Eisen Lab Blog

Graduate Student Opportunity in Marine Biology /Environmental Sequencing of micro eukaryotes

Posting a grad student opportunity for a new project I’m involved in – The project will be using high-throughput sequencing techniques to study microbial eukaryotes in Arctic sediments.

Graduate Student Opportunity in Marine Biology / Biological Oceanography
UAF School of Fisheries and Ocean Sciences, Fairbanks, Alaska USA

We are seeking a graduate student research assistant for a project applying high-throughput DNA sequencing techniques in the study of meiofaunal communities in the Arctic. The student will take a lead role in sample processing and data analysis, including both standard microscopic analysis and morphological taxonomy and high-throughput sequencing approaches. Data will be used to assess meiofaunal community structure and diversity in the US Arctic, and identify possible environmental drivers of community structure. Skills developed will include DNA extraction, purification, and next-generation sequencing methods, and analysis of sequence data. Prior experience in molecular methods is desirable, but not essential. The student may also have the opportunity to participate in research cruises in the Arctic.

Prospective students are encouraged to apply at either the MS or PhD level (PhD candidates would be expected to develop additional research objectives that complement the project, and to work with the advisor in pursuing additional funding sources). The position will be based at the University of Alaska, Fairbanks, but the student will be expected to travel for extended periods to University of California, Davis to receive training in sequencing methods and data analysis. Funding is available for 2.5 years, including tuition, stipend (starting at ~$21,000 / year for MS students), and basic health insurance. The successful candidate will be expected to enroll in the graduate program in Spring 2014, but may be hired as a staff research technician as early as Oct. 1, 2013 if available.

To apply:
Application materials and general information about the graduate program are available at http://www.sfos.uaf.edu/prospective/graduate/. Application deadline for spring enrollment is October 15, 2013. Required materials include three letters of recommendation, general GRE scores, and transcripts from all institutions attended. If interested, or for additional information about the project or the position, contact Sarah Hardy (smhardy@alaska.edu) or Holly Bik (hbik@ucdavis.edu).

Search for Executive Director, UCSD Center for Bioinformatics Analysis

Just got this by email. Seems like an interesting job —

———- Forwarded message ———-

Date: Tue, Jul 30, 2013 at 6:49 PM
Subject: Search for Executive Director, UCSD Center for Bioinformatics Analysis
To: jaeisen@ucdavis.edu
Dear Jonathan Eisen,

I am writing to seek your assistance in identying a director of a new center being established at UC San Diego, the Center for Bioinformatic Analysis. This center will establish a world-class program of bioinformatics research, collaboration and service. Its mission is to develop and apply technology for integrating diverse ‘omics data sets and to establish the means by which this information can be translated to the clinic to promote human health and prevent disease. To lead the Center for Bioinformatic Analysis we are looking for an Executive Director who has a PhD in Bioinformatics or related discipline with substantial team management experience in industry or academia. S/he will be responsible for the overall planning, function and long-term support of the Center. Key responsibilities involve interacting with UC San Diego life sciences faculty and engaging them in collaborative research projects; management of Center staff dedicated to collaboration or software development; reporting to UC San Diego faculty leadership and advisory boards; establishing the Center business model and lead in outreach and fundraising efforts. Under the leadership of the Director, the Center will be staffed by several dozen bioinformatics personnel that carry out the key functions of the center. I would greatly appreciate it if you could forward this notice and alert any candidates who might be interested. The job application is online at the UCSD web portal: http://jobs.ucsd.edu/bulletin/job.aspx?cat=search&sortby=rank&jobnum_in=67358&search=bioinformatics Thanks for your help!

 

Misleading microbial headline of the month: Bacteria in Brains Suggest Alzheimer’s-Gum Disease Link

Wow.  Check out this story from Bloomberg: Bacteria in Brains Suggest Alzheimer’s-Gum Disease Link – Bloomberg.  The title suggests that there is some connection between Alzheimer’s and Gum Disease.  And so does the story.  Plus check out these other stories:

All based on the same work.  Sounds like a real connection was made in this new work showing a link between bad dental hygiene and Alzheimer’s, and also between the bacterium Porphyromonas gingivalis and Alzheimer’s.  These would both be a big big deal.  After all – tooth decay is something you can do something about.  And if tooth decay causes Alzheimer’s – then – well – we could probably prevent Alzheimer’s.

Sounds awesome.  Was going to go invest in companies that are working on this topic.  Then I made a dreadful mistake.  I decided to look at the paper that all of this is based on: Determining the Presence of Periodontopathic Virulence Factors in Short-Term Postmortem Alzheimer’s Disease Brain Tissue.

Hmm .. that is weird.  The paper does not seem to have anything in it really closely tied to all the claims in the news stories. Here is the Abstract:

The aim of this study was to establish a link between periodontal disease and Alzheimer’s disease (AD) with a view to identifying the major periodontal disease bacteria (Treponema denticola, Tannerella forsythia, and Porphyromonas gingivalis) and/or bacterial components in brain tissue from 12 h postmortem delay. Our request matched 10 AD cases for tissue from Brains for Dementia Research alongside 10 non-AD age-related controls with similar or greater postmortem interval. We exposed SVGp12, an astrocyte cell line, to culture supernatant containing lipopolysaccharide (LPS) from the putative periodontal bacteria P. gingivalis. The challenged SVGp12 cells and cryosections from AD and control brains were immunolabeled and immunoblotted using a battery of antibodies including the anti-P. gingivalis-specific monoclonal antibody. Immunofluorescence labeling demonstrated the SVGp12 cell line was able to adsorb LPS from culture supernatant on its surface membrane; similar labeling was observed in four out of 10 AD cases. Immunoblotting demonstrated bands corresponding to LPS from P. gingivalis in the SVGp12 cell lysate and in the same four AD brain specimens which were positive when screened by immunofluorescence. All controls remained negative throughout while the same four cases were consistently positive for P. gingivalis LPS (p = 0.029). This study confirms that LPS from periodontal bacteria can access the AD brain during life as labeling in the corresponding controls, with equivalent/longer postmortem interval, was absent. Demonstration of a known chronic oral-pathogen-related virulence factor reaching the human brains suggests an inflammatory role in the existing AD pathology.

Alas, even via UC Davis Libraries I do not have access to the full article.  So my inferences will have to be based on the abstract (note to authors, if you want people to judge your full papers not just your abstracts, well, it would be good to have your paper be available).  From what I can tell – what they showed in this paper is that antibodies that are known to find to lipopolysaccharide (LPS) from P. gingivalis showed positive binding to brain material from a few patients who had Alzheimer’s and did not show binding to brain material from controls.  So let’s ask and try to answer a few questions about this:

  • Does LPS from a specific organism in the brain mean that the organism was in the brain: I don’t think so – LPS could move around?
  • Does binding by the antibody they used mean that there is LPS from P. gingivalis there?  Definitely no – there could be cross reactivity with other LPSs or even other molecules?
  • Did they do any more specific tests (e.g., DNA)? Doesn’t seem like it.

But let us just assume that they really did detect P. gingivalis in the brains of Alzheimer’s patients.  Would this mean PG causes Alzheimer’s? Obviously it does not mean that. Let us even assume (ridiculously) that PG causes Alzheimer’s.  Would this mean the periodontal disease leads to Alzheimer’s? No – PG could come into brains in other ways.

I could go on and on.  There are so so so so so so so many jumps that are needed to go from the limited results presented in this paper to getting anywhere near supporting a hypothesis that periodontal disease causes Alzheimer’s that it makes we want to scream.  The news reporting here is awful.  The scientists involved seem to be overhyping their work to extremes with risky, dangerous possible consequences (e.g., – oh – so you have Alzheimer’s – it’s your fault for not taking care of your teeth … we need more money for dental care to prevent Alzheimer’s; everyone should take prophylactic antibiotics to prevent Alzheimer’s and so on).

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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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Summer microbial ecology course 2014 in Sydney, Australia

Center for Marine Bio-Innovation is accepting applications for its Summer Course in Microbial Ecology for 2014 in Sydney, Australia.

February 17-28, 2014

For more information see http://www.cmb.unsw.edu.au

CMB Summer Course Feb. 2014.pdf

Another genomics meeting featuring men men men and men: International Forum on "Genomics, Innovation and economic growth"

Well this is just peachy.  Saw this tweet

And my first thought was – please – please – please let this meeting have a decent gender ratio. I am so so sick of genome meetings that have gender ratio issues. Alas, then I went to their site: International Forum “Genomics, Innovation and economic growth”

11 plenary speakers. All of them men.  See here.
Forum president: 1 man
Advisory Board: 5 men

Crap crap crap. What is WRONG WITH PEOPLE?

Nothing else to say really.  But I will not be going I guess I can say that.

——–
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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Cool open science project: rOpenSci just got 180K funding boost

Just a quick post here.  Just found out from Carl Boettiger that this cool project “rOpenSci” in which he is involved just got a boost in funding with a grant from the Alfred P. Sloan Foundation – see rOpenSci – What we hope to accomplish with the new funding.  The goals of the project are summarized on their site

“At rOpenSci we are creating packages that allow access to data repositories through the R statistical programming environment that is already a familiar part of the workflow of many scientists. We hope that our tools will not only facilitate drawing data into an environment where it can readily be manipulated, but also one in which those analyses and methods can be easily shared, replicated, and extended by other researchers. While all the pieces for connecting researchers with these data sources exist as disparate entities, our efforts will provide a unified framework that will be quickly connect researchers to open data.”

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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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Worst science by press release of the year: nitrogen fixation in crops

Well, this is one heck of a science – by – press release case.

Was pointed to this press release: World-Changing Technology Enables Crops to Take Nitrogen from the Air which comes to us from the University of Nottingham.  It makes some really bold claims like

A major new technology has been developed by The University of Nottingham, which enables all of the world’s crops to take nitrogen from the air rather than expensive and environmentally damaging fertilisers

And

This ground-breaking development potentially provides every cell in the plant with the ability to fix atmospheric nitrogen. The implications for agriculture are enormous as this new technology can provide much of the plant’s nitrogen needs.

And

Applied to the cells of plants (intra-cellular) via the seed, it provides every cell in the plant with the ability to fix nitrogen. Plant seeds are coated with these bacteria in order to create a symbiotic, mutually beneficial relationship and naturally produce nitrogen.

And

N-Fix is a natural nitrogen seed coating that provides a sustainable solution to fertiliser overuse and Nitrogen pollution. It is environmentally friendly and can be applied to all crops. Over the last 10 years, The University of Nottingham has conducted a series of extensive research programmes which have established proof of principal of the technology in the laboratory, growth rooms and glasshouses.

And

There is a substantial global market for the N-Fix technology, as it can be applied globally to all crops. N-Fix has the power to transform agriculture, while at the same time offering a significant cost benefit to the grower through the savings that they will make in the reduced costs of fertilisers. It is a great example of how University research can have a world-changing impact.

And

The proof of concept has already been demonstrated. The uptake and fixation of nitrogen in a range of crop species has been proven to work in the laboratory and Azotic is now working on field trials in order to produce robust efficacy data. This will be followed by seeking regulatory approval for N-Fix initially in the UK, Europe, USA, Canada and Brazil, with more countries to follow.

Sounds f$*@#$# awesome.  So awesome that it was picked up by multiple news sources including
The only problem is – they don’t present any evidence.  None.  No data.  No paper.  No poster.  Nothing.  It is simply a press release with a bunch of words. Ridiculous.  I think I am going to announce I have a way to not only get all crops to fix nitrogen, but that it will work by telepathy.  This is one of the worst science-by-press-release cases I have ever ever seen.

UPDATE 7/27/13

Richard Conniff, who was the one who pointed me to the PR has a post about this too: http://strangebehaviors.wordpress.com/2013/07/27/best-news-ever-in-agriculture-or-utter-bullshit/

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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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Postdoc position in innovating scholarly communication at #UCDavis w/ me, Mario Biagioli & Mackenzie Smith

7/26/13

Postdoc Position in Innovating Scholarly Communication

A new UC Davis initiative on “Innovating the Communication of Scholarship” is hiring a 3-year postdoctoral fellow, starting September 1, 2013. This is a cross-disciplinary project to study the future of academic publishing, involving faculty from the Center for Science and Innovation Studies, the Library, the Genome Center, and the School of Law (with additional collaborators in Computer Science, English, Philosophy, and the Graduate School of Management). Research topics include open access models, peer review, new forms of quality metrics, data publication, use of social media, and new forms of misconduct.
The successful candidate will conduct research, collaborate on or lead organization of conferences, workshops, pedagogical activities, and grant writing. A Ph.D. is required in a relevant field such as Science and Technology Studies, Library and Information Sciences, Communication, Law, Science, or English. Other disciplines will be considered depending on the specific focus of the candidate?s research and other experience. Qualified applicants will have experience working successfully in teams and managing multi-year projects. He or she will possess excellent written and oral communication and administrative skills.
Salary is based on experience and qualifications according to UC Davis guidelines.
To apply: E-mail a PDF file containing your CV, short description of your research experience relevant to this position, and contact details for three references to Mario Biagioli, MacKenzie Smith, Jonathan Eisen.
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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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Another quick post – condoms and probiotics

Another quick post.  Just read this article in LiveScience about a new PLOS One paper: Condoms May Boost Beneficial Vaginal Bacteria | LiveScience.  Am wondering – when will condoms start coming with probiotics in them?  Anyone out there know if this has been done yet?  I mean, I do not want to oversell the microbiome but hey it seems like there could be something to do here …

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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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Quick post – very interesting interview of Peter Suber by Richard Poynder

For those interested in Academic Publishing and OpenAccess issues this is really worth a read: Open and Shut?: Peter Suber on the state of Open Access: Where are we, what still needs to be done?.  It is an interview of Peter Suber by Richard Poynder.

UPDATE 10 minutes later – not saying I endorse or support everything Suber says (I am much more enthusiastic about gold open access than green OA which I find limited in use).  But the interview is worth a read.

——–
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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