Saturday, April 27, 2013

Yes, the human microbiome has truly arrived: on Wait Wait Don't Tell Me

So cool.  Yesterday on "wait wait ... don't tell me" Kai Penn (actor) was enticed to play the game "Ahhh! Get It Off Me!" in regard to microbes: Not My Job: Kal Penn Takes A Quiz On The Microbiome : NPR

Hat tip to Jenna Lang for pointing me to this.

Trying to sort out all the STEM and STEM related departments, graduate programs , at #UCDavis

Well, I was in a meeting yesterday for the UC Davis ADVANCE program.  This program is an NSF funded project to improve presence of women and underrepresented minorities on the faculty in Science, Technology, Engineering and Math (STEM).  So I decided to see - how many departments at UC Davis might participate in such an initiative.  And, well, wow.  I knew there were a lot of STEM or STEM-related departments at UC Davis but I did not know there were this many.

Here is a list I compiled of UC Davis STEM or STEM-related Departments.  I included medical departments here since many people in such departments do medical/science research.  But clearly this is a broad definition of STEM.  But nevertheless, this gives some picture of the scope of science and medicine and related departments at UC Davis.

Vet School departments in Yellow
Med School departments in Red
College of Biological Sciences Departments are In Green
College of Agricultural and Environmental Sciences in Orange
College of Letters and Science in Light Blue
College of Engineering in Grey
  1. Anatomy, Physiology & Cell Biology
  2. Anesthesiology
  3. Animal Science
  4. Anthropology
  5. Applied Science
  6. Biochemistry and Molecular Medicine
  7. Biological and Agricultural Engineering
  8. Biomedical Engineering
  9. Cardiovascular Medicine
  10. Cell Biology and Human Anatomy
  11. Chemical Engineering and Materials Science
  12. Chemistry
  13. Civil and Environmental Engineering
  14. Computer Science
  15. Dermatology
  16. Electrical and Computer Engineering
  17. Emergency Medicine
  18. Entomology
  19. Environmental Science and Policy
  20. Environmental Toxicology
  21. Evolution and Ecology
  22. Family and Community Medicine
  23. Food Science and Technology
  24. Geology
  25. Human and Community Development
  26. Infectious Diseases
  27. Internal Medicine
  28. Land, Air and Water Resources
  29. Linguistics
  30. Mathematics
  31. Mechanical and Aeronautical Engineering
  32. Medical Pathology
  33. Medical Microbiology & Immunology
  34. Medicine and Epidemiology
  35. Microbiology and Molecular Genetics 
  36. Molecular and Cellular Biology
  37. Molecular Biosciences
  38. Nematology
  39. Neurobiology, Physiology and Behavior
  40. Neurological Surgery
  41. Neurology
  42. Nursing
  43. Nutrition
  44. Obstetrics and Gynecology
  45. Ophthalmology
  46. Pathology
  47. Pathology, Microbiology & Immunology
  48. Pediatrics
  49. Pharmacology
  50. Physical Medicine and Rehabilitation
  51. Physics
  52. Physiology and Membrane Biology
  53. Plant Biology
  54. Plant Pathology
  55. Plant Sciences
  56. Population Health and Reproduction
  57. Psychiatry
  58. Psychology
  59. Public Health Sciences
  60. Statistics
  61. Surgery
  62. Surgical and Radiological Sciences 
  63. Urology
  64. Viticulture & Enology
  65. Wildlife, Fish and Conservation Biology

And then of course UC Davis has a TON of graduate groups and almost all of these are separate from departments.  They do not hire faculty but they are a key part of the atmosphere and academics at UC Davis.  And there are an enormous number of these in STEM or STEM-related fields.  See below

Bad Ome-like word of the week: symbiome

Well I got pointed to this paper: Transgenerational Transmission of the Glossina pallidipes Hytrosavirus Depends on the Presence of a Functional Symbiome

And as many might guess - the word "symbiome" did not sit well with me.  Alas, they don't define it in the paper.  So I can't really quibble with their definition.  But I did find some other stuff out there that, well, at least helps see how other people are using the word:
I can't really tell from most of these if "symbiome" can be a useful term or not sometimes.  Certainly the iPhylo example above has potential.  But in general, the word seems awkward at best.  Now - as far as I can tell, nobody is using it in the context of "genomics" so this does not fit in with my "badomics" obsession.  But it still does not make me feel warm and fuzzy so I am going to give it a pseudo-award - the Bad Ome-like word award.


Thursday, April 25, 2013

So cool - NSF has a program to provide supplemental funds when CAREER PIs go on family leave

Just got pointed to this by Siobhan Brady from UC Davis:

US NSF - Dear Colleague Letter: FY 2013 Career-Life Balance (CLB)-Faculty Early Career Development Program (CAREER) Supplemental Funding Requests (nsf13075)

It is an NSF program to
"The purpose of this DCL is to announce the continuation of the supplemental funding opportunity initiated in FY 2012 for PIs supported in the CAREER program. CAREER Principal Investigators (PIs) are invited to submit supplemental funding requests to support additional personnel (e.g., research technicians or equivalent) to sustain research when the PI is on family leave. These requests may include funding for up to 3 months of salary support, for a maximum of $12,000 in salary compensation. The fringe benefits and associated indirect costs may be in addition to the salary payment and therefore, the total supplemental funding request may exceed $12,000."
This is part of a larger program on Career-Life Balance:
Instituted in 2012, NSF’s Career-Life Balance (CLB) Initiative is an ambitious, ten-year initiative that will build on the best of family-friendly practices among individual NSF programs to expand them to activities NSF-wide.  This agency-level approach will help attract, retain, and advance graduate students, postdoctoral students, and early-career researchers in STEM fields.  This effort will help reduce the rate at which women depart from the STEM workforce.  By the end of this ten-year initiative (2021), it is expected that women will represent 41 percent of newly tenured doctoral S&E faculty—the same percentage as the available pool of women S&E doctorate recipients in 2009; and that women of color will comprise 17 percent of newly tenured faculty, the same percentage of their PhD production rate in 2009.  Further information on the CLB initiative may be found on the Foundation’s website.  
The primary emphasis of NSF’s CLB initiative in FY 2012 was focused on opportunities such as dependent-care issues (child birth/adoption and elder care).  These issues initially were addressed through NSF’s Faculty Early Career Development (CAREER) program, where career-life balance opportunities can help retain a significant fraction of early career STEM talent.  In FY 2013, the Foundation intends to further integrate CLB opportunities through other programs such as the Graduate Research Fellowship and postdoctoral fellowship programs, as well as expand opportunities such as dual career-hiring through the Increasing the Participation and Advancement of Women in Academic Science and Engineering Careers (ADVANCE) program.  Each of these opportunities will be described and implemented separately.
I am involved in the UC Davis ADVANCE program (minor advisory role) and am always on the lookout for ways that institutions and fundings agencies try to increase representation of women and minorities in STEM fields so if you know of other examples - please post details.

If you are into microbial diversity and use R this may be worth checking out: phyloseq

Just got pointed (by the lead author) to this new paper: PLOS ONE: phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

Abstract:


Background
The analysis of microbial communities through DNA sequencing brings many challenges: the integration of different types of data with methods from ecology, genetics, phylogenetics, multivariate statistics, visualization and testing. With the increased breadth of experimental designs now being pursued, project-specific statistical analyses are often needed, and these analyses are often difficult (or impossible) for peer researchers to independently reproduce. The vast majority of the requisite tools for performing these analyses reproducibly are already implemented in R and its extensions (packages), but with limited support for high throughput microbiome census data.
Results
Here we describe a software project, phyloseq, dedicated to the object-oriented representation and analysis of microbiome census data in R. It supports importing data from a variety of common formats, as well as many analysis techniques. These include calibration, filtering, subsetting, agglomeration, multi-table comparisons, diversity analysis, parallelized Fast UniFrac, ordination methods, and production of publication-quality graphics; all in a manner that is easy to document, share, and modify. We show how to apply functions from other R packages to phyloseq-represented data, illustrating the availability of a large number of open source analysis techniques. We discuss the use of phyloseq with tools for reproducible research, a practice common in other fields but still rare in the analysis of highly parallel microbiome census data. We have made available all of the materials necessary to completely reproduce the analysis and figures included in this article, an example of best practices for reproducible research.
Conclusions
The phyloseq project for R is a new open-source software package, freely available on the web from both GitHub and Bioconductor.

Seems similar in some ways to the WATERs Kepler Workflow that we released a few years ago.   Anyway - if you use R and are into microbial diversity studies this may be worth checking out.  As a bonus - it has a strong emphasis on reproducibility - which is a good thing.

Quick post: interesting article in Smithsonian on the human microbiome by Richard Conniff

Just q quick post here.  There is an interesting article about the human microbiome worth checking out: Microbes: The Trillions of Creatures Governing Your Health.  By Richard Conniff in Smithsonian Magazine. It also comes with some related videos and pictures. See for example and And it references my "Overselling the microbiome" award ...
When a scientific team recently suggested that changes in gut bacteria could protect against stroke, Jonathan Eisen of the University of California at Davis lambasted them for “absurd, dangerous, self-serving claims that completely confuse the issue of correlation versus causation.” Eisen, a specialist in microbial genomics, now regularly presents “overselling the microbiome” awards on his blog. He says he doesn’t doubt the ultimate importance of the microbiome: “I believe the community of microbes that live in and on us is going to be shown to have major influences.” But believing that “is different from actually showing it, and showing it doesn’t mean that we have any idea what to do to treat it. There is danger here.”
And it even discusses a fecal transplant-like treatment called RePOOPulate. What could be better? Anyway - definitely worth checking out.

Wednesday, April 24, 2013

Announcement: Intntl. BioInformatics Workshop on Virus Evolution & Molecular Epidemiology

This looks pretty good:


18th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology
University of Florida, Emerging Pathogens Institute
Gainesville, Florida, USA.
August 25th - August 30th, 2013

Bioinformatics Methods Applied to Virology and Epidemiology

We are announcing the organization of the international workshop on Virus Evolution and Molecular Epidemiology (VEME) in 2013, hosted by the Emerging Pathogens Institute in the warm city of Gainsville and sponsored by several local partners.
We plan to organize a 'Phylogenetic Inference' module that offers the theoretical background and hands-on experience in phylogenetic analysis for those who have little or no prior expertise in sequence analysis. An 'Evolutionary Hypothesis Testing' is targeted to participants who are well familiar with alignments and phylogenetic trees, and would like to extend their expertise to likelihood and Bayesian inference in phylogenetics, coalescent and phylogeographic analyses ('phylodynamics') and molecular adaptation. A 'Large Dataset Analysis' module will cover the more complex analysis of full genomes, huge datasets of pathogens including Next Generation Sequencing data, and combined analyses of pathogen and host. Practical sessions in these modules will involve software like, PHYLIP, PAUP*, PHYML, MEGA, PAML or HYPHY, TREE-PUZZLE, SplitsTree, BEAST, MrBayes Simplot and RDP3.
We recommend participants to buy The Phylogenetic Handbook as a guide during the workshop, and to bring their own data set.
For further information and applications we refer to a dedicated website that will be announced here soon.
Abstract and application deadline is April 30th.
Selections will be made by end of May 2013.
The registration fee of 1000 USD covers attendance, lunches and coffee breaks.
Participation is limited to 25 scientists in each module and is dependent on a selection procedure based on the submitted abstract and statement of motivation. A limited number of grants are available for scientists who experience difficulties to attend because of financial reasons.
For further information and applications we refer this website: http://conferences.dce.ufl.edu/vemei/http://conferences.dce.ufl.edu/veme/ 

Guest post: Kevin Carpenter on his new microbial photo exhibit at the Exploratorium in SF #SoCool

Special guest post from Kevin Carpenter who has microbe photos featured at the Exploratorium.


One of my colleagues who does research on the microbes that live in the hindguts of lower termites once remarked that interesting organisms can be found in the most unusual of places. And the lower termite hindgut, by almost anyone’s estimation, is certainly an unusual place. It is also a fascinating place for anyone interested in biology, ecology, evolution, biochemistry, or beautiful natural forms and patterns.

Since my undergraduate days in the early 90s, I have had a deep interest in the tree of life, especially eukaryote phylogeny. After a Ph.D. in Plant Biology at U.C. Davis, I headed off to the University of British Columbia to work in Patrick Keeling's lab to pursue these interests. Anyone who has this peculiar obsession (actually, I think it's peculiar not to have this obsession!) knows that the eukaryote tree comprises mostly protists, and they arguably encompass greater structural, cell biological, biochemical, (and certainly evolutionary!) diversity than all plants, animals, and fungi combined.

In Patrick's lab I developed methods for SEM and TEM imaging of these microbes to investigate their phenotypic character evolution, functional morphology, and symbioses with bacteria in the light of molecular phylogenetic data. In addition to a number of publications (with more to come) and talks in Russia, Germany, Norway, etc. my electron micrographs have been featured on numerous journal covers, textbooks, and invited artistic presentations in Canada and Germany.

On 17 April 2013, a collection of 11 of my scanning electron micrographs of lower termite hindgut protists and their bacterial symbionts will go on permanent exhibit at the Exploratorium museum as they open their new $300 million dollar location on Pier 15 in San Francisco. This is a large (12' x 4') installation in the East Gallery (overlooking the bay):




The waterfront location, the architecture, the exhibits, and sustainable technology (rooftop solar panels, etc) are all amazing, and I encourage anyone with any interest in science/biology, art, experimentation, tinkering, and beautiful views to come out for a visit. For more information on the exhibit, the organisms, additional images and other resources (including a blog!), please visit my website at: KevinJCarpenter.com

As for the organisms...

The hindgut of wood-feeding lower termites--comprising approximately 1000 species (out of a total of several thousand species of termites)--is densely packed with symbiotic protozoa (protists), many of which engulf and enzymatically degrade wood fragments making their way to the termite hindgut. Far from being parasites, numerous studies have shown this to be a mutualsitic symbiosis, by demonstrating that the termites will starve and die if deprived of their protist symbionts. The symbiosis between lower termites and their hindgut protists is one of the longest-studied and best-known examples of microbial symbiosis, dating back nearly a century and a half to the work by Joseph Leidy and others.

YAMMGM: Yet another mostly male genomics meeting

Just got an email from Illumina - key parts are below:

2013 Illumina Scientific Summit

Dear Jonathan,

Illumina's third annual Scientific Summit will be held June 3rd through 7th in charming New Orleans, Louisiana, at the Loews Hotel. Described by a past attendee as, "an upscale Gordon Conference", the Scientific Summit is an invitation-only meeting of 120 leading scientists and thought leaders plus the Illumina executive and R&D leadership teams. 

Plenary sessions will be focused on the Genetic Etiology of Cancer and Genetic Diseases, The Changing Landscape of Medical Genetics, Microbial Detection, and Epigenetics. The formal presentations will be complemented by attendee-driven discussion sessions on a variety of topics ranging from workflow bottlenecks to future applications of Next Generation Sequencing in single cells and diagnostics.

The following distinguished scientists are scheduled to speak:

Dr. Mark Adams, Scientific Director, J. Craig Venter Institute

Dr. Kenneth J. Bloom, Chief Medical Officer, Clarient

Dr. David Craig, Deputy Director of Bioinformatics, Associate Professor and Director, Neurogenomics Division, Head Neurobehavioral Research Unit, TGen

Dr. Richard Gibbs, Wofford Cain Chair in Molecular and Human Genetics, Professor, Department of Molecular and Human Genetics, Professor, Programs in Translational Biology & Molecular Medicine, Baylor College of Medicine

Dr. David Goldstein, Director, Duke Medical Center for Human Genome Variation, Duke University

Dr. Steven Jones, Head of Bioinformatics and Associate Director, Michael Smith Genome Sciences Centre, BC Cancer Agency 

Dr. Michael Katze, Professor, Microbiology, University of Washington

Dr. Jim Knowles, Professor and Associate Chair for Research and Psychiatry and the Behavioral Sciences, USC

Dr. Peter Laird, Director, USC Epigenome Center, Professor of Surgery,Biochemistry and Molecular Biology, Keck School of Medicine, USC

Neil Miller,  Director of Informatics and Software Development, Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City

Dr. Steven Musser, Director, Office of Regulatory Science, FDA Center for Food Safety and Applied Nutrition

Dr. Charles Perou, Distinguished Professor of Genetics, Professor, Pathology & Lab Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine

Dr. Jonathan Sebat, Chief, Beyster Center for Genomics of Neuropsychiatric Diseases, Associate Professor, Department of Psychiatry & Cellular and Molecular Medicine, University of California, San Diego

Dr. George Weinstock, Professor of Genetics and Molecular Microbiology, Washington University

Dr. Liz Worthey, Director of Genomic Informatics, Medical College of Wisconsin

I love Illumina sequencing toys.  I really do.  No so impressed with the gender ratio of this meeting however.  Would not have gone anyway ... but if I COULD have attended I would not have.  I wonder -did they even think about whether there might be some bias here?  There certainly are plenty of female candidates they could have invited. Maybe they did not invite women? Maybe all the women said no?

Monday, April 22, 2013

Do we need naming regulations for computer software?

Well, just saw this new paper: BMC Bioinformatics | Full text | Bellerophon: a hybrid method for detecting interchromo-somal rearrangements at base pair resolution using next-generation sequencing data.  Seems potentially interesting.  But one part of it struck me as very awkward.  You see, there already is a Bellerophon software program used by many in my field: Bellerophon: a program to detect chimeric sequences in multiple sequence alignments.  Seems like a very bad idea to have a new program with the same name as an existing (and still used) one in a similar general field (DNA sequence analysis).

This leads me to the following question - do we need some sort of naming guidelines or regulations for computer software?  We have all sorts of naming regulations and conventions for genes, for species, for other groups of taxa, and more.  Why not software tools?  But seriously, I don't think we need such a thing - we just need people to use Google and to do a little searching before they invent / publish a software package in case it's name is, well, already used.

Thursday, April 04, 2013

Cool #OpenAccess paper from McTavish et al. on Domestication of New World Cattle

Sort of randomly bumped into this one via Google Scholar Alerts I have set up and being from UC Davis the title caught my eye: New World cattle show ancestry from multiple independent domestication events.  Yes, we think about cows a lot here OK.  And then the second thing that caught my eye were the authors - including David Hillis - who I did not know was working on cattle.  I mean - I knew he lived in Texas - so maybe I should have guessed this was coming at some point.

And then I noticed the first author is someone I follow on Twitter.  Ok - enough.  I got the message.  So I looked over the paper.

From the Abstract:

Previous archeological and genetic research has shown that modern cattle breeds are descended from multiple independent domestication events of the wild aurochs (Bos primigenius) ∼10,000 y ago. Two primary areas of domestication in the Middle East/Europe and the Indian subcontinent resulted in taurine and indicine lines of cattle, respectively. American descendants of cattle brought by European explorers to the New World beginning in 1493 generally have been considered to belong to the taurine lineage. Our analyses of 47,506 single nucleotide polymorphisms show that these New World cattle breeds, as well as many related breeds of cattle in southern Europe, actually exhibit ancestry from both the taurine and indicine lineages. In this study, we show that, although European cattle are largely descended from the taurine lineage, gene flow from African cattle (partially of indicine origin) contributed substantial genomic components to both southern European cattle breeds and their New World descendants. New World cattle breeds, such as Texas Longhorns, provide an opportunity to study global population structure and domestication in cattle. Following their introduction into the Americas in the late 1400s, semiferal herds of cattle underwent between 80 and 200 generations of predominantly natural selection, as opposed to the human-mediated artificial selection of Old World breeding programs. Our analyses of global cattle breed population history show that the hybrid ancestry of New World breeds contributed genetic variation that likely facilitated the adaptation of these breeds to a novel environment.

There is some really fascinating stuff in here.  And some great figures.

Definitely worth a look if you are interested in cattle, domestication, population genetics, and more ...

Wednesday, April 03, 2013

WWWD - What would Wolbachia do? Not always male destruction. Not always mutualism. Sometimes they disappear.

Interesting paper in Nature Genetics: Genomics of Loa loa, a Wolbachia-free filarial parasite of humans : Nature Genetics : Nature Publishing Group.  It is "Open" due to the NPG policy for papers reporting genome data.

Anyway - the paper deals in parts with the biology of the interaction between Wolbachia and filiarial nematodes.  Wolbachia are these fascinating intracellular bacteria that are found to infect a diversity of invertebrate species.  In 2004 we published the genome sequence of the first Wolbachia genome - a strain that infects Drosophila melanogaster and causes male specific detrimental effects (see summary here and our paper here and a general review here).  Many of the Wolbacia that are well studied have male specific effects leading us to jokingly call them "WMDs" the Wolbachia of male destruction.

Interestingly, Wolbachia also infect filarial nematodes, such as the ones that cause various nasty diseases.  And these Wolbachia not only do not have any obvious male specific detrimental effects, they appear to be mutualistic symbionts of the nematodes.  That is where this paper comes in.  The authors sequenced the genome of a filarial nematode that does not have any Wolbachia.  The premise here is - if Wolbachia are needed for other nematodes maybe one can figure out what Wolbachia do by identifying features in the Wolbachia-free nematode that are not in the ones with Wolbachia. 

They write

Loa loa, the African eyeworm, is a major filarial pathogen of humans. Unlike most filariae, L. loa does not contain the obligate intracellular Wolbachia endosymbiont. We describe the 91.4-Mb genome of L. loa and that of the related filarial parasite Wuchereria bancrofti and predict 14,907 L. loa genes on the basis of microfilarial RNA sequencing. By comparing these genomes to that of another filarial parasite, Brugia malayi, and to those of several other nematodes, we demonstrate synteny among filariae but not with nonparasitic nematodes. The L. loa genome encodes many immunologically relevant genes, as well as protein kinases targeted by drugs currently approved for use in humans. Despite lacking Wolbachia, L. loa shows no new metabolic synthesis or transport capabilities compared to other filariae. These results suggest that the role of Wolbachia in filarial biology is more subtle than previously thought and reveal marked differences between parasitic and nonparasitic nematodes.

Anyway - the paper is worth checking out.

Figure 3: Phylogenomic analysis of nematodes.. Maximum likelihood, parsimony and Bayesian methods all estimated an identical phylogeny using the concatenated protein sequences of 921 single-copy orthologs. To the left of each node are likelihood bootstrap support values/parsimony bootstrap support values/Bayesian posterior probabilities. The distributions of genes in the ortholog clusters are shown to the right of the phylogeny. Core genes are encoded by all genomes, shared genes are encoded by at least two but fewer than all genomes, and unique genes are found only in one genome. Orthologs specific to the nonparasitic (C. elegans, C. briggsae and P. pacificus) and filarial nematodes are also highlighted. Of the 6,280 L. loa genes with no functional assignment, 3,665 are unique to L. loa and 1,158 are filarial specific. From http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.2585.html

Tuesday, April 02, 2013

Microbes and obesity - more connections

A couple of recent papers on weight-loss surgery and microbes have gotten a lot of attention to the idea that obesity and microbes have a more than just coincidental connection.

Some of the news stories on the topic are below. A few of them are a bit over the top but the new work seems pretty sound so this is definitely worth a look.

Storify of Day 1 of "An open digital global south meeting" at #UCDavis

I made a Storify of Tweets and some pictures from the "An open digital Global South" meeting that I am a co-organizer of. This was...