It may have been a flawed #OpenAccess "Sting" but WE ROCKED IT so submit to our journal …

I suppose I knew this was coming … but did not expect it so soon … see the email I received below.  Focus in particular on the part highlighted in yellow …. 

Dear Colleague, 

British Biotechnology Journal (BBJ) is an OPEN peer-reviewed, OPEN access, INTERNATIONAL journal, inspired from the great OPEN Access Movement. We offer both Online publication as well as Reprints (Hard copy) options. Article Processing Charge is only 50 US$ as per present offer. This journal is at present publishing Volume 4 (i.e. Fourth year of operation). 

2. Transparent and High standard Peer review:
In order to maintain highest level of transparency and high standard of review, this journal presently follows highly respected and toughest Advanced OPEN peer-review system(Example Link1, Link2, Link3, Link4, Link5, Link6, Link7, Link8, Link9, Link10,Link11, etc). We hope that you will appreciate this Advanced OPEN peer-review system, which is expected to give doubtless scholarly benefit and impact to the authors in long run. Additionally we strongly encourage and promote “Post-publication Peer review” by ourcomment section. 

As per a recent report (Link) of Science journal (present Impact factor 31), one of our journal passed a stringent test of quality of Peer review by rejecting a fake article (Link1,Link2, Link3). We applaud the dedication and hard-work of our peer reviewers and editors to maintain the high standard of our journals. It was reported that only few journals (20), out of total 304 journals tested, rejected the fake article after substantial peer review. We are happy that our journal was among these few successful journals along with industry leaders like PLoS One, Hindawi, etc. We believe that the result of this experiment also proved the efficacy of our Advanced OPEN peer review and ‘post publication’ peer review system. Though the report is debated, as it did not include subscription journals, we normally support any effort to improve the quality and transparency of peer review. 

3. Proposed Time Schedule:
Submission to first editorial decision with review comments: 3 weeks
Submission to publication: 6 weeks
State-of-the-art ‘running issue’ concept gives authors the benefit of ‘Zero Waiting Time’ for the officially accepted manuscripts to be published.
4. Abstracting/indexing:
Many respected abstracting/indexing services covered our journals.

  • HINARI
  • (United Nation’s Database)

  • AGORA
  • (United Nation’s FAO database)

  • OARE
  • (United Nations Environment Programme (UNEP), Yale University, etc.)

5. Authors’ profile:
Considering high peer review standard, quality control, etc. our journals have been chosen by academicians of many famous universities, institutes, etc. A glimpse of authors’ profileis provided here

6. Testimonials:
Appreciation of our esteemed satisfied authors is the greatest inspiration behind the hard-work of our editorial team. Some of the testimonials are available here

7. Article Processing Charge (or Publication Charge):
Article Processing Charge (or Publication Charge): Manuscript submitted within 1st July, 13 — 30th September, 2013 will be eligible for 90% discount on normal Article Processing Charge (APC) of 500 USD. (i.e. Effective APC: 50 USD). For more information visit here

7.1. Reprints (Hard copy):
Reprints (Hard copy) are also available at extra cost. For detailed information please see here (Reprint information link). 

8. Sample papers:

  1. Antibacterial and Antiviral Activities of Essential Oils of Northern…..
  2. African Cassava: Biotechnology and Molecular Breeding to the Rescue
  3. Growth Inhibition of Some Phytopathogenic Bacteria by Cell-Free Extracts fromEnterococcus sp
  4. Primary Somatic Embryos from Axillary Meristems and Immature Leaf Lobes of Selected ..
  5. Effects of Initiating Antihypertensive Therapy with Amlodipine or Hydrochlorothiazide on Creatinine Clearance in Hypertensive Nigerians with Type 2 Diabetes Mellitus
  6. Preparation of Protein Extraction from Flower Buds of Solanum lycopersicum for Two-Dimensional Gel Electrophoresis
  7. Diversity of Bacterial Community in Fermentation of African Oil Bean Seeds (Pentaciethra macrophylla Benth) by comparison of 16S rRNA Gene Fragments
  8. The Application Development of Plant-Based Environmental Protection Plasticizer
  9. Genetic Variability, Heritability and Genetic Advance in Pearl Millet (Penisetum glaucum [L.] R. Br.) Genotypes

9. Highly qualified Editors:

  • Prof. Y. Dai,
  • Associate Director of Research, Revivicor Inc. Blacksburg, USA

  • Prof. Viroj Wiwanitkit, Department of Laboratory Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
  • Dr. Jean-Marc Sabatier, Université de la Méditerranée-Ambrilia Biopharma inc., France
  • Dr. Robert L. Brown, Food and Feed Safety Research Unit, USDA-ARS-SRRC, New Orleans, USA
  • Dr. Giuseppe Novelli, Università di Roma Tor Vergata, Rome, Italy
  • Dr. Juan Pedro Navarro – Aviñó, Technical University of Valencia, Spain
  • Dr. Nikolaos Labrou, Department of Agr. Biotechnology, Agricultural University of Athens, Greece.

10. Manuscript submission 

Option 1:
Online submission (recommended): Subcentral (http://www.sciencedomain.org/login.php)
Option 2:
Email attachment to the editorial office at submission@sciencedomain.org.

General Guideline for Authors: http://www.sciencedomain.org/page.php?id=general-guideline-for-authors
To download MS word SDI paper template click here
To download SDI Manuscript Submission form click here
To download Latex paper template click here

with regards,
Ms. Samapika Mondal
British Biotechnology Journal : An OPEN peer reviewed journal
www.sciencedomain.org; E-mail: editor.60@sciencedomain.org
Reg. Office:
UK: SCIENCEDOMAIN international, Third Floor, 207 Regent Street, London, W1B 3HH,UK,Registered in England and Wales, Company Registration Number: 7794635, Fax: +44 20-3031-1429
USA: SCIENCEDOMAIN international, One Commerce Centre, 1201, Orange St. # 600, Wilmington, New Castle, Delaware, USA, Corporate File Number: 5049777, Fax: +1 302-397-2050
India: SCIENCEDOMAIN international, U GF, DLF City Phase-III, Gurgaon, 122001, Delhi NCR, Corp. Firm Registration Number: 255 (2010-11), Fax: +91 11-66173993

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.

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 BiagioliMacKenzie SmithJonathan Eisen.

I am highly skeptical of the CHORUS system proposed by scientific publishers as an end run around PubMed Central

Just read this news story … Scientific Publishers Offer Solution to White House’s Public Access Mandate – ScienceInsider

It reports on an effort by various scientific publishers to create something they call “CHORUS” which stands for “Clearinghouse for the Open Research of the United States.” They claim this will be used to meet the guidelines issued by the White House OSTP for making papers for which the work was supported by federal grants available for free within 12 months of being published.

This appears to be an attempt to kill databases like Pubmed Central which is where such freely available publications now are archived.  I am very skeptical of the claims made by publishers that papers that are supposed to be freely available will in fact be made freely available on their own websites.  Why you may ask am I skeptical of this?  I suggest you read my prior posts on how Nature Publishing Group continuously failed to fulfill their promises to make genome papers freely available on their website.

See for example:

We need to make sure such papers are freely available permanently and the only way to do this is via making them available outside of the publishers own sites.  Pubmed Central seems to be a good solution for this.  I would be happy to hear other possible solutions – but leaving “free” papers under the control of the publishers is a bad idea.

UPDATE 6/27/2013

Saw this Tweet

//platform.twitter.com/widgets.js Seemed potentially really interesting. Read the story and got pointed to a new Nature paper on the ancient horse genome. I guess not so surprisingly, despite the fact that they report a new genome sequence, it is not openly available. We really cannot trust Nature on this can we? They could say “Well, this is a draft genome, and we did not mean to apply our policy to draft genomes.” Well, that would be weird since, well, they have applied this to draft genomes before. And then I decided to search for other examples … and in about ten minutes I found a few. See

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

Quick post – Nature Publishing Group buys into #OpenAccess publisher Frontiers

In case you have not hear – Nature Publishing Group continues to play around with open publishing and other open science initiatives (when they switch some of their big journals to fully OpenAccess I will stop referring to it as playing around …).  The latest is that Nature has bought into the Frontiers publishing group which publishes a series of Open Access journals.  For more on this see:

Hat tip to many people who have sent this info to me.  Not 100% sure what to make of it, but it is interesting …

A day to think, to pause, to ponder

Today is not an easy day for me.

I pause today to think about a person in my life.  A person who was dedicated to science and discovery and improving the human condition.  A person who was idealistic and sensitive and also had some mental health issues.  A person who was pushed over the edge by an overly aggressive, misguided investigation.  A person who became lost in some sort of downward spiral triggered by this investigation.  A person who then took their own life and in one moment created a catastrophic ripple in the world around them.

This person was not Aaron Swartz, though I am thinking of him today too. The person I refer to was my father.  On this day, February 7, 1987, my father Howard J. Eisen took his own life.  I was a freshman in college then.  Enjoying life on my own at Harvard.  Exploring the world of new friends, academic pursuits, and the usual college antics.  And then it all exploded.  The details are a bit of a blur and most are not really important for what I write about here.  But suffice it to say I was devastated.

I flew home to Maryland with my brother and slowly the details emerged.  My father was a researcher at the NIH.  A paper was being prepared for publication by a post doc who worked for a colleague / boss of my father and who my father also worked with.  My father was apparently asked to look at the paper and some “discrepancies” were noted and my father helped launch an investigation into the work.  The NIH panel that was brought in to investigate the work of this post doc was very aggressive – very unpleasant – and even though no accusations of wrong doing were made against my father – the style and tone of the investigation pushed him over the edge.  And he could not dig himself out.  Some people knew he was having trouble with the whole incident but others (e.g., myself) were not in the loop at all.  I knew nothing.  Perhaps people thought I had enough going on as a freshman in college or perhaps it just never came up.  But all I knew was discovered after finding out my father had died, by taking his own life, on February 7, 1987.

Losing my father at the age of 18 was devastating.  Still is.  The fact that he killed himself made it even worse of course.  There were even news stories for a while about it – in the Washington Post, and New York Times, and the Associated Press and Nature and such.  Some of the stories helped in a way because they did not accuse my father of any wrong doing.  For example the Washington Post reported

“Dr. Howard J. Eisen, a respected scientist at the National Institutes of Health, committed suicide at his Bethesda home last week while under pressure from an investigation he helped initiate of alleged scientific fraud by a coworker. 

The suicide has shocked the NIH community and outraged some scientists there, who think that the stress of the investigation triggered Eisen’s death. They view it as a case of the system making a responsible scientist suffer even though he acted aggressively to uncover possible dishonesty in his laboratory. Eisen’s friends and family acknowledged that his personality-he was intensely idealistic and unusually sensitive-made him vulnerable.”

And the Nature article, by Joe Palca, reported “NIH made no allegations against Eisen.” Did these make me feel better?  I suppose.  But of course, not really.  Suicide is brutal for those left behind (and I am sure for those who commit it).  I have never recovered.  But I note – the life and death of my father, and the story of the investigation, have shaped my life.  It is why, when I went to graduate school, my #1 criterion for choosing a PhD advisor was that they were a good, kind person.  After struggling with some of the people I worked with I found such a person in Phil Hanawalt and, really, never wanted to leave his lab.  I see so many examples of scientists and MDs and administrators abusing their positions of power and finding someone who does not do any such things can sometimes be a challenge.

The story behind my father’s death is also why, a few years ago, when I realized my father’s publications were not freely and openly available that I got so angry.  My father had, in a way, died over his research.  And for it to not be available pained me to no end.  When David Dobbs wrote a story about my quest to Free my Father’s publications I felt some peace that I had done something in his name.  And when I finally made them all available a week later, I was truly happy.

The story behind my father’s death is also why, when people have pointed out to me that I have been a bit over the top in critiquing others, that I back off.  And I have tried to get others on the web and in my arena to be much more careful about avoiding personal attacks (e.g, see here).

I also note that the story behind my father’s death is why the death of Aaron Swartz hit home so hard to me.  I knew Aaron a tiny bit (having met a SciFoo many years ago) but not in any deep way.  I read the stories about his JStor download and even wrote about it a little bit.  But I was not aware of the demented, aggressive prosecution of him and when I read about his death I was devastated.  The story reminded me a great deal of my father.  I wrote about Swartz and about the follow up PDFTribute movement (here and here) but it felt a bit awkward since I did not know quite how to discuss my own personal feelings about this story.  So I said nothing.  But now, in tribute to my father, I am trying to not ignore the facts around his death.  They are a part of his life and a part of why I am the way I am.  So I write this post.  And I call for others out there to remember – life is fragile.  Be careful with your words and your actions.  No – one cannot blame everyone – or anyone really – for complex things like suicide.  But we can all do a little bit to improve how we treat others.  And on this day, when I am 44, the same age as my father was when he died, that is what I think about.

My father, Howard J. Eisen

UPDATE 2/8: See my brother’s nearly simultaneously written post about this topic (which we did not discuss – typical – here).

Storification of responses

From iSEEM project: Phylogenetic Diversity Theory Sheds Light on the Structure of Microbial Communities

Quick post.  Another paper is out based on the Gordon and Betty Moore Foundation funded iSEEM project I co-ran with Jessica Green and Katie Pollard.

PLOS Computational Biology: Phylogenetic Diversity Theory Sheds Light on the Structure of Microbial Communities.

O’Dwyer JP, Kembel SW, Green JL (2012) Phylogenetic Diversity Theory Sheds Light on the Structure of Microbial Communities. PLoS Comput Biol 8(12): e1002832. doi:10.1371/journal.pcbi.1002832.

It has one of my favorite paper figures ever.

Figure 1. The local community and metacommunity framework casts local biodiversity of coexisting species in terms of a sampling process from a larger reference pool, or metacommunity. 

And the paper is definitely worth checking out.

10 things you can do to REALLY support #OpenAccess #PDFTribute

I wrote a post earlier today in relation to the #PDFTribute movement: Ten simple ways to share PDFs of your papers #PDFtribute.  I wrote it largely to give people an outlet and information and ideas about how to better share PDFs of their academic work.  I think the more people share the better.

However, I also got shit from my brother Michael – co founder of PLoS on Twitter about how this is partly a “feel good” action.  I do think he underestimates the surge of anger over the death of Aaron Swartz and the momentum right now in the semi-civil disobedience being seen in the #PDFTribute movement.  But I also think he is right in part. So, I thought I would follow up with suggestions for what people should do in the future to really support full and open access to the academic literature.

  1. Only publish in fully open access journals.  See DOAJ — Directory of Open Access Journals.
  2. Do not do ANY work for non open access journals. That includes reviewing, suggesting reviewers, etc. 
  3. Cancel all subscriptions to closed access journals. The subscription model is part of the problem. 
  4. Work for open access journals. 
  5. Embrace openness in other aspects of your academic work. See for example Open science – Wikipedia, the free encyclopedia and Open Humanities Alliance
  6. Learn the difference between “open” and “freely available.” See Peter Suber, Open Access Overview (definition, introduction) and Open Access | PLOS
  7. Reward people in job hiring, merits and promotions for their level of openness.  Do not reward them for closed activities.
  8. Lobby for more open access requirements at the Federal, State, and Institutional level.  Make sure they are not mealy mouthed or mediocre. See What the UC “open access” policy should say for example.
  9. Embrace other changes in scientific publishing such as post-publication review that enable more rapid sharing of publications (see The Glacial Pace of Change in Scientific Publishing). 
  10. Read up on what else you can do (e.g., Peter Suber, What you can do to promote open access) and come up with your own ideas.  Oh and share them.  Openly.

Related posts from The Tree of Life



Other ideas? Please post in comments.


Story behind the paper: Corey Nislow on Haloferax Chromatin and eLife

This is fun.  Today I am posting this guest post from Corey Nislow in my continuing “Story behind the paper” series.  The history of this post is what is most fun for me.  A few weeks ago I received this email from Corey:

Hi Jonathan, I hope this mail finds you well.
I wanted to alert you to a study from our lab that will be coming out in the inaugural issue of eLIFE.
After reading your PLoS ONE paper on the Haloferax volcanii genome (inspiration #1) I ordered the critter, prepared nucleosomes and RNA and we went mapping. Without a student to burden, I actually had to do some work…
Anyhow, we found that the genome-wide pattern of nucleosome occupancy and its relation to gene expression was remarkably yeast like. Unsure of where to send the story, we rolled the dice with the new open access journal eLIFE (inspiration #2) and the experience was awesome. I’m quite keen to pursue generating a barcoded deletion set for Hfx.
here’s the paper (coming out Dec. 10) if you’re curious.

And a PDF of the paper was attached.

And I wrote back quickly in my typically elegant manner:

completely awesome

But then I thought better of it and wrote again

So – can I con you into writing a guest post for my blog about the story behind this paper?  Or if you are writing a description somewhere else I would love to share it

And he said, well, yes.  And with a little back and forth, he wrote up the post that it below.  Go halophiles.  Go Haloferax.  Go open access.  Go science.


Chromatin is an ancient innovation conserved between Archaea and Eukarya  – The story behind the story
By Corey Nislow

My group first became interested in understanding the global organization of chromatin in early 2005 when Lars Steinmetz (now program leader at the EMBL) led a team effort at the Stanford Genome Center to design a state-of-the-art whole genome tiling microarray for Saccharomyces cerevisiae. These were heady times at Ron Davis’ Genome Technology shop and the array was another triumph of technology and teamwork. The array has over 7 million exceedingly small (5 µm²). The history of how this microarray transformed our understanding of the transcriptome began in 2006. As Lars’ group dug deeper, the extent of antisense transcription and its role in the regulation of expression became clear.

The availability of this array and its potential for asking interesting questions inspired me to convince William Lee, a new graduate student in my group (now at Memorial Sloan-Kettering) to embark on a seemingly simple experiment. The idea was to ask if we could use the classic micrococcal nuclease assay to define nucleosome positioning on a DNA template. But rather than using a short stretch of DNA that could be assessed by radioactive end-labeling and slab gel analysis, we decided the time was right to go “full-genome”. Accordingly, the template was all ~12.5mB of the yeast genome. Will systematically worked out conditions appropriate for hybridization, wrote the software to extract signal off the array (we were flying blind as the array did not come with an instruction manual) and producing an output that was compatible with the genome browsers of the time. Will’s computational background proved critical here (and at several later stages of the project). The result of this experiment was a map of the yeast genome with each of its approximately 70,000 nucleosome’s charted with respect to their occupancy (the length of time that the nucleosomes spend in contact with the DNA) and positioning (the location of a particular nucleosome relative to specific sequence coordinates) in a logarithmically growing population of cells (the paper). Both occupancy and positioning regulate access of most trans-acting factors for all DNA transactions. Working with my new colleague Tim Hughes at the University of Toronto, we began to mine this data focusing first on how the diverse occupancy patterns correlated with aspects of transcription, e.g. the presence of transcription factor binding sites, the level of expression of particular genes, and the like. With this data for the entire genome, we could systematically correlate nucleosome positioning/occupancy with functional elements, sequence logos and structural features. Des Tillo, a graduate student in Tim’s lab and now a research fellow with Eran Segal, was able to build a model that could predict nucleosome occupancy. The correlation (R=0.45) was not great but it was miles better than anything that existed at the time. Tim and Eran’s labs, work with Jason Lieb and Jonathan Widom, refined the model to greater accuracy 2009 model.

Our original study (essentially a control experiment to define the benchmark nucleosome map in yeast) has been widely cited- many of these cites have come from what were two opposing camps, the sequence advocates and the trans-acting proponents. The sequence folks posed that nucleosome position is directed by the underlying sequence information while the trans-acting folks see chromatin remodelers as having the primary role. Having last worked on chromatin in 1995 as a postdoc in Lorraine Pillus’ lab (cloning yeast SET1), it has been a scientific treat to be both a participant and observer in this most recent renaissance of chromatin glory.

The protocol

As a reminder, the micrococcal nuclease (MNase) assay relies on the preference of this nuclease to digest linker DNA. By chemically crosslinking histones to DNA with formaldehyde, digesting with MNase, then reversing the crosslinks and deproteinizing the DNA, you obtain 2 populations of DNAs, those protected by digestion (and presumably wrapped around nucleosomes in vivo) and a control sample that is crosslinked but not digested (genomic DNA). The former sample becomes the numerator and the latter the denominator and you take the ration between the two. Initially we compared the microarray signal intensities, now next generation sequence counts are used to define nucleosomal DNA. This cartoon depicts the array based assay, but simply swap in an NGS library step for the arrays to upgrade to the current state-of-the-art.  

In 2007 we were restricted to array-based assays (as were most genomic studies) and frankly, the 4bp resolution of the arrays was pretty amazing. But the introduction of Next-generation sequencing opened up the possibility of charting nucleosomes in worms or wildebeest or almonds, there was nothing to stop you other than the short read lengths at the time. The read length issue has since disappeared as the “short-read” platforms can easily cover the length of a nucleosome protected DNA fragment of ~150bases.

So that brings me to the paper I’d like to highlight today, which asks the question: if (and how) chromatin is organized in the archae, and further, is there any correlation of archae chromatin architecture to gene expression?

My extreme background
Just like the universal fascination of kids with dinosaurs, I was captivated by the discovery of life in extreme environments like boiling water or in acid that could melt flesh on contact. Teaching intro bio, I would try to provoke the students by claiming that discovering extraterrestrial life will be a letdown compared to what we can find on earth. So while my students were occupied with classifying yeast nucleosome and transcriptome profiles in different mutants and drug conditions, I had the rare opportunity to indulge my curiosity. Jonathan E’s talks on the dearth of information on microbes, combined with my re-discovery of the early papers from Reeve and Sandman (see review) had me hooked. Reading the literature was like discovering the existence of a parallel chromatin universe. Archae histone complexes were tetramers (as opposed to the octamers of eukaryotic nucleosome core particles) but most everything else was similar- they wrapped DNA (60-80 bases compared to 147 for yeast) and although archael histones did not share primary sequence similarity to eukaryotic nucleosomes, at the structural level they resembled histone H3 and H4 in eukaryotes.

Working from ignorance
Choosing the particular archaeon to study was dictated by one criterion, the ability to grow it in the lab easily without resorting to anaerobic conditions or similar calisthenics. Again, I was fortunate in that the halophilic arcaeon Haloferax volcanii fit the bill, but more importantly, there was a wealth of literature on this critter, including a well-annoted genome (thanks again Jonathan!) and an impressive armamentarium of genomic tools. Indeed the work of Allers, Mevarech and Lloyd and others have established Hfx. volcanii as a bona fide model organism with excellent transformation gene deletion gene tagging and gene expression tools.


Home for Haloferax volcanii


This photograph shows salt pillars that form in the dead sea which borders Jordan to the east and Israel and the West Bank to the west. The salt concentration in the water can exceed 5M!

So cool, now all we had to do was prepare nucleosomal DNA and RNA from Haloferax, sequence the samples, build a map and see where it led us. With everyone in the lab otherwise occupied, I tried to grow these critters. At first I was convinced I’d been out of the lab too long as nothing grew. Actually I just needed to be a little patient. Then the first cell pellets were so snotty that I aspirated them into oblivion. Finally, I had plenty of pellets and my talented yeast nucleosome group adapted their protocols such that we got nice nucleosome ladders.

This was a pleasant surprise and one we did not take for granted given the high CG content of the genome (65%). We then turned to isolating RNA. Without polyA tails for enrichment, our first attempts at RNA-seq were 95% ribosomal. Combining partially successful double-stranded nuclease (DSN) treatment with massive sequencing depth we were able to get fairly high coverage of the transcriptome. Here’s where Ron Ammar, a graduate student supervised by me, Guri Giaever and Gary Bader stepped in and turned my laboratory adventures into a wonderful story. Ron mapped the reads from our nucleosome samples to the reference genome and found what to my eyes looked like a yeast nucleosome map only at half scale.

Here were well-ordered arrays in the gene bodies and nucleosome depleted regions at the ends of genes. The Haloferax genome is a model of streamlining and as a consequence, intergenic regions are tiny and hard to define. With little published data to guide the definition of archea promoters and terminators the transcriptome map saved us. Ron focused on the primary chromosome in Haloferax and hand curated each transcription start and stop site based on the RNA-seq data. This is when we realized we had something interesting. Here were nucleosome depleted promoters and nucleosome depleted terminators and when we constructed an average-o-gram of all the nucleosome signatures for each promoter on the main chromosome, it looked like this….

The take home

The data strongly suggested that archae chromatin is organized in a matter very similar to eukaryotes. And further, the correlation between gene expression and nucleosome positioning, particularly with respect to the +1 and -1 nucleosomes was conserved. This conservation begs some interesting speculation. According to Koonin and colleagues the common ancestor of eukaryotes and archea predates the evolutionary split that gave rise to euryarchael and crenarchael lineages. Both of these branches have bona fide nucleosomes, therefore it would seem parsimonious to assume that the ancestor of these two branches also organized its genome into chromatin with anucleosomal scaffold. The similarities between the chomatin in archaea and eukaryotes, and the correlation between nucleosome occupancy and gene expression in archaea raise the interesting evolutionary possibility that the initial function of nucleosomes and chromatin formation might have been to regulate gene expression rather than for packaging of DNA. This is consistent with two decades of research that has shown that there is an extraordinarily complex relationship between the structure of chromatin and the process of gene expression. It also jives with in vitro observations that yeast H3/H4 tetramers can support robust transcription, while H2A/H2B tetramers cannot.

It is possible, therefore, that as the first eukaryotes evolved, nucleosomes and chromatin started to further compact their DNA into nuclei, which among other things, helped to prevent DNA damage, and that this subsequently enabled early eukaryotes to flourish. This observation is so exciting to me because it brings up so many questions that we can actually address such as- if there are nucleosomes comprised of histones, where are the histone chaperones? And further- despite the conventional wisdom that archael nucleosomes are not post translationally modified- this remains to be confirmed (or denied) experimentally. If conventional wisdom is correct and archea histones are not post countries post-translational and modified, then when did this innovation arise? There are more than enough questions to keep the lab buzzing!

Publishing the paper
Because I truly believed that this result “would be of general interest to a broad readership” we prepared a report for Science which was returned to us within 48 hours. The turnaround from Nature was even faster. I had received emails from eLIFE several months previously, and after reading the promotional materials and the surrounding press, we took our chances s at eLIFE and hoped for the best. The best is exactly what we got. Within a few days the editors emailed that the manuscript was out for peer review and four weeks later we received the reviews. They were unique. They outlined required, non-negotiable revisions (including a complete resequencing of the genome after MNase digestion but without prior cross-linking) but contained no gray areas and required no mind-reading. With all hands on deck and we resubmitted the manuscript in four weeks and were overjoyed with its acceptance. Of course with N=1, combined with a positive outcome it’s hard to be anything but extremely positive about this new journal. But I think the optimism is defendable- the reviews were transparent, and the criticisms made it a better paper. The editorial staff was supportive gave us the opportunity to take the first stab at drafting the digest which accompanies the manuscript.

NOTE ADDED BY JONATHAN EISEN.  A preprint of the paper is available here.  Thanks to the eLife staff for helping us out with this and encouraging posting prior to formally going live on the eLife site.

What’s next and what’s in the freezer
This work represents the Haloferax reference condition, with asynchronously growing cells in rich, high-salt media. We recently collected samples of log phase cultures exposed to several environmental stresses and samples from lag, log and stationary phases of growth to chart archael nucleosome dynamics. We are also refining a home-made ribosomal depletion protocol to make constructing complementary transcriptome maps considerably cheaper. Finally, it is exciting to contemplate a consortium effort to create a systematic, barcoded set of Haloferax deletion (or disruption) mutants for systematic functional studies.

Mille grazie to Jonathan E. for inspiring me to looking at understudied microbes and for encouraging me to walk the walk with respect to publishing in open access forums. And for letting me share my thoughts as a guest on his blog

The tree of life from Haloferax’s perspective Artwork by Trine Giaever

PhD Comics @phdcomics animated cartoon on #OpenAccess interview of me & Nick Shockey

I assume if you pay any attention to science satire/humor you are familiar with PhD Comics by Jorge Cham. If not, you must check it out. It is simply brilliant stuff. And thus I was completely floored when I was contacted about whether I wanted to be interviewed by Jorge for a video he was commissioned to make as part of Open Access week activities. I mean – I figging say no to almost everything these days but I said yes to this almost immediately. And so I did a phone interview with him and Nick Shockey from SPARC. And then Jorge worked his magic — and here it is.