Friday, July 03, 2015

Yet another mostly male meeting (YAMMM) from Cold Spring Harbor

I guess this would go down in "You Can't Make This Stuff Up" or something like that. A few weeks ago, I posted an anonymous guest post about the lack of female speakers at the Programming for Biology workshop at Cold Spring Harbor Labs: Guest post on Yet Another Mostly Male Meeting (YAMMM) - Programming for Biology.  This got a response from Cold Spring Harbor on Twitter claiming they do work to have diverse speakers at their meetings.

Then I got an email last week inviting me to Cold Spring Harbor meeting on the History of DNA Sequencing with a truly awful gender ratio.  So I wrote a blog post about that: Cold Spring Harbor presents the men's only view on the evolution of sequencing.  And also started a discussion about this on Twitter.

And in response to some comments from some of the CSHL Meeting people I decided to look into the past meetings in the same history of science series and was saddened with the incredibly low # of female speakers at all the meetings in this series. So I posted about that ...

And had more discussions on Twitter where CSHL made some claims about these History of Science meetings being a special case (not buying their argument, just reporting what they said).

And I thought I could have a relaxing Fourth of July weekend not spending my time dealing with Cold Spring Harbor Meetings.  And then, well, I got an email from CSHL that I just looked at a few minutes ago.  This email invited me to one of their "CSHL Asia Conferences".


I clicked on the link and when to the meeting site: Biological Rhythms and sadly I got sucked into YAMMM (yet another mostly male meeting) land.  Here are the details on the organizers and presenters as far as I could sort out.  I have labelled people I infer to be likely male in yellow and likely female in green.  (I note I accept that a binary male vs. female representation of gender is less than ideal but I think in general this is a useful thing to look and to make some hypotheses for to assess meetings).

Organizers:
  1. Carla Green, UT Southwestern, USA
  2. Michael Hastings, MRC Laboratory of Molecular Biology, UK
  3. Joseph Takahashi, HHMI/UT Southwestern, USA
  4. Hiroki Ueda, University of Tokyo/RIKEN, Japan
  5. Han Wang, Soochow University, China
Speakers
  1. Joseph Takahashi, HHMI/UT Southwestern Medical Center, USA 
  2. Ravi Allada, Northwestern University, USA 
  3. Joseph Bass, Northwestern University Feinberg School of Medicine, USA 
  4. Deborah Bell-Pedersen, Texas A&M University, USA 
  5. Nicolas Cermakian, Douglas Mental Health University Institute, CANADA 
  6. Xinnian Dong, Duke University, USA 
  7. Yoshitaka Fukada, University of Tokyo, JAPAN 
  8. Carla Green, The University of Texas Southwestern Medical Center, USA 
  9. Jinhu Guo, Sun Yat-Sen University, China 
  10. Fang Han, Peking University People’s Hospital of Beijing, CHINA 
  11. Qun He, China Agricultural University, China 
  12. John Hogenesch, University of Pennsylvania School of Medicine, USA 
  13. Zhili Huang, Fudan University, China 
  14. Takao Kondo, Nagoya University/Div. of Biological Science, JAPAN 
  15. Katja Lamia, The Scripps Research Institute, USA 
  16. Cheng Chi Lee, University of Texas Health Science Center Houston, USA 
  17. Yi Liu, UT Southwestern Medical Center, USA 
  18. Chang Liu, Nanjing Normal University, China 
  19. Hugh Piggins, University of Manchester, UNITED KINGDOM 
  20. Till Roenneberg, Ludwig-Maximilians-University Munich, GERMANY 
  21. Louis Ptacek, HHMI/University of California San Francisco, USA 
  22. Hiroki Ueda, RIKEN Kobe Institute, JAPAN 
  23. David Virshup, Duke-NUS Graduate Medical School, SINGAPORE 
  24. Han Wang, Soochow University, China 
  25. Charles Weitz, Harvard Medical School, USA 
  26. David Whitmore, University College London, UNITED KINGDOM 
  27. Ying Xu, Soochow University, China 
  28. Xiaodong Xu, Hubei Normal University, China 
  29. Erquan Zhang, National Institute of Biological Sciences, China 
  30. Zhangwu Zhao, China Agricultural University, China

So that is 30 speakers.  Only 29 of which could I find information on the web to make a hypothesis of gender.  Of those 29, I inferred 6 - or 20% to be female.  That is just really low for biological sciences.  I am sorry Cold Spring Harbor but you are just not doing a good enough job with diversity.  Scratch that, you are doing a bad job.  Sad to see.  

Thursday, July 02, 2015

Kudos to California Academy of Sciences for Responding (Well) to Gender Bias Issue at Meeting They Are Hosting

Just a quick post of a Storify relating to a meeting at the Calacademy:

Friday, June 26, 2015

Cold Spring Harbor presents the men's only view on the evolution of sequencing

On June 5 I posted a guest blog post by an anonymous person writing about the Programming for Biology workshop at Cold Spring Harbor Labs: Guest post on Yet Another Mostly Male Meeting (YAMMM) - Programming for Biology 


And this post generated some responses including yesterday a series of responses from whomever is behind the Cold Spring Harbor Meetings Twitter account.






Sounds great.  And I retweeted all of these.

And then I got an email invite to a new Cold Spring Harbor Meeting: The Evolution of Sequencing Technology: A Half Century of Progress


With a long long list of speakers.  Alas, the gender ratio here of speakers is abyssmal.  I have highlighted men in yellow and women in green (with the caveat that I always try to giver that assigning gender from names or appearance or records is not always accurate)

  1. Mark Adams, J. Craig Venter Institute
  2. Gillian Air, University of Oklahoma
  3. Shankar Balasubramanian, University of Cambridge, UK
  4. Hagan Bayley, Oxford Nanopore Technologies, Ltd.
  5. David Bentley, Illumina Cambridge, Ltd
  6. Sydney Brenner, Salk Institute for Biological Studies
  7. Nigel Brown, University of Edinburgh, UK
  8. George Brownlee, University of Oxford, UK 
  9. Graham Cameron, Bioinformatics Resource, Australia EMBL
  10. Piero Carninci, RIKEN Ctr.for Life Science Technologies, Japan
  11. Norman Dovichi, University of Notre Dame
  12. J. William Efcavitch, Molecular Assemblies, Inc.
  13. Miguel Garcia-Sancho, University of Edinburgh, UK
  14. Mark Gerstein, Yale University 
  15. Jack Gilbert, University of Chicago
  16. Walter Gilbert, Harvard University
  17. Philip Green, University of Washington
  18. Leroy Hood, Institute for Systems Biology
  19. Clyde Hutchison, J. Craig Venter Institute
  20. James Kent, University of California, Santa Cruz
  21. Jonas Korlach, Pacific Biosciences
  22. Victor Ling, BC Cancer Agency, Canada
  23. David Lipman, NCBI/NLM National Instiutes of Health 
  24. James Lupski, Baylor College of Medicine
  25. Thomas Maniatis, Columbia University Medical Center
  26. W. Richard McCombie, Cold Spring Harbor Laboratory
  27. Joachim Messing, Waksman Institute, Rutgers University
  28. Gene Myers, Max Planck Institute of Molecular Cell Biology & Genetics, Germany
  29. Richard Myers, HudsonAlpha Institute for Biotechnology
  30. Debbie Nickerson, University of Washington
  31. James Ostell, NLM/NCBI
  32. Stephen Quake, Stanford University/HHMI
  33. Charles Richardson, Harvard Medical School
  34. Richard Roberts, New England BioLabs
  35. Jane Rogers, The Genome Analysis Centre, UK
  36. Mostafa Ronaghi, Illumina, Inc.
  37. Yoshiyuki Sakaki, University of Tokyo
  38. Jay Shendure, University of Washington
  39. Melvin Simon, Caltech
  40. Hamilton Smith, J. Craig Venter Institute
  41. Lloyd Smith, University of Wisconsin-Madison
  42. J. Craig Venter, J. Craig Venter Institute
  43. Robert Waterston, University of Washington
  44. James Watson, Cold Spring Harbor Laboratory 
  45. Jean Weissenbach, Genoscope, France
  46. Barbara Wold, Caltech
  47. Huanming Yang, Beijing Genomics Institute, China
That is right.  47 speakers.  4 of which are female.  For a whopping 7.8 % female speakers.  This is one of the most extreme skews I have seen for any meeting.  This truly makes me sick to my stomach.   Since there are plenty of women who have had and still have fundamentally important roles in the field of sequencing and sequencing technology I infer that this most likely reflects some type of bias in the meeting organization and planning process.

The meeting page lists the organizers as
  • Mark Adams, J. Craig Venter Institute       
  • Nigel Brown, University of Edinburgh, UK
  • Mila Pollock, Cold Spring Harbor Laboratory     
  • Robert Waterston, University of Washington
And one of the major sponsors as Illumina.

I think they all have some explaining to do.

One last note - the meeting description says "The opening session will include a tribute to Frederick Sanger, the father of DNA sequencing, and will cover the early efforts in protein, RNA and DNA sequencing."  Really?  The father of DNA sequencing?  Seems perfect for this meeting I guess.




UPDATE 6/29/15 7 PM PST

Apparently this meeting is part of a series on the history of molecular biology.  The meeting page says
The CSHL/Genentech Center Conferences on the History of Molecular Biology & Biotechnology (http://library.cshl.edu/hosted-meetings) aim to explore important themes of discovery in the biological sciences, bringing together scientists who made many of the seminal discoveries that began the field with others whose interests may include the current status of the field, the historical progress of the field, and/or the application of these techniques and approaches in biotechnology and medicine. Previous meetings in the series have included:  
Biotechnology: Past, Present & Future (2008)
History of Restriction Enzymes (2013)
Messenger RNA: From Discovery to Synthesis and Regulation in Bacteria and Eukaryotes (2014)
Plasmids: History & Biology (2014)
So I decided to take a peek at these meetings I started with Biotechnology: Past, Present & Future (2008).

Organizers
  1. Mila Pollock 
  2. Jan Witkowski
Advisors
  1. Sydney Brenner
  2. Peter Feinstein
  3. Lee Hood
  4. Tom Maniatis
  5. Richard Roberts 
Speakers are listed below:
  1. Garen Bohlin
  2. Robert Bud 
  3. Don Comb 
  4. Peter Feinstein
  5. Maryann Feldman 
  6. Herbert Heyneker 
  7. John H. Leamon
  8. Yuk-Lam Lo 
  9. Alan McHughen 
  10. Stelios Papadopoulos 
  11. Rich Roberts
  12. Robert Steinbrook
  13. Kenneth Thibodeau 
  14. Marc Van Montagu
  15. Charles Weissmann 
  16. Julie Xing
For speakers that comes to 14:2 male:female or 12.5 % female



Next I went to History of Restriction Enzymes (2013).

Organizers
  1. Herb Boyer, University of California, San Francisco
  2. Stu Linn, University of California, Berkeley
  3. Mila Pollock, Cold Spring Harbor Laboratory
  4. Richard Roberts, New England BioLabs
Speakers are listed below:
  1. Aneel Aggarwal, Mount Sinai School of Medicine
  2. Werner Arber, University of Basel, Switzerland
  3. Tom Bickle, University of Basel, Switzerland
  4. Herb Boyer, University of California, San Francisco
  5. Jack Chirikjian, Georgetown University
  6. Steve Halford, Bristol University, United Kingdom
  7. Ken Horiuchi, The Rockefeller University
  8. Clyde Hutchison, J. Craig Venter Institute
  9. Arvydas Janulaitis, Institute of Biotechnology, Lithuania
  10. Stu Linn, University of Califoria, Berkeley
  11. Bill Linton, Promega
  12. Arvydas Lubys, Institute of Biotechnology, Lithuania
  13. Matthew Meselson, Harvard University
  14. Rick Morgan, New England BioLabs
  15. Andrzej Piekarowicz, Warsaw University, Poland
  16. Alfred Pingoud, Institute of Biochemistry - Giessen, Germany
  17. Mila Pollock, Cold Spring Harbor Laboratory
  18. Rich Roberts, New England BioLabs
  19. John Rosenberg, University of Pittsburgh
  20. Ham Smith, J. Craig Venter Institute
  21. Bruno Strasser, Yale University & University of Geneva
  22. Geoff Wilson, New England BioLabs
OK that is 21:1 or 4.5 % women. Well, I guess this makes the meeting on sequencing look good.




Organizers:
  1. James Darnell, The Rockefeller University
  2. Adrian Krainer, Cold Spring Harbor Laboratory
  3. Mila Pollock, Cold Spring Harbor Laboratory
Speakers
  1. Arnold Berk, University of California, Los Angeles
  2. Douglas Black, HHMI, University of California, Los Angeles
  3. George Brawerman, Tufts University School of Medicine
  4. Sydney Brenner, Janelia Farm Research Campus, HHMI
  5. Stephen Buratowski, Harvard Medical School
  6. Louise Chow, University of Alabama
  7. Juan Pablo Couso, University of Sussex, UK
  8. James Darnell, The Rockefeller University
  9. Gideon Dreyfuss, HHMI, University of Pennsylvania
  10. Grigorii Georgiev, Russian Academy of Sciences, Russia
  11. Adrian Krainer, Cold Spring Harbor Laboratory
  12. Tom Maniatis, Columbia University Medical Center
  13. James Manley, Columbia University
  14. Lynne Maquat, University of Rochester Medical Center
  15. Matthew Meselson, Harvard University
  16. Melissa Moore, University of Massachusetts Medical School
  17. Bernard Moss, National Institute of Allergy & Infectious Diseases
  18. Arthur Pardee, Dana Farber Cancer Institute
  19. Mila Pollock, Cold Spring Harbor Laboratory
  20. Rich Roberts, New England BioLabs
  21. Robert Roeder, The Rockefeller University
  22. Mike Rosbash, Brandeis University
  23. Robert Schleif, John Hopkins University
  24. Robert Singer, Albert Einstein College of Medicine
  25. Nahum Sonenberg, McGill University, Montré, Quéc, Canada
  26. Joan Steitz, Yale University/ HHMI
  27. David Tollervey, Wellcome Center for Cell Biology; University of Edinburgh, UK
  28. Jonathan Warner, Albert Einstein College of Medicine
  29. James Watson, Cold Spring Harbor Laboratory
So so much better no? 24:5 Male: Female or 17% female (for the speakers).



Finally I checked out Plasmids: History & Biology (2014)

Organizers
  1. Dhruba Chattoraj, National Cancer Institute, Bethesda, MD
  2. Stanley N. Cohen, Stanford University
  3. Stanley Falkow, Stanford University
  4. Richard Novick, New York University
  5. Chris Thomas, University of Birmingham, UK
  6. Jan Witkowski, Cold Spring Harbor Laboratory, NY
Speakers
  1. Peter Barth, Helsby, Cheshire UK
  2. Susana Brom, Universidad Nacional Autonóma de México, Cuernavaca, Morelos Mexico
  3. Ananda Chakrabarty, University of Illinois
  4. Mike Chandler, Université Sabatier, Toulouse, France
  5. Dhruba Chattoraj, National Cancer Institute, Bethesda, MD
  6. Don Clewell, University of Michigan, Ann Arbor, MI
  7. Stanley N. Cohen, Stanford University
  8. Fernando de la Cruz, Universidad de Cantabria, Spain
  9. R. Curtiss III, Arizona State University, Tempe, AZ
  10. Julian Davies, University of British Columbia, Canada
  11. Stanley Falkow, Stanford University
  12. Laura Frost, University of Alberta, Edmonton, Alberta, Canada
  13. Barbara Funnell, University of Toronto, Toronto, Ontario, Canada
  14. Mathias Grote, Technische Universität Berlin, Germany
  15. George A. Jacoby, Lahey Clinic, Burlington, MA
  16. Mark Jones, Life Sciences Foundation, San Francisco, CA
  17. Saleem Khan, University of Pittsburgh
  18. Bruce Levin, Emory University, Atlanta, GA
  19. John Mekalanos, Harvard Medical School
  20. Marc van Montagu, Ghent University, Belgium
  21. Richard Novick, New York University
  22. David Sherratt, University of Oxford, UK
  23. David Summers, University of Cambridge, UK
  24. Chris Thomas, University of Birmingham, UK
  25. Eva Top, University of Idaho, Moscow, ID
  26. Gerhart Wagner, Uppsala University, Sweden
  27. Michael Yarmolinsky, National Cancer Institute, Bethesda MD
  28. Peter Young, University of York, UK
That comes to 24:4 for speakers or 14% female.



Notice any patterns?  The totals for these meetings come to 17 women out of 142 speakers.  Or ~12 %.  That is a dismal record for Cold Spring Harbor Labs and certainly does not convince me that they are trying at all to have diversity represented at their meetings.  I note - I truly love many things about CSHL.  This is definitely not one of them.






UPDATE 2 - Some discussion of this post on Twitter









UPDATE 3: Made a Storify w/ some of the discussions

Wednesday, June 17, 2015

Hoss Cartwright from Bonanza rocks the science world by joining many editorial boards

A few years ago I wrote about a brilliant and scary real world satire done by Burkhard Morgenstern:

Scary and funny: fake researcher Peter Uhnemann on OMICS group Editorial Board #JournalSPAM | The Tree of Life



Well he has done it again.  This time he has gotten a Hoss Cartwright, a fictional character from Bonanza onto the editorial board of many journals.






There he is listed as 

Dr. Hoss Cartwright, Senior Research Fellow, Ponderosa Institute for Bovine Research, Nevada, United States.

A little Googling found this blog post with more detail


So funny and painful at the same time.


Wednesday, June 10, 2015

Guest Post on Open Source Hacker Insulin by Anthony Di Franco

Last night I had a minor freak out episode.  My insulin pump alarm sounded at like 1:30 in the morning (I have type 1 diabetes). It was out of insulin (well, the alarm said "No Delivery" which is what it does when it is out of insulin.  So I got up, barely alert, and went to the fridge to get a bottle from my insulin supply.


This is not a usual occurrence.  Usually, I pay attention to the warning alarms saying my pump is running low.  But this time I had ignored them.  I guess I thought it would last through the night.  Oops.  But, in the grand scheme of things, this is not that big a deal.  All I have to do is get a new cartridge for the insulin, fill it, and then rewind the pump and load the new cartridge and prime the pump.  Except, this time, I took out the last bottle I have of insulin for my pump from the fridge, and as I turned around to the kitchen island, my hand carrying the insulin wacked into the fridge door, and the bottle flew out of my hand.  It went up a bit and then headed down to our brutally hard tile floor.  I instinctively reached out with my foot and somehow the bottle landed on my foot, not the floor (this is probably related to the daily soccer I have been doing with my son for the last year or so).  My foot-eye coordination never used to be so good.  And thankfully the bottle did not break.  And I loaded up my pump and primed it and headed back to bed.  But I could not sleep.  I was wondering - what would I do if I ran out of insulin or my last bottle broke.  I guess I would go to a 24 hour pharmacy or an emergency room.  Or I would use the now expired back up insulin I had in the fridge.  And then I wondered, what would I do if I could not get any insulin from a drug store or a hospital.

It seemed to me that the best solution would be to have some sort of freeze dried supply of insulin at home that I could rehydrate in an emergency.  So I started Googling that.  And not much came up that seemed right.   And since I was pretty tired, I onyl spent a few minutes at the computer and then I went back to bed.  But to say this ate at me would be an understatement.

This morning I got up, not as early as normal and took my son to school and then headed off to this workshop that was happening on campus hosted by my ICIS (Innovating Communication in Scholarship) Project on "The Social Life of Medical Data"


And bizarrely and amazingly, the topic of making DIY insulin came up part way through the meeting.


What a coincidence. Although the speaker said he was not going to focus on this, after I posted the Tweet, a response came implying that someone was working on this
Well, wow. I had no idea. It makes sense, but I had no idea. And I wondered, is this anyone I know at the Counter Culture Labs doing this. And a few minutes later the answer came to that when I got an email from Patrik D'haeseleer - a friend, colleague, collaborator, and co-author
Hi Jonathan,  
We're actually trying to get Anthony's piece on Open Source Hacker Insulin guest posted somewhere before our kickstarter for Counter Culture Labs ends tomorrow (under the motto "if it's worth doing, it's worth doing last-minute")  
Would you be interested in hosting it as a guest blog post?

And so I said yes.  And, well, here it is.


Open Source Hacker Insulin

Anthony Di Franco


The effects of untreated diabetes include blindness, impotence, nerve damage and necrosis in the extremities, kidney failure, cardiovascular disease, coma, and death—all good reasons to assure the broad and consistent availability of insulin with decentralized production. Illustration by Zach Weiner of "Saturday Morning Breakfast Cereal."

Hi, I'm Anthony Di Franco. I'm a member of Counter Culture Labs, a biohacker collective in Oakland. (We're currently running a Kickstarter campaign to cement the core capabilities we need to pursue research – more on that below!) I also have type I diabetes. My general interest in biohacking is part of my interest in technological STEMI compression: making technology more efficient and effective and making it work at smaller scales, so that it empowers individuals more and more. My more specific interest is in doing this for the technologies that treat diabetes: mainly those for measuring blood glucose levels and making, purifying, and administering insulin. I've written previously about these topics in Biocoder magazine, among several others, where I suggested a variety of possibilities that might be well-suited to decentralized hackerspace development.


Right now I'd like to focus on insulin production and purification, without which measurement is mostly moot. The goal of producing insulin aligns well with the goals of the broader DIYbio movement for two reasons. First, because recombinant insulin was the first major commercial success of synthetic biology at scale, and set an early example of tools and techniques that shaped the future development of biologics. Second, irrespective of the role they happened to play in history, the tools involved are fundamental to biology and medicine and cover the core functions needed for all serious DIYbio research and other community goals: production and purification of biologics.

Open sourcing treatments is also important because pharmaceuticals in general and insulin and insulin pumping specifically suffer from perverse economic incentives that, at least in part, favor keeping people on the treatments with the most disposable or consumable supplies possible, at the highest price relative to the cost of manufacturing. In terms of the famous razor/blade business model, patients are the razors, and the treatments we need are a long stream of blades with a reliable revenue stream attached. Open source efforts could develop incentives more attuned to encouraging innovations that improve patient outcomes and constitute progress toward a definitive cure, in contrast with the current model which encourages corporations to sit on profits harvested by keeping patients addicted to consumable supplies.

With all that in mind, I'm pleased to announce a new collaboration between members of Counter Culture Labs and Arcturus Biocloud to develop generic insulin. Despite there being no formal barriers to its development, there remains no generic insulin on the market, a perplexing puzzlement pondered in context by Jeremy A Greene in his article in the New England Journal of Medicine. Now, we're preparing to address this problematic situation directly. Arcturus biocloud will provide the means to economically produce the insulin, but we'll still need to develop the means to purify it, eventually to the point where we need not fear the catastrophic consequences of injecting it in impure form – fulminant or chronic allergic reaction to insulin, both of which carry fatal risks. Even though we’re producing the insulin for research purposes only, and certainly aren’t intending to inject it into any living beings in the foreseeable future, a main goal is to demonstrate that we can achieve usable levels of purity in a DIY setting, and to document how we do and share the knowledge. To do that, we'll need to equip Counter Culture Labs with the basics for isolating and purifying biologics, and for that we'll need our kickstarter campaign to succeed. Fortunately, we’ve recently met our base goal, which will let us cover the basics of staying in the building and keeping things up to code. But we’ll still need much more to equip ourselves to work on projects like insulin purification, so we hope we can rely on your support as we pursue our stretch goals.

Please also consider becoming a member and donating via our regular website after our kickstarter ends as that is how we fund DIY insulin and projects like it in the long term.


Anthony Di Franco works at the intersections of complex adaptive systems, economics, and computing. He is a board member of the East Bay biology hackerspace, Counter Culture Labs, where he teaches and organizes events on topics at the intersection of computation and biology. He is also the author of the transgressive historical wuxia manhua, Three Sovereigns.

Monday, June 08, 2015

Guest post by Katie Dahlhausen on her project on "The effect of antibiotics for chlamydia on koalas and their microbiomes"

This is a guest post by Katie Dahlhausen, a PhD Student in my lab.


Koala populations across Australia are on a rapid decline due to many culprits including habitat loss, being hit by cars, attacks by dogs, and the Chlamydia infection. Yes, that’s right, Chlamydia. And when koalas are brought into wildlife hospitals, they are treated with antibiotics to cure their Chlamydia infection. Although ridding koalas of Chlamydia, the antibiotics also kill off important gut microbes that are essential to the koala’s life biology. Koalas eat a diet solely of eucalyptus leaves, which would be poisonous to the koalas if it wasn’t for the tannin-protein-complex-degrading enterobacteria that break down the toxic components of the koala’s diet. Brace yourself, because the koala’s biology gets even more interesting! Mother koalas feed their young joeys a substance called pap, a fecal matter more concentrated in nutrients and microbes than normal feces. This form of a natural fecal transplant allows the joeys to colonize the critical gut microbes necessary for them to eat noxious eucaplytus leaves. But what does this mean for joeys whose mothers have been administered antibiotics?

My name is Katie Dahlhausen and I am A PhD student in Jonathan’s lab. I am crowd-funding a project to study this fascinating koala biology, as well as investigate alternative infectious disease treatment where antibiotics are not a viable option. Want to help out these adorable critters? You can support the Indiegogo campaign here, which is live until June 16, 2015. More information about the project is available on the crowdfunding page, and in these recent articles published in Scientific American and the Washington Post.

So how did I get into this project? Well, When I was at the Australia Wildlife Zoo in Australia last September, there was a sign next to the koala exhibit with picture of a joey whose mouth was covered in a brown substance. The sign read something like "It's not chocolate!" and explained the pap part of the koala's biology.



The moment I read this I knew there was some fascinating microbiology questions that were begging to be answered. While researching the microbiology behind this behavior, I found a study the recorded the detrimental effects antibiotics had on a koala's eating habit and inability to maintain weight, but the question of how antibiotics were effecting the microbial composition of koala's guts remained unsolved. That is how this whole project started. Like most people, I think koalas are cute and appreciate how iconic they are to Australia. Otherwise, I'm not very attached to koalas - they are actually quite mean and antisocial! But koalas are a fantastic model system - one food source, plenty of sampling opportunities (in Australia at least), frequently given antibiotics, and clear mechanism of the transfer of microbes from mother to offspring. The implications of the study are vast, but are aimed at the care for animals in captivity and foster changes in how/when we administer antibiotics.

Sunday, June 07, 2015

Guest post from Student Alex Martin on Kittybiome & Animal Shelters

We are nearing the end of our Kitty Kickstarter to fund research on the microbiome of cats (only three days left).  We have received some requests to learn more about our work with animal shelters. Here is a blog post by Alex Martin, a UC Berkeley junior who is working with us to study shelter cats in Berkeley.



The Berkeley Animal Shelter takes in all cats from within Berkeley city limits. Thus, cats who once varied markedly with regards to diet and home environment come to live under a fairly uniform set of conditions. It typically houses between fifteen and forty cats, but has held as many as seventy during the peak of breeding season. Recently we have begun collecting samples from cats at the Berkeley shelter in order to better understand their gut microbiomes.

A major dichotomy in the shelter cat population is the one separating house cats from feral cats. Both are considered domestic cats, members of the species Felis catus. If a kitten during its first few months of life is not exposed to humans, it develops behaviors to facilitate surviving in the wild, and grows up to become a feral cat. Some see feral cats as a nuisance, but the animals also tend to live difficult lives, enduring food shortages and a lack of medical care. Thus, a relatively new effort referred to as “trap-neuter-return” (TNR) aims to spay and neuter feral cats to slowly and humanely diminish the size and number of feral cat colonies. Differences in the gut microbiomes of feral cats versus their tamer counterparts is perhaps expected, as the two groups have vastly different diets and levels of environmental exposure. However, these differences have yet to be characterized.

In addition to the differences between feral and house cats, a small but important FIV (Feline Immunodeficiency Virus) population can potentially serve as an interesting point of comparison. Much like Human Immunodeficiency Virus, FIV attacks the immune system of infected individuals, making them markedly more susceptible to other infections. We think that this virus will affect the microbiome of FIV-positive cats in measurable ways. By identifying any differences, we will gain a better understanding of FIV as a whole and will hopefully be better positioned to one day develop more effective methods of treatment.




Geronimo is one Berkeley shelter cat whose gut microbiome will be analyzed. He was picked up as a stray just a few blocks from the shelter, and is three years old. Geronimo is exceptionally friendly, and loves playing with his wand toy and hiding in his cat tree to nap. He gets along well with other cats and was even introduced to a rabbit without incident. After spending about two weeks in the shelter, Geronimo was adopted into a loving home.

Friday, June 05, 2015

Guest post on Yet Another Mostly Male Meeting (YAMMM) - Programming for Biology

I have posted on Twitter and other places saying that I would be willing to share here anonymous postings about meetings with skewed gender ratios.  I generally am not overly fond on anonymity on the web but realize it has some very important and powerful uses, including protecting people from retribution.  So in the case of meetings with skewed gender ratios, I know from personal experience that posting about them can lead to serious vitriol, threats, and possible repercussions.  I feel confident enough in my status and position to mostly ignore these responses but I know that not everyone is so blessed.

So - here is one such anonymous post I received.
-------------------------------------------------

Last year I was looking around for good workshops to learn programming for biology
(http://programmingforbiology.org/index.html) and
about genome assembly and annotation. I came across the Cold Spring Harbor Laboratory
course called "Programming for Biology" and applied as they have a good reputation.
I was happy to get in and overall really enjoyed the course. I learnt how to program in
Perl (not Python what I regret a bit), a lot of background on downstream genome analysis
and had a mostly pleasant time. An interesting slogan of the meeting was
"It's not only what you learn here, but also who you meet that makes this workshop so special"
(I am paraphrasing here a bit). Great! But wait are all big players in the field of bioinformatics
guys?

Out of the 10 Guest Lectures ALL were male.

  • Scott Cain             Ontario Institute for Cancer Research
  • Brian Haas            Broad Institute
  • Winston Hide        Harvard School of Public Health, South African National Bioinformatics Institute
  • Tomas Marques     Universitat Pompeu Fabra
  • Barry Moore          University of Utah
  • William Pearson    University of Virginia
  • James Robinson     Broad Institute
  • Michael Schatz      CSHL
  • Jason Stajich          University of California, Riverside
  • Paul Thomas          University of Southern California
Only 2 out of the 7 instructors and tutors were female

  • Simon Prochnik DOE - Joint Genome Institute, Walnut Creek, CA
  • Sofia Robb         University of California, Riverside
  • Steven Ahrendt University of California, Riverside
  • Dave Messina Cofactor Genomics
  • Shawn Rynearson University of Utah
  • Deborah Triant University of Virginia
  • Ken Youens-Clark University of Arizona


This means only 2 out of 17 teachers were actual women. This together with the fact that
the meeting was also sold as 'who you meet here is important' was the most disappointing
fact. There are so many talented and great female bioinformatics out there it would be
great to see at least some of them present at this workshop in 2015.

P.S.: Don't get me wrong Simon and Sofia are great and organize a lovely meeting. So this
goes under the category 'even when it hurts'.

Thursday, June 04, 2015

Holly Ganz @hollyhganz on Why She Started the @Kittybiome Cat Microbiome Project

The Story Behind the Launch of the Kittybiome Cat Microbiome Project

Guest Post by Holly Ganz (Project Scientist in the Eisen Lab)



Recently a group of us launched a Kitty Kickstarter campaign where we offer to sequence the bacteria in your cat’s gut microbiome as part of a long term research project to learn more about how microbes may affect cat health, behavior and evolutionary history (and vice-versa). Jonathan has written about the origins story here. This project complements our interests in the microbiology of animal shelters and the evolution of bacterial communities in the Felidae. In addition, we thought that other people like cats too and might be interested in learning more about the hidden life of their cats. We have had an overwhelming response that vastly exceeded our expectations (and we are still welcoming more kitty “pawticipants”).



We have been asked “Why cats?” Personally I think it’s hard not to be fanatical about cats. The diversity of cats is astonishing and most people agree that cheetahs, leopards, lions and tigers are amazing. And when you see a lion in the wild for the first time, it’s hard not to see some of your house cat in there, in the way that it walks, naps, yawns, and even pounces (but not so much the roar). Also it’s really interesting that domestic cats have been associated with people for something like 10,000 years. Several years ago I decided to take what I learned from studying microbial ecology in soil (and how it might affect the transmission of anthrax in zebras) and apply it towards understanding the microbial ecology of the animals themselves. I believe that research in the microbiome of cats (and humans) will eventually lead to useful interventions.

In our kittybiome project, we aim to sequence the gut microbiome of 1,000 cats and by doing so begin to capture the variation in gut bacteria in different populations of cats (both domestic and wild). In domestic cats, we will compare cats living in houses with cats living in shelters and feral cats. We are starting to compare cats with different health conditions and have had some cats with diabetes and IBD join the project. This aspect of the project is really important because these conditions are fairly common and there is a lot of room for improvement in how cats suffering from IBD in particular are treated.



We are also collaborating with Adrian Tordiffe at the University of Pretoria, South Africa and the Africat Foundation on a study on how the diet of captive cheetahs might affect the gut microbiome. Here we hypothesize that the unnatural diet of captive cheetahs produces changes in the gut microbiota that may result in some of chronic diseases common in captive cheetahs.




In addition to being fanatical about cats and passionate about poop, I am especially interested in how social behavior affects the composition and function of microbial communities in cats (in their poop and their anal glands!). (My life was changed by reading about hyena scent gland bacteria.) The evolution of the interaction between cats and their symbiotic scent gland bacteria fascinates me. In the Serengeti, residential territorial cheetahs have been observed scent marking on an hourly basis. Domestic cats are really interesting because feral cats form social colonies. The only other cats that are social are lions (who form prides) and cheetahs (who form coalitions). We are comparing these cats with some social structure with some of their close relatives who are solitary (black-footed cats, leopards, and pumas).

Monday, June 01, 2015

Guest Post: 5 Things You Probably Didn't Know About Jonathan Eisen


5 Things You Probably Didn't Know About Jonathan Eisen 

  1. He doesn't know how to play Minecraft
  2. He mailed grass when he was a little kid
  3. His new phone is "precious" to him
  4. He loves Let it Go and Taylor Swift
  5. He has very ugly pink boots 
by his bored daughter A. I. Eisen