbes can be lost, but some microbes are required as a compelling reason for
why the holobiont and hologenome concepts are relevant and novel. We know that
the microbes need to be there to some degree and with some specificity, but we
also know that any given microbe many not be required. Fascinating!<br style="mso-special-character: line-break;" />
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Anonymoushttp://www.blogger.com/profile/15985401261412486690noreply@blogger.com0tag:blogger.com,1999:blog-6592300489643662663.post-22391098401143391852015-11-19T15:32:00.001-06:002015-11-19T15:32:34.779-06:00This Is What Congressional Support For Science Looks LikeSTUNNING! (While it is only for NIH, it is still welcome news.)<br />
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<br />Anonymoushttp://www.blogger.com/profile/15985401261412486690noreply@blogger.com0tag:blogger.com,1999:blog-6592300489643662663.post-23684245108062272202015-11-19T09:25:00.000-06:002015-11-19T09:27:40.580-06:00Dependent Care Travel Policy for Colleges and Universities<div class="MsoNormal">
<span style="font-size: 15px;">Academia is a profession that can require a substantial amount of travel - from serving on grant review panels to attending conferences and more. While it is a tremendous opportunity to see the world and meet new people, it is also problematic for some. Faculty, staff, and students with families or dependents cannot readily travel, and yet they are often measured in job interviews or tenure and </span><span style="font-size: 15.277776718139648px;">promotion</span><span style="font-size: 15px;"> reviews on the extent to </span><span style="font-size: 15.277776718139648px;">which</span><span style="font-size: 15px;"> </span><span style="font-size: 15.277776718139648px;">they</span><span style="font-size: 15px;"> have spoken at conferences or served on panels. In response to this problem, </span><span style="font-size: 15.277776718139648px;">several universities have earned my respect in leading the way with travel assistance policies. </span></div>
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<span style="font-size: 15px;"><br /></span></div>
<div class="MsoNormal">
<span style="font-size: 15px;">I wrote </span><span style="font-size: 15.277776718139648px;">the letter below to bring a similar policy to fruition at Vanderbilt. It is a work in progress as it moves through leadership and adminsitratorion (with some progress), but perhaps this letter will help others in the same pursuit.</span><span style="font-size: 11pt;"> </span><br />
<span style="font-size: 11pt;"><br /></span></div>
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<span style="mso-tab-count: 5;"><br /></span>
<span style="mso-tab-count: 5;">EXAMPLE LETTER </span><span style="mso-spacerun: yes;"> </span><o:p></o:p></div>
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<br /></div>
<div class="MsoNormal" style="text-align: justify;">
Dear Colleagues:<o:p></o:p></div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="MsoNormal" style="text-align: justify;">
Thank you for taking the time to
read this proposal on behalf of Vanderbilt University's single and dual-career
parents and other dependent caretakers. From research staff to faculty, professionals
in academia often struggle to find the work-life balance and financial
resources to attend national and international meetings because the costs of
airfare and care services for dependents (children, elderly, ill, or disabled
family) are prohibitive. As a result, their scholarship is at a disadvantage
relative to others who are not juggling dependent care in academia. Indeed,
childcare is one increasing and welcome trend at large meetings, yet without
the support to travel to conferences, staff and faculty parents must restrict
their professional development and networking. <o:p></o:p></div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="MsoNormal" style="text-align: justify;">
In response to this escalating
demand, universities are pioneering Family-Friendly Travel Policies (see five
examples below with web links). Each one supports employees with financial assistance
for airfare and/or care services for dependents per fiscal year. At a time when
single and dual-career parents and caretakers are rising, it seems that a
similar policy at Vanderbilt would not only lift the burden of current scholars
with families, but also serve as a recruiting tool for those that consider
family policies in their job search. Indeed, there appears to be no existing
policy after discussing this topic with colleagues in the Schools of Arts and
Science, Law, Medicine, Nursing, and Peabody. <span style="color: #262626; mso-bidi-font-family: Arial;">A reduced opportunity to speak, meet colleagues, and hear
about the latest work in the field translates for many to reduced career
growth. We can eliminate this bias and at the same time lift the spirit around
family-friendly policies at Vanderbilt.<span style="mso-spacerun: yes;"> </span></span><o:p></o:p></div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="MsoNormal" style="margin-left: .5in; mso-layout-grid-align: none; mso-list: l0 level1 lfo1; mso-pagination: none; text-autospace: none; text-indent: -.25in;">
<!--[if !supportLists]--><span style="color: #262626; font-family: "wingdings"; mso-bidi-font-family: Wingdings; mso-fareast-font-family: Wingdings;"><span style="mso-list: Ignore;">Ø<span style="font: 7.0pt "Times New Roman";">
</span></span></span><!--[endif]--><span style="mso-bidi-font-family: Arial;"><a href="https://hr.cornell.edu/life/support/faculty_dependent_care.html"><span style="color: #680e17; text-decoration: none; text-underline: none;">Cornell
University</span></a><span style="color: #262626;"> | Faculty Dependent Care
Travel Fund | $1000 per year<o:p></o:p></span></span></div>
<div class="MsoNormal" style="margin-left: .5in; mso-list: l0 level1 lfo1; text-align: justify; text-indent: -.25in;">
<!--[if !supportLists]--><span style="font-family: "wingdings"; mso-bidi-font-family: Wingdings; mso-fareast-font-family: Wingdings;"><span style="mso-list: Ignore;">Ø<span style="font: 7.0pt "Times New Roman";"> </span></span></span><!--[endif]--><span style="color: #262626; mso-bidi-font-family: Arial;"><a href="http://vpf.berkeley.edu/policies-and-programs/dependent-care-travel-policy"><span style="color: #680e17; text-decoration: none; text-underline: none;">UC Berkeley</span></a>
| Dependent Care Travel Policy | Covers all costs + 70% more than actual costs
to offset taxes that will be deducted</span><o:p></o:p></div>
<div class="MsoNormal" style="margin-left: .5in; mso-layout-grid-align: none; mso-list: l0 level1 lfo1; mso-pagination: none; text-autospace: none; text-indent: -.25in;">
<!--[if !supportLists]--><span style="color: #262626; font-family: "wingdings"; mso-bidi-font-family: Wingdings; mso-fareast-font-family: Wingdings;"><span style="mso-list: Ignore;">Ø<span style="font: 7.0pt "Times New Roman";">
</span></span></span><!--[endif]--><span style="color: #262626; mso-bidi-font-family: Arial;"><a href="http://www.northwestern.edu/provost/faculty-resources/career-life/dependent-care-professional-travel-grant-program.html"><span style="color: #680e17; text-decoration: none; text-underline: none;">Northwestern
University</span></a> | Dependent Care Professional Travel Grant Program | $750
per year<o:p></o:p></span></div>
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<!--[if !supportLists]--><span style="color: #262626; font-family: "wingdings"; mso-bidi-font-family: Wingdings; mso-fareast-font-family: Wingdings;"><span style="mso-list: Ignore;">Ø<span style="font: 7.0pt "Times New Roman";">
</span></span></span><!--[endif]--><span style="color: #262626; mso-bidi-font-family: Arial;"><a href="https://www.lsa.umich.edu/facstaff/academicaffairs/policiesandprocedures/tenuredandtenuretrackfaculty/familyfriendlypoliciesandprocedures/lsachildtravelexpensepolicy_ci"><span style="color: #680e17; text-decoration: none; text-underline: none;">University of
Michigan</span></a> | Child Travel Expense Policy | $1000 per year<o:p></o:p></span></div>
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</span></span></span><!--[endif]--><span style="color: #262626; mso-bidi-font-family: Arial;"><a href="http://www.brown.edu/about/administration/dean-of-faculty/dependent-care-travel-fund"><span style="color: #680e17; text-decoration: none; text-underline: none;">Brown University</span></a>
| Dependent Care Travel Fund | $750 per year<o:p></o:p></span></div>
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Anonymoushttp://www.blogger.com/profile/15985401261412486690noreply@blogger.com0tag:blogger.com,1999:blog-6592300489643662663.post-69962767544114964942015-10-28T09:12:00.003-05:002015-10-28T09:12:51.559-05:00Important Message About Funding PostdocsI received this university-wide message today about potentially big changes to how we fund postdocs. Its unclear what will happen, but it is an important message for labs with postdocs.<br />
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<span style="font-size: 11pt; letter-spacing: -0.05pt;">The Fair Labor Standards Act (FLSA) is the federal law governing minimum wages and overtime pay. It currently requires that most* employees making less than $23,660 record their hours and must be paid for overtime at 1.5 times their usual rate for any hours worked over 40. The federal government has proposed a revision to the FLSA which would increase this minimum threshold to $50,440. This proposed change, which will likely take effect before November 2016, will apply to the wages we are federally required to pay postdoctoral scholars.</span><o:p></o:p></div>
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<span style="font-size: 11pt; letter-spacing: -0.05pt;">Most of our postdocs currently receive salaries of $42,000 or more, and are therefore within roughly $8,000 of the proposed new minimum. Most postdocs regularly work more than 40 hours/week, and it would make financial sense to increase these salaries to the new federal minimum rather than pay overtime. Yet even for postdocs who do not regularly work more than 40 hours, university leaders believe that redefining postdocs as hourly workers would undermine the professional nature of their work.</span><o:p></o:p></div>
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<span style="font-size: 11pt; letter-spacing: -0.05pt;">Changes to the FLSA, if enacted, would have a significant impact upon department budgets, grant budgets, and more. There are still many details to be clarified, and numerous offices across the university are working to determine possible and best courses of action. The final rule will determine the actions we need to take. In the meantime, we want to be prepared for the likely scenario of needing to increase postdoctoral salaries. </span><o:p></o:p></div>
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<span style="font-size: 11pt; letter-spacing: -0.05pt;">For the present, please do two things:</span><o:p></o:p></div>
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1.<span style="font-family: 'Times New Roman'; font-size: 7pt;"> </span><span style="font-size: 11pt; letter-spacing: -0.05pt;">Alert all necessary members of your department to take these proposed changes into account as needed (for example, budgeting, writing grant proposals, making new offers to postdoctoral scholars, etc.) Again, changes will likely take effect before November 2016 but the final regulation has not been published yet. No immediate changes to salaries need to be made at this time.</span><o:p></o:p></div>
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2.<span style="font-family: 'Times New Roman'; font-size: 7pt;"> </span><span style="font-size: 11pt; letter-spacing: -0.05pt;">Provide resources for those who have questions:</span><o:p></o:p></div>
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a.<span style="font-family: 'Times New Roman'; font-size: 7pt;"> </span><span style="font-size: 11pt; letter-spacing: -0.05pt;">The documents attached to the email provide some further information.</span><o:p></o:p></div>
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b.<span style="font-family: 'Times New Roman'; font-size: 7pt;"> XXXXX </span><span style="font-size: 11pt; letter-spacing: -0.05pt;">is the primary contact person for specific questions. She is available for meetings with faculty groups. </span><o:p></o:p></div>
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c.<span style="font-family: 'Times New Roman'; font-size: 7pt;"> </span><span style="font-size: 11pt; letter-spacing: -0.05pt;">Remind those with questions that this is an open issue which is subject to change and for which the university is still exploring options.</span><o:p></o:p></div>
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<i><span style="font-size: 10pt; letter-spacing: -0.05pt;">*The law provides certain exceptions, including executives, MDs, teachers, lawyers, and trainees. Postdocs whose <u>primary</u> duty is teaching could be defined as holding a teaching position and receive this exception. The federal definition of “trainee” includes that trainees may not receive wages, so this designation is not an option for most postdocs with the exception of those on NIH NRSA training grants.</span></i></div>
Anonymoushttp://www.blogger.com/profile/15985401261412486690noreply@blogger.com0tag:blogger.com,1999:blog-6592300489643662663.post-54728838980082868692015-10-13T21:48:00.002-05:002015-10-13T21:50:19.943-05:00My phage talk at North Carolina State UniversityJust got back from North Carolina State University last week. <a href="http://www.microbiology.ncsu.edu/people/faculty/Miller.html">Eric Miller</a> invited me out for a lecture in his Department of Plant and Microbial Biology. Eric has been involved with various bacteriophage projects over the years, including most recently the HHMI phage genome sequencing project and phages that might be useful for killing bee pathogens. I was really impressed with NCSU and how linked in they are with the various industries of Research Triangle. Nearly every person I spoke to had a collaborative, educational, or financial relationship of some kind with them. I don't often see this kind of collaboration between industry and academia, and it is clearly a model for other universities to follow. As a side note, NCSU just launched a major initiative on <a href="https://jobs.ncsu.edu/postings/59240?utm_content=bufferf9b75&utm_medium=social&utm_source=twitter.com&utm_campaign=buffer">hiring new faculty</a> in the area of non-human microbiomes.<br />
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Anyway, I presented our long-term studies and recent @<a href="https://twitter.com/srbordenstein">srbordenstein</a> work on <i>Wolbachia</i>'s phage WO, which has some very interesting features that are unique to the viral world. This work is currently in review. I also covered work by <a href="https://twitter.com/JMetcalfVU">@JMetcalfVU</a> and <a href="https://twitter.com/DNAdiva87">@DNADiva87</a> on bioprospecting Archaea for new antibiotics that originally stemmed from our investigations of phage WO (<a href="http://elifesciences.org/content/3/e04266">link to paper</a>). Here's the <a href="https://www.youtube.com/watch?v=gguUoMoKxHY">talk</a> that I recorded in Keynote, exported to Quicktime, and posted to YouTube. Comments and questions are most welcome. </div>
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Anonymoushttp://www.blogger.com/profile/15985401261412486690noreply@blogger.com0tag:blogger.com,1999:blog-6592300489643662663.post-30406594723821305892015-10-09T10:50:00.002-05:002015-10-09T10:50:28.811-05:00The War on Science<span style="font-size: large;">There will always be a war on science. Such is the nature of humanity. This <a href="https://www.youtube.com/watch?v=8e1XX-ngJcc">video</a> is worth your next five minutes. It speaks for itself....</span><br />
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<span style="font-family: Helvetica; font-size: 18px;">"Somwhere, something incredible is waiting to be known" - Carl Sagan</span>Anonymoushttp://www.blogger.com/profile/15985401261412486690noreply@blogger.com0tag:blogger.com,1999:blog-6592300489643662663.post-35218515667280784682015-10-02T10:39:00.000-05:002015-10-02T10:39:00.885-05:00Wolbachia Milestone: "Video Game" StatusThere are many reasons why <a href="http://eol.org/pages/976559/overview" style="font-style: italic;">Wolbachia </a>bacteria are one of the most amazing microorganisms that you'll ever read about (and why scientists have studied them for almost a century now). For starters, they curiously dwell inside the cells of animal gonads (testes and ovaries) spanning insects to filarial worms. Second, they can change the gender or reproduction of those insects. Third, they can not only prevent mosquitoes from passing on dengue virus to humans, but they may also be a target for curing diseases such as lymphatic filariasis or river blindness. Fourth, they are one of the best cases of how infectious microorganisms can assist the origin of new species. <div>
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Among many other astounding facts, <i>Wolbachia</i> have become so famed apparently in the popular news that they are also now featured in the video game series <a href="http://www.theverge.com/2015/10/1/9431725/mgs5-review">Metal Gear Solid 5</a>. A friend pointed me to this sound track yesterday with the quote "can't escape it - <i>Wolbachia</i> are now making appearances in video games. <i>Wolbachia</i> in this game are used by the enemy to create a pathogen that kills people speaking only certain languages". </div>
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The full video / sound track is here:<br /><div>
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The two clips where Wolbachia are featured are:</div>
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Anonymoushttp://www.blogger.com/profile/15985401261412486690noreply@blogger.com0