Thursday, November 29, 2012

Convoluted title, cool paper in #PLoSGenetics on relative of insect mutualists causing a human infection

Saw this tweet a few minutes ago:

The title of the paper took me a reread or two to understand.  But once I got what they were trying to say I was intrigued.  And so I went to the paper:  PLOS Genetics: A Novel Human-Infection-Derived Bacterium Provides Insights into the Evolutionary Origins of Mutualistic Insect–Bacterial Symbioses.  And it is loaded with interesting tidbits.  First, the first section of the results details the history of the infection in a 71 year old male and his recovery and the isolation and characterization of a new bacterial strain.  Phylogenetic analysis revealed this was a close relative of the Sodalis endosymbionts of insects.

And then comparative genomics revealed a bit more detail about the history of this strain, it's relatives, and some of the insect endosymbionts.  And plus, it allowed the authors to make some jazzy figures such as

And this and other comparative analyses revealed some interesting findings.  As summarize by the authors
Our results indicate that ancestral relatives of strain HS have served as progenitors for the independent descent of Sodalis-allied endosymbionts found in several insect hosts. Comparative analyses indicate that the gene inventories of the insect endosymbionts were independently derived from a common ancestral template through a combination of irreversible degenerative changes. Our results provide compelling support for the notion that mutualists evolve from pathogenic progenitors. They also elucidate the role of degenerative evolutionary processes in shaping the gene inventories of symbiotic bacteria at a very early stage in these mutualistic associations.
The paper is definitely worth a look.

Playing with Impact Story to look at Alt Metrics for my papers, data, etc

The future of science will include in part better evaluations of the impact of individual scientists, individual papers and individual other units such as data sets, software, presentations, etc.

 There are many efforts in this area of "Alt Metrics" and one I have been playing around with recently is Impact Story. It used to be called Total Impact but they changed their name and some of their focus. It is pretty easy to use.

 One thing you can do is to create "A Collection." To do this you go to their site, you register, and then you select "Create Collection". And you add some information there

Among the information you can include: 

  • ORCID ID: ORCID is a new system for unique author IDs.  Once you get your unique ID you can curate / update your papers at the site (the site needs some work ... some issues there with duplication).  I have gotten my ORCID ID and updating my publications there.
  • Articles from Google Scholar profile.  This allows one to upload a Bibtext fuile of one's publication list from Google Scholar.  To get this, you need a Google Scholar page.  I have one here.  I have been playing a lot with Google Scholar recently: The Tree of Life: Wow - Google Scholar "Updates" a big step forward ... and The Tree of Life: Thank you Google Scholar Updates for finding me ... but did not realize it had a Bibtex export function until now.  From the drop down menu one selects "Export" and then can export ones publications (in the screen capture below the default option is Actions).  Once you get a Bibtex file you can upload it to ImpactStory.
  • Article and Dataset IDs.  Here one can Pubmed IDs or DOIs for other publications or datasets. Since most / all of my papers are in my Bibtext export and Orcid ID what I imagine using this for is data from places like Figshare and DataDryad
  • Webpage URLs.  One can include URLs here.  But so far my experience has been that they do not have a good system of assessing webpages.
  • Slideshare username.  If you are not posting slides and other materials on Slideshare, get with the program.  I post all my talks there.  And other things.  
  • Github Username.  A good place to post code/software.  We are doing this more and more in my lab.  I have a username though I don't do much there myself.  
And then give your collection a name and click go.  It takes a bit of time to finish the initial collection creation with my list of materials.  But it is fascinating and very useful once done.  Here is a link to a collection "Jonathan Eisen try #3" I recently made.  I have not added everything to it but it is still a good record of how many of my contributions are being used.

My favorite thing to do so far is to click "expand all" from the menu which then shows the detailed Alt Metrics for everything.  

  • PDF views.
  • HTML Views. 
  • Facebook shares.  
  • Twitter shares.  
  • And much more. 

It does not seem perfect - not sure how the metrics are quantified for things like Twitter and Facebook.  But it gives a decent indication of how much chatter and use there is of various materials.

And you can export all the information for your own private use.  I can imagine this being VERY useful for promotion/tenure/other review actions.

I also sniffed around the site and found some nice features from their api page.  I especially like the embed function for specific DOIs.  You copy their text and change the DOI and you get a nice graphical summary of Alt Metrics for that DOI.  See an example at the bottom of the post.  Am probably going to add this to my publication lists on the web.

It is important to realize this is a BETA version. Still needs some work. But LOTS of cool things to play with. The future is here and I like it. Time to end reliance on indirect measures of the impact of papers and data (e.g., Journal Impact Factor). Time to measure actual impact. And this is a good tool to help do that.


Wednesday, November 28, 2012

Returning to Walt Whitman High School, home of supposed overachievers

And now for something completely different ... But I thought this might have some connection to the theme of this blog here since this was a bit about education ...

Yesterday I was a member of panel of alumni from my high school Walt Whitman High School in Bethesda, MD discussing the book "The Overachievers".

Why on Earth was there a panel of alumni from my high school discussing a book?  Well, there is a course at UC Davis "Integrated Studies Honors Seminar" which was for this quarter discussing the book The Overachievers. The book is by a WWHS alum (Alexandra Robbins) about WWHS students.  Anyway, Sharon Knox, a WWHS alum heard about this course and suggested to the instructor Jim Shackleford the idea of a panel of WWHS alumni to discuss WWHS with the students.  And thus the WWHS panel was born.

I got an email from Sharon a month or so ago inviting me to participate and found out there would be three other WWHS alums who are in the area involved.  Sue Greenwald (ex mayor of Davis and husband of one of my faculty colleagues Michael Syvannen.  Max Chertok - a UC Davis physics professor.  And Kim Addonizio a poet/artist living in Oakland.

Anyway .. the panel discussion was at 4 PM yesterday on campus at UCD.  I showed up a few minutes early, and eventually went into the room where I was the first of the WWHS alumni to arrive.  Eventually the others showed up as did the ~ 100 students and we had a somewhat interesting discussion of Whitman (we covered the 60s, 70s and 80s pretty well with the different people on the panel).  Most of what we discussed was whether we thought WWHS was somehow different in producing overachievers in some way.  Most of the panel felt that it was not really about the school - that it was really more about the demographic (in general this apparently agrees with the message of the book which also said WWHS was no unique in any special way).

Anyway - I don't want to bore people with discussions of WWHS.  But one thing came up in the discussion with the students that was quite interesting and disturbing.  This relates to the excessive march towards having everything in K-12 be about preparing for college and about getting in to college.  Students are clearly more stressed these days about their futures.  They (on average -- not everyone obviously) get tested and prodded and tested some more.  They have coaches and counselors and parents and others all telling them what they need to do.  And it seems they are less and less doing things they are passionate about and more and more doing things they think they should do.  This sounds bad.  Amazingly and sadly I even see this in my kids school.  And my kids are five and seven years old.  In Davis, there is, for example a "GATE" program for the supposedly gifted and talented students.  And kids get tested for this and if they score highly they can move into a completely separate "GATE" program - segregated from the other kids.  This program is very controversially right now in our town (e.g., see here)  and I personally think it should be dumped.  I must say I am pretty shocked by all of this.  Don't we want kids to be able to just be kids.  To have fun?  To play a little bit?  Do they really have to have second graders getting stressed out about how they will do on a test to determine if they are gifted?  Uggh.  I mean - I am all for doing well in school and for education for educations sake.  But to plot out your kids lives when they are seven seems wacky beyond recognition.

Anyway - going to probably expand more into K-12 education issues here on the blog as my kids get more into the school system ...

Saturday, November 24, 2012

A badomics word for good purposes: new paper on the "ridiculome"

Quick post here.  There is a new paper in BMC Biology which uses a bad omics word in the paper and in the title: BMC Biology | Full text | Logic modeling and the ridiculome under the rug.  Fortunately they are using the term to poke a bit of fun at people who think genomics will solve all of their research problems.

Friday, November 23, 2012

A scientific study of gender bias in scientific conferences: new #PLoS One paper from #UCDavis

Well, this is certainly very interesting especially given my recent obsession with gender biases in scientific conferences (e.g., see The Tree of Life: Q-Bio conference in Hawaii, bring your surfboard and your Y chromosome because they don't take a XX) ....  A press release from UC Davis (see here: Science, still a man's world? (VIDEO) :: UC Davis News & Information) describes a newly published study on gender bias in science conferences.  The study was published in PLoS One a few days ago:

Isbell LA, Young TP, Harcourt AH (2012) Stag Parties Linger: Continued Gender Bias in a Female-Rich Scientific Discipline. PLoS ONE 7(11): e49682. doi:10.1371/journal.pone.0049682

The most disturbing piece of data is shows in Figure 2

Figure 2. Proportion of women as first authors of posters, talks, and symposia at AAPA meetings. The average proportion for all presentations with women as first authors over a 21-year period of annual meetings of the American Association of Physical Anthropologists is indicated by the solid black line. F-Org. Symp.: symposia organized by women only; F/M Org. Symp.: symposia organized jointly by women and men; M-Org. Symp.: symposia organized by men only.
So this seems to suggest that when men organize conferences women are much more underrepresented than they could / should be based on #s in the field. Similar to my observations in certain areas.

Some other things I have written on this topic:

Thursday, November 22, 2012

A call, on Thanksgiving, for unrestricted References and Acknowledgements sections for papers

On this Thanksgiving 2012 I am calling for a change in the way we acknowledge the contributions of others to our academic work.  We all stand upon the shoulders of those who have come before us.  And in the digital age we have the power to track much more completely what prior work has contributed to ours and also what people have helped along the way who are not reflected in author lists.  It is time for journals to do more to record these contributions.  So I am making a call here for a few simple things we can all do in this regard:

1. Reference EVERYTHING you can in your works if it is relevant.  

Use a computer program for some of your work?  Make sure you cite the program in some way.  Use some data as a key part of your analyses?  Cite the source of the data.  (For example, in my area people are really bad about citing genome data).  Got an idea from some paper about how to do an analysis?  Cite that paper.  I find it absurd that some journals arbitrarily restrict the number of citations one can use in a paper.  Sure, don't overcite things that are trivial.  Don't overcite yourself either.  But cite everything that matters.

2. Write complete and detailed Acknowledgement sections.  

Describe in as much detail as possible whomever contributed in some way to the work.  Sure, in printed papers a long Acknowledgement section may be a bit much.  But this is the web era.  Many journals already have online methods sections that are longer than those in the printed version.  It is time to do the same thing for Acknowledgements.  

3. Annotate in detail the contributions of authors on a paper.  

Most journals (at least in the sciences) now have a section on "Author's Contributions" although some of them have arbitrary categories one is supposed to use.  Don't follow those silly categories.  Write a section that details what authors ACTUALLY did and put it in your paper.  Many journals will allow one to replace the arbitrary categories with one's own text.  

It is by detailing the actual contributions to one's work that we can really show the spirit of Thanksgiving in academic work. 

Wednesday, November 21, 2012

American Gut Project: Food, crowd sourcing, citizen science, open science, and MICROBES - what could be better?

A press release just came out announcing the American Gut Project: New public gut bacteria study expected to reach around world | University of Colorado Boulder.  From Rob Knight, Jeff Leach and others this project aims to engage the public in a large scale study of the connection between diet and the human gut microbiome.  Read more about it in the press release and I am sure more will come out soon.  Full disclosure - I have agreed to be a collaborator on the project - though as a fully open project I think pretty much anyone could be a collaborator.  Anyone this is definitely worth checking out.

As an aside - this is not the only crowd sourcing microbiome project out there.  I just became aware of another one called uBiome and I am working on getting a guest blog post from the organizers.  The American Gut project has got dozens of the major players in microbiome research involved.  And with Rob Knight being one of the key players one can expect it to big, cutting edge things.  Not sure about the scope / plans of uBiome but hopefully we will find out more soon.

Tuesday, November 20, 2012

Thank you Google Scholar Updates for finding me two new papers to read

Am really liking the Google Scholar Updates system.   Have written about it before: The Tree of Life: Wow - Google Scholar "Updates" a big step forward ... and continue to be impressed.  Today the system suggested two papers for me

Dead on accurate in terms of papers I would be interest in.  #1 is on Drosophila associated microbes and it is a paper from Dmitri Petrov's group: Bacterial diversity associated with Drosophila in the laboratory and in the natural environment.  #2 is on computational normalization of shotgun genome sequence data from Titus Brown and others.  As these are both preprints I almost certainly never would have found them without Google Scholar Updates.

Sunday, November 18, 2012

The evil germy pacifier story is getting out of hand - w/ Dr. Glass misleading the charge

From Wikipedia
Oh for crying out loud.  This is getting out of control.  Two weeks ago I wrote about an over the top story in US News and World Report about pacifiers and microbes: The Tree of Life: Germophobia 101: there are microbes on pacifiers ....  The culprit in this story was a Dr. - Dr. Tom Glass - who was the lead presenter of some study at a meeting.  His study involved counting the number of colony forming units on used vs. new pacifiers.  And low and behold used ones were covered in germs.  Amazingly, this led Glass to say ridiculous things like

In the long run, it may be that what you do now [using a pacifier] may have a lot to do with whether a child ends up developing atherosclerosis or type 2 diabetes.
Completely misleading and deceptive and dangerous I would say.  And alas, the story has been crawling it's way around the web picking up speed.  Now it is at Time.Com with another story about Glass' work: Bacteria on Binkies: A Recipe for Crankiness |  Glass apparently is now blaming biofilms of pacifiers for all the problems.  And again Dr. Glass is (mis)leading the charge against pacifiers.
A lot of times when a child is cranky, the first thing a parent does is reach for a pacifier,” says Dr. R. Tom Glass, the study’s principal investigator and a professor of forensic sciences, pathology and dental medicine at Oklahoma State University. “But what are you using to treat the crankiness? It’s a vicious cycle.
"biofilms can potentially increase the likelihood of colic or ear infections and could possibly heighten the risk of allergies or asthma, says Glass."
The reporter does present some skepticism from parents and from the literature.  But come one - why even report this crap from Glass.  I mean - I am all for keeping babies from getting sick and pacifiers very well may be a source of some nasties.  But let's think about the big picture here.  Parents buy pacifier.  Parents open package.  Parents give to baby.  Baby puts in mouth.  Baby drops pacifier and it gets dirt on it as well as some germs.  Baby puts back in mouth.  Pacifier gets left on counter.  Things from babies mouth grow on pacifier.  Baby puts pacifier back in mouth.  And so on.  Tell me again where the pacifier introduces bad germs to this system?

UPDATE: some reading material

Saturday, November 17, 2012

My new microbe art corner w/ three works by @artologica

Must read microbiome paper of the month: defined microbioata treatment of Cdiff infections

This is a must read: PLOS Pathogens: Targeted Restoration of the Intestinal Microbiota with a Simple, Defined Bacteriotherapy Resolves Relapsing Clostridium difficile Disease in Mice

This is the paper I referred to in a previous post: Mouse study of fecal transplants to treat Cdiff infection.  This post was about a BBC News story that appeared to have jumped the embargo.  And then the news article disappeared and the scientific article was missing.  Thankfully the paper is now out.

The article has gotten some press that was not retracted.
More on fecal transplants and bacteriotherapy from my blog can be found below:

Thursday, November 15, 2012

Microbes, art and a bit of satire all in one place - Design Interactions at the RCA

Got pointed to an interesting site recently - "Design Interactions at the RCA"  This is a program (or as they call it - a programme) at the Royal College of Art in London.  One of the current students - Lana Porter - contacted me about a possible project she was working on involving microbes.  She also pointed me to some past projects connected to microbes from the program.  The two she pointed to are:
  • Viruses, close enemies or distant cousins? | Design Interactions at the RCA. From Mikael Metthey.  It appears to be from a few years ago but I am not sure.  Regardless, it is pretty humorous.  It is basically a description of an attempt to create "more intimate ways to approach the process of vaccination" by having poxteddy bears and cowpox rides and vaccination playgrounds.
  • The Race.  From Michael Burton.  Also from a few years ago. This one is about antibiotics and microbial evolution and the hygiene hypothesis.  
And then browsing around the site led to some other interesting concepts:
Seems like a fun programme (or program) ...

Monday, November 12, 2012

Fermentation microbiomes part 2 from #UCDavis: American coolship ale microbiome

 From Nick Bokulich: This is an image of the "coolship" where the cooling wort
(pre-fermented beer) is left overnight and presumably where wild
microbes are introduced to kick off the fermentation. This is the
morning after, still full of wort.
Just a quick follow up to my recent post on How did I miss this? The botrytized wine microbiome ... from #UCDavis colleague David Mills.  There is a similar paper from the same group also in PLoS One from about the same time: PLOS ONE: Brewhouse-Resident Microbiota Are Responsible for Multi-Stage Fermentation of American Coolship Ale.  What a job --- microbes, ales and wines, and sequencing.  One of the few times when reading a paper where I have said "I wish that was me doing that work." ... must look into getting involved in such studies ...

How did I miss this? The botrytized wine microbiome ... from #UCDavis colleague David Mills

From here.
Fun use of next generation sequencing in this paper: PLOS ONE: Next-Generation Sequencing Reveals Significant Bacterial Diversity of Botrytized Wine.  They used sequencing to characterize the diversity of microbes associated with botrytized wine (wine produced from grapes infected with the mold Botrytis cinerea.  They focused in particular on Dolce wine (not 100% sure what this is but I think it is wine from the Dolce winery ...).  And they focused in particular on the bacteria associated with this wine as it was being produced.  Anyway ... I am no food/drink microbiologist .. but this seems cool.

Saturday, November 10, 2012

Overselling the microbiome award of the month: Integrative medical group of Irvine

Wow.  Just discovered this site: Fecal Transplantation | Integrative Medical Group of Irvine.  Not sure how long it has been out there.  But this is one of the more aggressive and perhaps egregious overselling of the power of the human microbiome that I have seen. They are promoting fecal transplants at their clinic as a way to cure a diverse array of ailments from ulcerative colitis to obesity and imply they can be used for cardiovascular health, emotional status, bone health, and more.  My "favorite" part:
As our understanding of the enormous importance of bowel micro-biota (bacteria) grows, the indications for fecal transplant will expand greatly and public acceptance will follow. But there is no reason for you to wait. Dr. Lee, our naturopathic doctor, is one of only a tiny handful of specialists certified in the use of fecal transplant. She can expertly manage your case.
Yes that is right.  We (the royal We of course) are on the verge of showing that the microbiota does EVERYTHING and therefore, if anything ails you, just wash your troubles away with some shit from a relative.  There is no reason to wait.  Come in to our clinic now.

And for the misleading nature of this site, I am giving this Integrative Medical Group of Irvine my coveted "Overselling the microbiome award."  Previous winners and discussions of this issue are listed below:

UPDATE September 2017

Was just looking back at this post.  Alas the link to the Irvine web site was dead.  But thankfully the Internet Archive indexed this page. See It is from 2013 but may be the same as what I was seeing.

I am copying the text below

Fecal Transplantation

The gastrointestinal (GI) system is largely responsible for the well-being of every other cell and system in the body. It absorbs the nutrients which all cells require, expels toxic wastes, nurtures the complex bacterial bio-matrix which produces essential enzymes and vitamins, protects the body from invading organisms, and participates in critical “cross-talk” with the brain and the immune system.
When the bacterial communities of the intestinal tract become altered or damaged, their essential processes malfunction and the health of the individual declines – sometimes slowly, but at other times with devastating speed. When this happens, we attempt to “heal the gut,” a process that involves elimination diets, healing supplementation and probiotics. This can take many weeks or longer.
Recently, however, a new treatment has been developed that is proving highly beneficial, amazing fast, and in many cases lifesaving. Though fecal transplantation sounds unappealing, this amazingly simple procedure rejuvenates the gastrointestinal (GI) system literally overnight by taking fecal material from a healthy donor (preferably a relative), carefully processing it, and then inserting it into the colon of the patient. This is a simple and safe procedure, and, of course, the donor is thoroughly screened for communicable diseases.
The most common application of fecal transplant is in patients suffering from a serious intestinal infection caused by Clostridium difficile bacteria. Usually infections with C. diff occur following oral administration of antibiotics, and with increasing frequency the resulting infection is resistant to all antibiotic therapies. Lives have been saved and transformed in a matter of days following a fecal transplant treatment.
Exciting novel applications are evolving for fecal transplant. One is for the treatment of ulcerative colitis (UC). Patients on the verge of having their colons removed or patients living in misery with UC have experienced dramatic remissions following fecal transplants.
Another novel application involves the use of fecal transplants in obese patients. It has been discovered that in these individuals, the GI bacteria differ from those found in thin, healthy people. These so-called “fat bacteria” can extract a significantly greater quantity of calories from the same amount of food as do normal bowel bacteria. There is great hope that doing a fecal transplant on an obese individual will stimulate more appropriate bacterial behavior, and weight loss will become much easier.
Data now exists that the bacteria in the gut impacts virtually all aspects of health. Cardiovascular well-being, emotional status, bone strength, as well as immune health are all dependent on a healthy bowel flora.
As our understanding of the enormous importance of bowel micro-biota (bacteria) grows, the indications for fecal transplant will expand greatly and public acceptance will follow. But there is no reason for you to wait. Dr. Lee, our naturopathic doctor, is one of only a tiny handful of specialists certified in the use of fecal transplant. She can expertly manage your case.
If you are interested in learning more about how fecal transplants can improve your health, we encourage you to call our office to schedule an appointment with Dr. Lee.

Teaching kept me from SF Giants playoff games; StubHub glitches are keeping me from my money ..

Well, as if not going to the game wasn't bad enough ...

A few weeks ago, I managed to buy some tickets to some San Francisco Giants playoff games (for the League Championship Series and the World Series). Alas, due to teaching activities for Intro Bio at UC Davis, I was unable to go (when I bought them the dates were not yet determined). I gave some to a neighbor (a belated thank you for them allowing construction workers to use their driveway and yard for months when we had a pool built last summer). And then I sold the others on StubHub. Generally I have always loved Stubhub. Great way to get tickets. Had never sold any there before but it was pretty smooth and painless (except for the relatively large commission but that is another story) and the tickets sold fast (I listed them at ticket price).

And then I waited to payment to go to my Paypal account. And waited. And waited. I finally wrote to StubHub
"Just trying to find out why it is taking so long to get payment from something from a few weeks ago"
The response was surprising:
Dear Jonathan,

Thank you for contacting StubHub.

I understand your concern regarding your payment. I'm sorry it has been delayed. We recently experienced a technical error where MLB payments were diverted to 'Credit My Team Account'. We are in the process of correcting these orders and issuing payments to the default payment method in the sellers account. Due to the widespread nature of this issue, it is taking longer than normal to change the payment method, as each one needs to be done manually. Unfortunately at this point, I am unable to give you a timeframe for receiving your PayPal payment. Rest assured we are working as quickly as possible on this issue.

Important & neglected aspect of lab studies of animals : effect of habitat change on microbiome

By Aaron Logan via Wikipedia 
Very very interesting paper came out recent from some colleagues at UC Davis: PLOS ONE: Routine Habitat Change: A Source of Unrecognized Transient Alteration of Intestinal Microbiota in Laboratory Mice

Abstract: The mammalian intestine harbors a vast, complex and dynamic microbial population, which has profound effects on host nutrition, intestinal function and immune response, as well as influence on physiology outside of the alimentary tract. Imbalance in the composition of the dense colonizing bacterial population can increase susceptibility to various acute and chronic diseases. Valuable insights on the association of the microbiota with disease critically depend on investigation of mouse models. Like in humans, the microbial community in the mouse intestine is relatively stable and resilient, yet can be influenced by environmental factors. An often-overlooked variable in research is basic animal husbandry, which can potentially alter mouse physiology and experimental outcomes. This study examined the effects of common husbandry practices, including food and bedding alterations, as well as facility and cage changes, on the gut microbiota over a short time course of five days using three culture-independent techniques, quantitative PCR, terminal restriction fragment length polymorphism (TRFLP) and next generation sequencing (NGS). This study detected a substantial transient alteration in microbiota after the common practice of a short cross-campus facility transfer, but found no comparable alterations in microbiota within 5 days of switches in common laboratory food or bedding, or following an isolated cage change in mice acclimated to their housing facility. Our results highlight the importance of an acclimation period following even simple transfer of mice between campus facilities, and highlights that occult changes in microbiota should be considered when imposing husbandry variables on laboratory animals.

I personally think that we as a community are going to have to come to grips with the fact that the microbial communities in / on research organisms (of all kinds) may have a profound effect on experimental results.  This may explain many of the differences seen in experiments between facilities or over time within a facility.  In general, I think either controlling the microbes more carefully in lab experiments (e.g., using defined flora) or at least monitoring them is going to be very important to best interpret studies of plants and animals in the lab (or for that matter - in the field too).  Anyway -this paper is a tiny window into one of the ways that controlling for microbiomes may be important in lab studies.

Citation: Ma BW, Bokulich NA, Castillo PA, Kananurak A, Underwood MA, et al. (2012) Routine Habitat Change: A Source of Unrecognized Transient Alteration of Intestinal Microbiota in Laboratory Mice. PLoS ONE 7(10): e47416. doi:10.1371/journal.pone.0047416

Thursday, November 08, 2012

Guest post on "CHANCE" ChIP-seq QC and validation software

Guest post by Aaron Diaz from UCSF on a software package called CHANCE which is for ChIP-seq analyses.  Aaron wrote to me telling me about the software and asking if I would consider writing about it on my blog.  Not really the normal topic of my blog but it is open source and published in an open access journal and is genomicy and bioinformaticy in nature.   So I wrote back inviting him to write about it.  Here is his post:

CHANCE: A comprehensive and easy-to-use graphical software for ChIP-seq quality control and validation

Our recent paper presents CHANCE a user-friendly software for ChIP-seq QC and protocol optimization. Our user-friendly graphical software quickly estimates the strength and quality of immunoprecipitations, identifies biases, compares the user's data with ENCODE's large collection of published datasets, performs multi-sample normalization, checks against qPCR-validated control regions, and produces publication ready graphical reports. CHANCE can be downloaded here.

An overview of ChIP-seq: cross-
linked chromatin is sheared,
enriched for a transcription factor
or epigenetic mark of interest
using an antibody, purified and

Chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq) is a powerful tool for constructing genome wide maps of epigenetic modifications and transcription factor binding sites. Although this technology enables the study of transcriptional regulation with unprecedented scale and throughput interpreting the resulting data and knowing when to trust the data can be difficult. Also, when things go wrong it is hard to know where to start when troubleshooting. CHANCE provides a variety of tests to help debug library preparation protocols.

One of the primary uses of CHANCE is to check the strength of the IP. CHANCE produces a summary statement which will give you an estimate of the percentage of the IP reads which map DNA fragments pulled down by the antibody used for the ChIP. In addition to the size of this signal component within the IP CHANCE reports the fraction of the genome these signal reads cover, as well as the statistical significance of the genome wide percentage enrichment relative to control in the form of a q-value (positive false discovery rate). CHANCE has been trained on CHIP-seq experiments from the ENCODE repository by making over 10,000 Input to IP and Input to replicate Input comparisons. The q-value reported gives then the fraction of comparisons between Input sample techinical replicates that report an enrichment for signal in one sample compared to another equal to the user provided sample or greater. CHANCE identifies insufficient sequencing depth, PCR amplification bias in library preparation, and batch effects.

CHANCE identifies biases in sequence content and quality, as well as cell-type and laboratory-dependent biases in read density. Read-density bias reduces the statistical power to distinguish subtle but real enrichment from background noise. CHANCE visualizes base-call quality and nucleotide frequency with heat maps. Furthermore, efficient techniques borrowed from signal processing uncover biases in read density caused by sonication, chemical digestion, and library preparation.

Monday, November 05, 2012

Germophobia 101: there are microbes on pacifiers; therefore pacifiers cause atherosclerosis & diabetes

Oh my God.  I hope upon hope that the quote in this story was unintended.  The story is from US News and World Report: Dirty Pacifiers May Make Infants Sick: Study - US News and World Report

It is excruciatingly painful to read.  First, the headline is misleading and way out of line.  US News should be reprimanded for this.  There is no evidence presented that pacifiers are making anyone sick.

What is the story about?  At a conference someone(s) presented results of taking used and new pacifiers and chopping them up and seeing what grew on different parts.  And they found - get ready - microbes on them.  And more microbes on the used ones than the new ones.  And they even found some microbes that were apparently resistant to antibiotics.

Scared yet?  You shouldn't be because of course  Fortunately the story does quote on sane person

Dr. Ben Hoffman, medical director of the Children's Safety Center at Oregon Health and Science University's Doernbecher Children's Hospital, said he can't think of an infection a child has had that he would attribute to a pacifier. 
"The majority of things you're going to find on a pacifier are things we'll find on our clothes, normal human flora," said Hoffman. "It's not a reason to demonize pacifiers if people find them useful."

But alas it also quotes the lead author of the study.
Glass doesn't recommend that parents use pacifiers to calm their babies and toddlers. "After doing the study, I say why take a risk? The key is to recognize that pacifiers can cause illness," he said. "In the long run, it may be that what you do now [using a pacifier] may have a lot to do with whether a child ends up developing atherosclerosis or type 2 diabetes."
What? The? Fu$*#? Pacifiers have microbes on them.  Therefore they cause atherosclerosis and diabetes?   Completely, unbelievably insane and irresponsible.  And I think US News should have made it clearer that this is just completely out of line.

Sunday, November 04, 2012

Thank you interwebs: help proving fungi are cool

Well, am teaching three lectures this week on Fungal Diversity for BIS002C at UC Davis. And I decided tonight to ask the internet for help finding cool new stories on fungi. And boy did the internet come through in the clutch. Thanks internet. See Storification of Twitter and Facebook discussions below:

Friday, November 02, 2012

Quick post: nice microbial genomes database: MGBD (hat tip to Google Scholar Updates)

Just discovered this paper: MBGD update 2013: the microbial genome database for exploring the diversity of microbial world.  Seems to be a useful microbial genomes database with some nice associated tools.  Among the potentially useful features:

General Ortholog Table
Select your own organisms for a Custom Ortholog Table
Add your own genome in My MBGD Mode

And more.  Anyway - worth checking out.

I note - I found out about this via Google Scholar Updates:

For more on Scholar Updates see here.

Thursday, November 01, 2012

Story behind the Paper: Functional biogeography of ocean microbes

Guest Post by Russell Neches, a PhD Student in my lab and Co-Author on a new paper in PLoS One.  Some minor edits by me.

For this installment of the Story Behind the Paper, I’m going to discuss a paper we recently published in which we investigated the geographic distribution of protein function among the world’s oceans. The paper, Functional Biogeography of Ocean Microbes Revealed through Non-Negative Matrix Factorization, came out in PLOS ONE in September, and was a collaboration among Xingpeng Jiang (McMaster, now at Drexel), Morgan Langille (UC Davis, now at Dalhousie), myself (UC Davis), Marie Elliot (McMaster), Simon Levin (Princeton), Jonathan Eisen (my adviser, UC Davis), Joshua Weitz (Georgia Tech) and Jonathan Dushoff (McMaster).

Using projections to “see” patterns in complex biological data

Biology is notorious for its exuberant abundance of factors, and one of its central challenges is to discover which among a large group of factors are important for a given question. For this reason, biologists spend a lot of time looking at tables that might resemble this one :

sample A
sample B
sample C
factor 1
factor 2
factor 3

Which factors are important? Which differences among samples are important? There are a variety of mathematical tools that can help distill these tables into something perhaps more tractable to interpretation. One way or another, all of these tools work by decomposing the data into vectors and projecting them into a lower dimensional space, much the way object casts a shadow onto a surface. 

The idea is to find a projection that highlights an important feature of the original data. For example, the projection of the fire hydrant onto the pavement highlights its bilateral symmetry.

So, projections are very useful. Many people have a favorite projection, and like to apply the same one to every bunch of data they encounter. This is better than just staring at the raw data, but different data and different effects lend themselves to different projections. It would be better if people generalized their thinking a little bit.

A soothing microbiome music video of sorts

For all you microbiome geeks out there here is a music video of sorts from Antonio Gonzalez Peña in Rob Knight's lab.