Eisen Lab Blog

#UCDavis Department of Evolution & Ecology Faculty Search for an "Ecologist"

ECOLOGIST, UNIVERSITY OF CALIFORNIA, DAVIS — The College of Biological Sciences, University of California, Davis invites applications and nominations for a tenure-track position in the Department of Evolution and Ecology at the ASSISTANT PROFESSOR level. Candidates must have a Ph.D. (or equivalent) in the biological sciences or related fields. We seek a terrestrial or freshwater ecologist with research interests that will complement and build upon existing faculty strengths to address important ecological questions. We welcome applicants who address important ecological questions at any spatial or temporal scale.   We seek a colleague who is committed to participating in the departmental community through collaborative teaching, research, service and graduate mentoring. Letters of recommendation should specifically address this aspect of the application. The successful candidate will be expected to teach in undergraduate and graduate programs, and should be committed to mentoring and fostering diversity. Applicants should submit materials online at
https://recruit.ucdavis.edu/apply/JPF00130
which contains additional information about the position. These should include: cover letter, curriculum vitae, description of current and projected research, summary of teaching interests and experience, and three publications. Applicants should also provide the information requested for three referees (fourth referee optional). Once entered, applicants will electronically request letters from referees who will then be prompted by email with upload instructions for their letters. Closing Date: Open until filled, but all application materials, including letters of recommendation, must be received by October 15th, 2013 to assure full consideration. Administrative contact: Carla Munoz (camunoz@ucdavis.edu). Faculty contacts: Jay Stachowicz (jjstachowicz@ucdavis.edu), Sharon Strauss (systrauss@ucdavis.edu). The University of California is an Equal Opportunity/Affirmative Action Employer with a strong institutional commitment to the development of a climate that supports equality of opportunity and respect for differences.
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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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Spammy journal Editorial Board invitation of the week – Avens Journal of Food Processing and Beverages

I get lots of semi-Spammy email invites to be involved in various new journals.  Here is one from this week.  I figure – the more I post such things, when people Google for the journal they will sometimes see my posts about how idiotic some of these journals are.  No idea how I ended up on their radar here ..



Dear Dr. Jonathan Eisen,
We are glad to invite you as an eminent editor for the Journal of Food Processing and Beverages (JFPB). Journal of Food Processing and Beverages is an international, non profit, open access, peer reviewed journal that is being recently launched by Avens Publishing Group with a commitment to serve the scientific community.

We are aware of your reputation and distinction in research in some of the fields relating to our journal and that is why you have been chosen as an Editorial Board Member of our Journal of Food Processing and Beverages.

Editorial Board benefits: 

1. Articles suggested by Editors will be provided a 50% discount.
2. We will be conducting conferences yearly; relating to happenings, advancements and breakthroughs in our Journal and editors will be playing a key role in suggesting titles, educating the young scientific community and also promoting our Journal.
3. The article’s fate i.e., both the acceptance or rejection of article is purely dependent on the Editor’s decision and the peer reviewing process will be confidential.
4. We will be providing scientific credits to all the Editorial board members based on their active participation towards our journal.

If you are interested, you can send your details such as: short biography (100 words), C.V, recent passport size photo (to display at our website), and complete working address (Department, University / institute) for our records.

With regards,
Managing Editor
Journal of Food Processing and Beverages
Avens Publishing Group
877 W 23rd st.,
Los Angeles, CA 90007,
USA.

Disclaimer: All works published by Avens Publishing Group are under the terms of the Creative Commons Attribution License and supports the Bethesda statement on Open Access publishing.

Note: This is not a spam message, and has been sent to you because of your eminence in the field. If, however, you do not want to receive any email in future from Avens Publishing Group, then please reply with your request.

——–
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.

——–

YAMMGM – yet another mostly male genomics meeting (series): Plant Genomic Congresses by Global Engage

Just got invited to the “Plant Genomics Congress Asia” meeting. As usual, the first thing I look at now is gender ratio.  From their web site I got a list of their speakers (so far) and their advisory board.  I highlighted in Yellow ones I am inferring are male and in green ones I am inferring are female.  For the meeting the ratio so far is 17:4 male to female.  Not the worst I have seen but still pretty bad.  Though if you look at their advisory board at least the ratio for the speakers is better — it is 17:0 for the Advisory Board.

  1. John Manners, Chief, CSIRO Plant Industry, Australia 
  2. Dave Edwards, Principal Research Fellow, School of Agriculture and Food Sciences, University of Queensland, Australia 
  3. Nagendra Singh National Professor-BP Pal Chair, National Research Centre on Plant Biotechnology, Indian Council of Agricultural Research, India 
  4. Han Zhao, Professor of Biology and Biotechnology, Institute of Biotechnology Jiangsu, Academy of Agricultural Sciences, China 
  5. Huaan Yang, Department of Agriculture and Food (DAFWA), Australia 
  6. Rajeev K. Varshney, Principal Scientist (Applied Genomics) & Director, Centre of Excellence in Genomics, ICRISAT, India 
  7. Apichart Vanavichit, Professor, The Rice Gene Discovery Unit, Kasetsart University, Thailand 
  8. Norman Warthmann, Senior Post Doc, Borevitz Laboratory, ANU College of Medicine, Biology and Environment, Australian National University, Australia 
  9. Chungui Lu Lecturer in Post-Genomics, Faculty of Science, Nottingham University, UK 
  10. Beng Kah (Bk) Song, Lecturer, Monash University, Sunway Campus, Australia/ Malaysia 
  11. Kenneth Olsen, Associate Professor Department of Biology, Washington St Louis University, USA 
  12. Yue-Ie Hsing, Distinguished Research Fellow, Institute of Plant and Microbial Biology, Academica Sinica, Taiwan 
  13. Meilina Ong Abdullah, Breeding and Tissue Culture Unit, The Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB) Malaysia 
  14. Yijun Ruan, Professor and Director, Systems Biology Center, HuaZhong Agricultural University, Wuhan, China 
  15. Sachiko Isobe, Head Applied Plant Genomics, Kaduza DNA Research Institute (KDRI), Japan 
  16. Yuan-Ming Zhang, Professor of Statistical Genomics, State Key Lab. of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, China 
  17. Parveen Chhuneja, Geneticist, Bioinformatics Centre School of Agricultural Biotechnology, Punjab Agricultural University, India 
  18. Shengyi Liu, Professor and Head, The Key Lab of Oil Crops Biology, the Ministry of Agriculture, PRC Department of Genomics, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, China 
  19. Wen-Hsiung Li, Director and Distinguished Research Fellow, Biodiversity Research Center, Institute of Plant and Microbial Biology, Academica Sinica, Taiwan 
  20. Graham King, Director, Southern Cross Plant Science Professor of Plant Genomics and Epigenetics, Southern Cross University, Australia 
  21. Ryan Lister, Professor/ARC Future Fellow, Plant Energy Biology ARC CoE, School of Chemistry and Biochemistry, The University of Western Australia 
  22. Amitabh Mohanty, Lead Trait Discovery, E.I. DuPont India Pvt Ltd. 

Advisory Board:

  1. Robin G Allaby, Associate Professor, School of Life Sciences, University of Warwick, UK
  2. Todd Blevins, Senior Postdoctoral Associate, Pikaard Lab, Indiana University
  3. Roger Bossé, Global Product Line Leader, PerkinElmer
  4. James Coomer, Senior Technical Advisor for Europe. Data Direct Networks
  5. Tamas Dalmay, Professor of RNA Biology, School of Biological Sciences, University of East Anglia, Norwich 
  6. Massimo Delledonne, Professor, Department of Biotechnology & Director, Functional Genomics Center,  University of Verona, Italy
  7. Joe Duran, Director – HPC Systems, Technology Solutions Division, Fujitsu
  8. Alberto Ferrarini , Biotechnology Professional, University of Verona 
  9. Keywan Hassani-Pak, Group Leader Applied Bioinformatics, Computational and Systems Biology, Rothamsted Research
  10. Julin Maloof, Professor, Department of Plant Biology, University of California, Davis
  11. Piotr Mieczkowski, Director of NGS Facility, Research Assistant Professor, University of North Carolina
  12. Stephen P. Moose, Associate Professor, Maize Genomics, Department of Crop Sciences,, Program Leader, Feedstock Genomics, Energy Biosciences Institute, University of Illinois at Urbana Champaign
  13. Lukas Mueller, Professor, Plant Breeding and Genetics, Boyce Thompson Institute, Cornell University
  14. Odd-Arne Olsen, Professor at Department of Plant and Environmental Sciences (IPM), Norwegian University of Life Sciences (UMB) , Faculty of Education & Natural Sciences, Hamar University College (HUC), Norway
  15. Chris Pires, Associate Professor Division of Biological Sciences, University of Missouri-Columbia
  16. Uwe Scholz, Group Leader, Research Group Bioinformatics and Information Technology, IPK
  17. Alan Schulman, MTT Agrifood Research and Institute of Biotechnology, University of Helsinki 
So after checking out this meeting I decided – at their suggestion to check out the meetings in Europe and the USA they are organizing.  The speakers for the US meeting are a whopping 33:4 male to female according to my count and the ratio for the European meeting is about the same (mind you I like some of the speakers – am not blaming them — but this meeting should be avoided in my opinion).  Definitely not impressed with the organizers here or the Global Engage organization behind these meetings.  Uggh. What is wrong with people?  It is really not actually that hard to do better than this.

——–
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.

——–

Institutional repository success story: Master’s on "War Eagles" contributes to amazing ring recovery story

Image from NPR.

So I just heard this amazing story on NPR. “Journey Of The Ring: Lost In WWII, Now Back With POW’s Son.”  In summary – a US Military member David Cox was taken as a POW in World War II in Germany.  While a captive he ended up trading a treasured ring for some chocolate. He returned home and made a replica of the ring but always felt bad about having had to trade the ring for food.  He passed away a few years ago.  Three or so weeks ago, two Americans – Mark and Mindy Turner – were invited to a dinner at the house of Martin and Regina Kiss and it turns out the Kiss’s had the ring.  But they did not know who the original owner was.  So the Turners did some searching based on the inscription on the ring and the figured out who the original owner was and it has now been returned to David Cox’s son.

So – how on earth is this a story connected to institutional archives.  Well, it turns out that the Turners figured out who the original owner of the ring was because their Google searches based on the ring’s inscriptions took them within a few minutes to this Master’s Thesis posted in 2006 at the NC State Digital Repository: War Eagles: A Bird’s Eye View of 305th Bomb Group and the Eighth Air Force from the experiences of David C. Cox and Joseph B. Boyle – NCSU Digital Repository.  The thesis was written by Norwood McDowell, who happens to be the younger Cox’s son in law.  And his thesis was about the elder Cox and had a brief discussion of the ring.

Kudos to all involved, including NC State and Norwood McDowell for making his Masters thesis available.

——–
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.

——–

Jobs in microbial genome informatics in Iddo Friedberg’s lab at Miami University

Two post docs are available in Iddo Friendberg’s lab.

Job 1: Post Doc

The Friedberg Lab at the is recruiting a postdoc to an NSF-funded project to investigate the evolution of gene clusters and operons in bacteria and archaea. This is a bioinformatics postdoc position, and the successful applicant would be required to perform research employing computational biology skills.

Requirements: A PhD in microbiology, bioinformatics, or a related field. Strong publication record in peer-reviewed journals. Strong programming skills (preferred: R, Python, SQL). Strong oral and written communication skills in English. Strong domain knowledge of molecular biology. Salary is competitive and commensurate with experience. The Friedberg lab is a computational biology lab equipped with high-end cluster computers and strong bioinformatics support.

Candidates should send a c.v. and statement of interest, and have three letters of reference sent independently by their authors to Dr. Iddo Friedberg at Friedberg.lab.jobs@gmail.com. All documentation must be in PDF format only. Screening of applications begins immediately and will continue until the position is filled.

Miami University is an EOE/AA employer with smoke- and tobacco-free campuses. Miami’s Annual Security and Fire Safety Report with information on campus crime, fires, and safety may be found at:http://www.MiamiOH.edu/righttoknow. Hard copy available upon request.

Job 2: Bioinformatics Programmer

We are recruiting a bioinformatics programmer to implement and maintain a genomic database web site; implement data management tools including relational database management applications for efficient storage and retrieval of genomic data; perform other duties as related to the position such as data and project management to ensure data are being processed in an efficient and timely manner; contribute to writing scientific manuscripts. Competitive salary offered for suitable candidates.

Required qualifications: BS or BA in Computer Science, bioinformatics, or a related discipline; demonstrated programming experience, particularly in Python and SQL databases; demonstrated web programming experience; knowledge of Linux/Unix; excellent spoken and written communication and documentation skills.

Preferred qualifications: an advanced degree (M.Sc. or Ph.D) or equivalent in Computer Science, Bioinformatics, Molecular Biology or a related discipline; experience in development of bioinformatic algorithms; knowledge of R programming; experience in development of or contribution to open source projects; experience in collaborative software development such as the use of version control software, writing and following software specifications, participation in code review; knowledge of basic molecular biology; experience with genomic browser programming, such as GMOD or equivalent.

Candidates should send a c.v. or resume and have three letters of reference sent independently by their authors to Dr. Iddo Friedberg at Friedberg.lab.jobs@gmail.com. All documentation must be in PDF format only. Screening of applications begins immediately and will continue until the position is filled.

Miami University is an EOE/AA employer with smoke- and tobacco-free campuses. Miami’s Annual Security and Fire Safety Report with information on campus crime, fires, and safety may be found at:http://www.MiamiOH.edu/righttoknow. Hard copy available upon request.

Strange emails about microbes: probiotic water

I get some strange emails about microbes.  Here is one I got today:

Dear Prof. Jonathan,

I am nothing, but I write my wish because of duty for the great future of Probiotics, which shall be big fortune of earth people.

I, by G-d’s grace, made Probiotics Multiplication “Water” at my kitchen to help my sister’s intestine problem.

And I soon found out how many many applications of the Probiotics Multiplication Water shall be opened for most peoples in the earth.

Please invite me at your cost and let me introduce the Probiotics Water and the vary applications in front of your team, then, I will show 100ml spray and mist of Probiotics Water to them.  It would be great great opportunity of your meeting if you will do.

You said in Video of TED website that we have to surround ourselves by good bacteria.
How?  I convince the Probiotics Water Mist and Spray is the answer. Easy and economic valuable answer!

– Probiotics Water’s color is plain, light pale yellow and near transparency white.
Smell is some sour, and disappeared immediately after spray. –

If you have questions, please send me your reply asap.

My smart phone number : XX-XX-XXXX-XXXX /Phone: XX-XX-XXXX-XXXX

Please send me your message before calling. Thanks very much,

XXXXXX, XX
Pohang City, South Korea 

——–
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.

——–

Sloan Research Fellowships in Ocean Sciences

Sloan Research Fellowships in Ocean Sciences

Just received this …

Dear colleague,

As a long-time consultant to the Alfred P. Sloan Foundation, I am reaching out to you today with the hope that you will join us in identifying the next class of remarkable scholars studying the Earth’s oceans. I am hopeful you will share this email and information about the Sloan Research Fellowships in Ocean Sciences with senior leaders at the science programs you support and others at the Moore Foundation.

The Alfred P. Foundation is now accepting nominations for the 2014 Sloan Research Fellowships. The Sloan Research Fellowships in Ocean Sciences, now in their third year, encompass ocean-related disciplines as diverse as microbiology and zoology, chemistry and Earth science. To be considered, the online nomination and submission process must be completed no later than September 16, 2013. To begin the online nomination and submission process, visit http://www.sloan.org/sloan-research-fellowships/apply-online/.

The two-year, $50,000 fellowships are awarded annually to researchers in the U.S. and Canada in recognition of distinguished performance and a unique potential to make substantial contributions to their fields.

To be eligible, candidates must:

· Hold a Ph.D. or equivalent in chemistry, computational or evolutionary molecular biology, computer science, economics, mathematics, neuroscience, ocean sciences (including marine biology), physics, or a related field;

· Hold a tenure track or equivalent position at a college, university or other degree-granting institution in the United States or Canada, and;

· Be no more than six years from completion of their most recent Ph.D. or equivalent, as of the nomination year, with some exceptions for candidates whose careers were disrupted due to military service, child-rearing, or change of field.

The Alfred P. Sloan Foundation welcomes nominations of all candidates who meet the traditional high standards of this program, and strongly encourages the participation of women and members of underrepresented minority groups.

Your help in spreading the word is greatly appreciated.

Closed access irony of the day: Who Will Pay for Access to Research Data? You Will …

Though I would share this with people who read this blog but don’t follow me on Twitter.  

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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.

——–

Summary of Undergraduate Genome Sequencing Project

(cross posted from microbe.net)

With the publication of the 6th and last genome paper to come out of our Undergraduate Genome Sequencing Project I thought this would be a good time to reflect on how it all went.

To summarize, we had a group of undergraduate students go out into the built environment and attempt to find microbes whose genomes had not been sequenced.  They then sequenced and assembled the genomes, followed by authoring a short Genome Announcement publication per genome.  The goal was two-fold, first to give the students a real research experience that encompassed both lab work and bioinformatics.  The second goal was to increase the number of reference genomes from the built environment.

It turned out to take a lot longer than we thought, and involved some dead ends along the way.  However, the project was ultimately a success and the students appreciated being part of a real research project.   I’ve since had several folks ask for details on the project, in order to do the same thing at their institutions.   What we’ve decided to do is create a detailed step-by-step protocol for starting with a swab in hand and finishing with a Genome Announcement publication describing the genome assembly.  In order to achieve this goal, we have a student, Madison Duntiz, here at UC Davis who is going to repeat the process from start to finish using some microbes left over from our Project MERCCURI collections.  Along the way she will document everything in detail and we will publish the results here on microBEnet for anyone to use.

While waiting for that to finish up, I thought I would at least post the outline of the steps that we would recommend for a similar project.  Obviously this is lacking a lot of detail, but I’d be happy to answer any questions while we work on the detailed version.

Basic outline of the protocol

-Collect microbes from your favorite built environment using sterile swabs

-Swab onto solid media plate, and grow the swabs in liquid to be plated out as well (note that the temperature of incubation and the type of media used will strongly influence the kinds of bugs you find)

-Dilution streak colonies of interest.  Dilution streak again (having a mixed culture is bad news)

-Grow colonies up as overnight cultures

-Perform colony PCR using 16S primers directly on the bugs from the overnight cultures.  The resulting PCR fragments get cleaned and then sent for Sanger sequencing either at a University or an outside company.

-Trim and align the resulting reads, and BLAST the consensus sequences to identify the organisms.  In most cases you’ll probably also have to made a phylogenetic tree of the results in order to accurately identify the bugs.  Choose a bug whose genome has not been already sequenced.

-Take that overnight culture and extract genomic DNA.  Where you go from here depends on your resources and budget.  Some people might give this DNA directly to a sequencing center, others (such as ourselves) might choose to do make sequencing libraries themselves.

-Create sequencing libraries, preferably using a kit although there are other options.

-Confirm the quality of the sequencing libraries and normalize between libraries using qPCR.   Submit the barcoded libraries for Illumina sequencing.

-Demuliplex the resulting reads and mentally prepare yourself for genome assembly.

-The process of trimming, error-correcting, assembling, scaffolding, and verifying the assembly is a whole field unto itself.  However, to avoid this morass we used the super awesome A5 Assembly pipeline which does all of those steps for you and creates really high-quality assemblies to boot  (full disclosure, this was developed in our lab… but is free, open-source, and easy to install and use).

-Submit the completed assembly to RAST for gene annotation.

-Submit the assembly to the NCBI, submit the reads to either SRA or someplace like Figshare.

-Take the information about the bug, the data from the assembly, the data from RAST and put together a Genome Announcements publication.  Don’t forget you can’t submit the publication until you have an Accession # from NCBI.

-Submit the paper

-Once the paper is accepted, share your results with the world.  Blog about it and enter the genome into the GOLD database.

 

 

Because it is there? (Why Larry Smarr freezes his feces)

http://www.bbc.co.uk/emp/worldwide/player.swf<!– Hat tip to …

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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.

——–