Author: Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

Faculty position in Microbiology at CSU San Bernardino

Got this by email and thought it would be of interest:

Tenure Track Faculty

Microbiology

The Department of Biology at California State University San Bernardino invites applications for a tenure track position at the rank of assistant professor in the area of microbiology. The successful applicant will develop an independent research program and is expected to excel in teaching courses related to microbiology, medical microbiology, microbial ecology, or immunology at the undergraduate and M.S. levels. Candidates must have a record of published research and show potential for developing and sustaining independent, externally funded research involving both undergraduate and M.S. students. Candidates must have a Ph.D., preferably in the biological sciences; postdoctoral experience is desirable. Application deadline is 1 November 2013, but applications will be accepted until the position is filled. Submit curriculum vitae, statement of research accomplishments and goals, statement of teaching philosophy, and three letters of reference to:

Dr. David Polcyn, Chair

Department of Biology

Attn: Microbiology Faculty Search

California State University

5500 University Parkway

San Bernardino, CA 92407

(909) 537-5305

Email: dreynold@csusb.edu

http://biology.csusb.edu

Really? Nature put the #HeLa genome paper behind a paywall? Time for Nature Publishing Group to return ALL money obtained from genome papers

This is just fucking ridiculous.  As I have written about many many times – Nature Publishing Group many years ago promised to make papers reporting genome sequence data freely available.  They do not generally live up to this promise well.  See for example

Today I discovered that not only are some important genome papers not freely available but one for the ages – the paper on the HeLa genome – reported with much fanfare recently as a triumph of an agreement with the family of Henrietta Lacks – is only available if you pay.

Once again I call on Nature Publishing Group to publicly disclose all financial gains that have come from people paying for the these genome papers and for the money to be returned.
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Faculty position at the Global Health Institute, EPFL, Switzerland in “microbiota of the gut”

Forwarding this:

Dear Colleagues,

Please find attached an announcement regarding an exciting career opportunity on the Microbiota at the Global Health Institute, EPFL, Switzerland.

I would be grateful if you would forward it to the members of your Institution.

With best regards,

Stewart Cole

Global Health Institute

EPFL, Switzerland

Faculty Position in Microbiota of the Gut.pdf

Can academics use the "copyright termination" system to recover academic works?

Heard an interesting story on copyright termination on NPR last night: Taking Back ‘Funkytown’: Songwriters Prepare For A Custody Battle  By Joel Rose.  This in turn led me to a New York Times article on the same general topic: A Copyright Victory, 35 Years Later – NYTimes.com.

The gist of these stories is that it turns out UC Copyright law has a “termination” provision which allows artists / writers / etc to terminate copyright agreements that they made for work they produced.  This is allowed 35 years after the copyright was assigned.  And many musicians are using this provision of copyright law to reacquire some works they made three and a half decades ago.

So – I am asking the world out there – could this same provision be applied to scientific or academic works?  Would this be a way to move a lot of material that is behind a wall back into the hands of authors and/or into the public domain?  I am looking into doing this with work published by my father as a test case (as part of my long struggle of  Freeing My Father’s Publications (since termination rights apparently transfer to family members if the holder passes away as my dad did in 1987).

So – anyone out there know if this termination has been used for scientific or academic works?

UPDATE: Other reading

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Story behind the paper guest post by Corey Nislow (w/ Metka Lenassi) on "Genomics w/o Borders"

Below is another in the “Story behind the paper” series of guest posts here.  This one is from Corey Nislow w/ Metka Lenassi.  If anyone else has published an open access paper on anything relating to this blog and would like to write a guest post on the Story behind the paper, please let me know.

Genomics without Borders: Genome Sequence of the Extremely Halotolerant Yeast Hortaea werneckii 

by Corey Nislow (with Metka Lenassi)

In this guest post (thank you Jonathan!) I wanted to tell the story behind a paper that my colleagues and I published two weeks ago in PLoS ONE. The story also offers an opportunity to talk about what role, if any, a middle author can play in a scientific study.

The story is set in Slovenia a beautiful country which was part of the former Yugoslavia and which is home to about 2 million inhabitants, 2400+ fungal species (thanks Wikipedia) and some very interesting environments. One of these environments is the Secovlje Salterns where one can find the yeast Hortaea werneckii.

A worker harvests sea salt in the Secovlje salterns, July 17, 2010. Some 2600 tons of salt is expected to be produced during the two and a half month season at the salterns.(Xinhua/Reuters Photo)

I hadn’t heard of Hortaea until I started googling around looking for a yeast extremophile that I can grow in the lab to dissect out its nucleosomes to ask questions regarding nucleosome occupancy and transcription in the face of extreme environments. Turns out it was not a crazy idea–

13 years ago a peculiar black yeast Hortaea werneckii was isolated from its natural habitat: waters containing so much salt, it would kill most living organisms instantly. Since then, two small (but enthusiastic) Slovenian groups have tried to understand its halotolerance. This demanded field trips to the beautiful Slovenian coast, but also a lot of hard work and inventiveness to optimizing protocols used for other organisms – and to do it on a low budget. The first important obstacle was actually cultural – to persuade the scientific community that such extreme yeast even exists in nature! You can see it below. We now have ample evidence as Hortaea has been isolated from many seawater-related environments, saline lakes, but also from surface layers of tropical microbial mats in salterns and even from spider webs in Atacama Desert caves. All these different Hortaea strains are now waiting in their freezer (the Ex culture collection) to be analyzed.

Hortaea werneckii growing happily on 2M salt.

The figure below summarizes what was known about halotolerance of Hortaea before the genome sequence was decoded. In brief, high salinity is detected by sensors of the HOG signaling pathway (green arrows), which modulate the expression of salt-responsive genes (underlined green). The expression of other genes also varies; genes with higher expression at high salinity are written in red, repressed genes in blue). The impact of a hyperosmolar environment is countered by increasing the energy supply to drive energy-demanding processes such as export of Na+ and H+, import of glycerol andthe synthesis of compatible solutes. Melanization of the cell wall reduces the leaking of solutes from the cells and restructuring of membrane lipids helps preserve the integrity of the cells. Read this paper if you want to know more: Gostinčar et al, Adv Appl Microbiol. 2011;77:71-96 .

Gostinčar et al, Adv Appl Microbiol. 2011;77:71-96

This critter, as our recent paper reports, is as interesting genotypically as it is phenotypically. The full genome sequence reported in the PLoS ONE paper shows that genome size is 51mB quite a bit larger than its closest relatives, and given the number of gene models detected (20,000!), for all intents and purposes it looks like Hortaea underwent whole genome duplication last weekend!

Piquing my interest, I immediately started searching for the the genome sequence to have a reference to map nucleosome sequencing reads. Turns out, I had requested the strain from Metka years ago, only to find that one of our lab mates, Uros, with whom I was collaborating at the University of Toronto, had performed some of the groundwork on Hortaea for his PhD. But the network connections don’t stop here, I moved to the University of British Columbia last year, and as it happened Hortaea is popular in Vancouver too! Our new colleagues at UBC were working together with the Slovenian team on sequencing and analyzing the Hortaea genome. In fact, the collaboration started in 2005, catalyzed by a poster at the Budapest FEBS conference were Metka, at that time still a PhD student, and Ivan Sadowski started a discussion about the interesting phenotypic switch that Hortaea undergoes between yeast and filamentous forms. So, by virtue of a convergence of curiosity, good luck and generous collaborators I had the good fortune of being an active participant in the study.

So how does this have anything to do with what a middle author does or doesn’t do on a manuscript? And why do I care? 

Well, I recently re-read the comments section of a fellowship application, and ginned up the guts to read the “supervisor/training environment” section. The chief criticism was that I have a lot of papers on which I am not the senior author. So to the skeptics, I would say- even middle authors play important roles in bringing a study to an audience. In my case my self-interests guided my actions, but along the way, I had the chance to learn about an extraordinary critter, and an amazing group of Slovenian scientists. Yeah, I needed the genome sequence, but I was also excited to help drafting the manuscript, have our sequencing facility prepare additional libraries to close some gaps, and now to bring attention to this extraordinary critter.

The genome sequence offers an exciting new start in studies of Hortaea werneckii. Going forward, the Slovenians want to study its transcriptome and proteome in response to increasing salinity. Preparing knock-out mutants is also a must, to find key genes important for halotolerance. We definitely want to take a closer look at all those cation transporters and their functions. It would also be fun to find its mating partner in one of those frozen Hortaea samples. And now that the genome sequence is available to everybody, the research on this extremely interesting species may start to gain more appeal even to researchers beyond the two stubborn Slovenian groups.

Although I might not get to Slovenia in the foreseeable future, I wouldn’t be surprised if one of my graduate students will meet up with the group at an upcoming yeast meeting. This particular student is dragging our lab into evolutionary genomics by trying to see if he can’t get Hortaea to lose some of its genome in long-term culture (I can’t help but think of “Amadeus” where Salieri is telling Mozart that the composition is fine but it has too many notes….). I’m sure the results will be surprising, and am also encouraged to see what our future collaboration will bring.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Nice show on KQED on Inspiring Girls and Women to Code #Diversity #STEM

Listened to a nice show on KQED this AM on my bike ride in to work (note – I listen with one earplug in, and one ear free to hear the world around me, and I listed on relatively low volume …).  We still need to do so much to make STEM fields and related fields more diverse …

Inspiring Girls and Women to Code:

  http://www.kqed.org/assets/flash/kqedplayer.swf

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Bay Area Malaria Meeting (BAMM) – Tuesday 17 September

Bay Area Malaria Meeting (BAMM)

RSVP by phone: monroe

Come join the ‘updated’ local Malaria Meeting to share your research, policy work, ideas on eliminating malaria, etc. Make your voice heard, network, collaborate and have fun!

Date: Tuesday, September 17th, 2013

Location: Amyris Inc, 5885 Hollis St., Emeryville

Street parking available, accessible by Emery-Go-Round & Amtrak

Time: 6 – 8pm

Format :1- (30 min) Keynote, 2- (15 min) presenters, 30min network

The Key to Malaria Control and Elimination,

Roly Gosling,UCSF- GHG

The Effects of Deforestation and Climate Change on Avian Malaria, Ravinder Seghal, SFSU

Light Refreshments will be served

Sponsored by:

http://berkeley-oakland.mosquitosquad.com/

Families that share everything: Health2Fit video on brother helping sister by being a donor for a fecal transplant

I guess today is fecal transplant day. So why not a little news story from Health2Fit about families that share everything …

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Fecal transplants taken up by American Hospital Association in letter to HHS about Medicare/Medicaid

Interesting discussion of Fecal Transplants is this letter from the American Hospital Association to HHS about Medicaid / Medicare: Marilyn Tavenner September 6, 2013 Page 1 of 33 September 6 …

Key text is below:

“FECAL MICROBIOTA TRANSPLANTATION
Fecal microbiota transplantation (FMT), also known as fecal bacteriotherapy, or human probiotic infusion, is a medical treatment for patients with Clostridium difficile (C. difficile) enteritis or ulcerative colitis. C. difficile infection occurs in patients who have been administered antibiotics for a long period of time. The antibiotics destroy important disease-fighting bacterial flora in the intestine. Fecal transplants are believed to restore the bacteria back to normal, and the patient can recover. The fecal transplant works by repopulating friendly flora in the infected intestines. The donated feces is screened for disease and then mixed with a saline solution to the consistency of a “milkshake.” FMT can be performed by various routes including nasogastric (NG) tube, nasojejunal tube, upper tract endoscopy (EGD), colonoscopically or by retention enema. However, based on an editorial published in the Journal of Clinical Gastroenterology (Volume 45, Number 8, September 2011), colonoscopic FMT is the preferred method for the vast majority of C. difficile infection patients, and if carried out early, may prevent development of severe infection.

Effective with the 2013 edition of the CPT manual, the American Medical Association developed the CPT code 44705 (Preparation of fecal microbiota for instillation, including assessment of donor specimen) that includes:

  • development of the intestinal instillate for the recipient; and
  • evaluation of the donor specimen, including the physician review of results of testing the donor’s specimen for infectious pathogens

The CPT manual instructions require that the actual instillation or fecal microbiota transplant be coded separately using CPT 44799 for either oro-nasogastric tube or enema. Additional instruction in the CPT manual identifies that all laboratory testing provided for the patient is to be reported separately. Based on this instruction and the intent of the CPT code 44705, this is an add-on or “list separately in addition to the primary procedure,” which would be the instillation procedure, e.g., the oro-nasogastric tube or enema.


By contrast, effective Jan. 1, 2013, CMS created HCPCS code G0455, Preparation with instillation of fecal microbiota by any method, including assessment of donor recipient, and assigned it to APC 00340, with a payment of $49.64. The payment for code G0455 appears only to cover the work related to the preparation of the donor fecal microbiota specimen, which may also include the review of the donor lab results for presence of pathogenic microbes. However, the payment does not appear to recognize the work to prepare the patient for the implantation or the instillation of the donor microbes, or the work performed and supplies consumed during the instillation procedure. The additional cost to perform this portion of the procedure would include the supplies, e.g., nasogastric tubes (approximately $5 each), enema tubes (approximately $25 each), other disposables including drapes, gloves, gowns (approximate cost of $20); the overhead expenses are not considered in these additional costs. In addition, if the microbiota instillation is performed via colonoscopy or EGD, the payment does not recognize the cost of the endoscopic procedure. This is demonstrated by the CPT codes and corresponding APC payments as follows:

  • Using EGD as method of instillation: Loss of APC 0141 for EGD with code 43200, Esophagoscopy, rigid or flexible; diagnostic, with or without collection of specimen(s) by brushing or washing (separate procedure), with a payment of $623.45 (minus Significant Procedure, Multiple Reduction, if performed with other procedures).
  • Using colonoscopy as method of instillation: Loss of APC 0143 for colonoscopy with code 45378, Colonoscopy, flexible, proximal to splenic flexure; diagnostic, with or without collection of specimens) by brushing or washing, with or without colon decompression (separate procedure), with a payment of $691.32 (minus Significant Procedure, Multiple Reduction, if performed with other procedures).
We recommend that CMS delete code G0455 and replace it with three new G codes:

  1. Create a new G code for “Preparation of fecal microbiota with instillation by oro- nasogastric tube or enema, including assessment of donor recipient,” and place it in a more appropriate APC to include the costs of the supplies. We prefer that a new code be created (rather than revise existing code G4055) since the meaning of the code would be significantly different and would confuse any future data analysis if the same code would include different methods of instillation.
  2. Create a second new G code for “Preparation of fecal microbiota with instillation by upper endoscopy, including assessment of donor recipient,” and place it in APC 0143, Level I Upper GI Procedures.
  3. Create a third new G code for “Preparation of fecal microbiota with instillation by colonoscopy, including assessment of donor recipient,” and place it in APC 0141, Lower GI Endoscopy. “
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Fecal transplant recruiting on Craigslist

See this Craigslist post for the Boston area: Are you a healthy adult, 18-50 years old? – copied below.  It seems that fecal transplants really are everywhere …

 Are you a healthy adult, 18-50 years old? (Massachusetts General Hospital)

Fecal Microbiota Transplant
Healthy adult volunteers 18-50 years old
Involves donation of stool samples and medical screening
Blood draws, complete medical exam
No medical problems
5-7 out-patient visits at MGH
Compensation up to $700 for completion of study
617-724-8625
  • Location: Massachusetts General Hospital
  • it’s NOT ok to contact this poster with services or other commercial interests
Posting ID: 4050676649

Posted: 2013-09-06, 4:04PM EDT

Updated: 2013-09-06, 5:09PM EDT
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–