August 2011 – Page 2 – Jonathan Eisen's Lab

Single annual cycle for the National Science Foundation’s MCB, DEB and IOS Divisions.

Just received this from NSF and thought it might be of interest to some:

Dear Colleagues:

The Directorate for Biological Sciences (BIO) of the National Science Foundation (NSF) has initiated new procedures for the submission and review of regular research proposals to the core programs within the Division of Molecular and Cellular Biosciences (MCB), Division of Environmental Biology (DEB), and Division of Integrative Organismal Systems (IOS). The changes for MCB were previously announced in a new solicitation (NSF-11-545).

Effective immediately, DEB and IOS will both operate on a single annual cycle of preliminary and full proposals. The initial deadlines for preliminary proposals will be in January, 2012 and the initial deadline for invited full proposals will be in August, 2012. New Solicitations NSF 11-573 (for DEB) and NSF 11-572 (for IOS) provide further details. Also see the Dear Colleague Letter NSF 11-078 and Frequently Asked Questions NSF 11-079 for additional information.

Both DEB and IOS will be hosting webinars to provide further information, please see the Division websites, (DEB) and (IOS), for details and contact information if you have questions or concerns.

More fun with Mendeley plug ins for reference management #thingsIshouldhaveknownabout

OK – so I am a bit slow. I have been using Mendeley a lot recently. It has all sorts of nice “Social Networking” features for sharing reference lists and publications. I have for example used it as part of my push to free up papers by my father: Freeing my father’s publications part 5: near completion of PDF collection at Mendeley (h/t @David_Dobbs). And I have created some groups on Mendeley for sharing publications relating to various topics in which I am interested including: Microbial Forensics, Microbiology of the Built Environment and Phylogenetic and related analyses of metagenomic data. I have experimented with other online reference management systems like CiteULike, Connotea, Zotero, etc and each have some nice features. I have even written up some more detail on how to use citeulike for one project: Introducing citeulike group on microbiology of the built environment ….

But it is the more elaborate social networking features that drew me to Mendeley and why I am using it more than the other online system. And I have focused for example on getting all my personal publication in there to share them with others. And I confess I did not pay attention to many of the other features.

Yesterday however I discovered that Mendeley has plug-ins for generating bibliographies in various word processing programs: Reference Manager | Mendeley. Obviously I probably should have known this. But I have been using EndNote forever and had not experimented with anything new in a while. But I tried out the Mendeley Plugin for MS Word and it is OK. Not perfect. Still needs some work. But it is another factor in why I will likely shift even more to using Mendeley over other system. Still will play with the other ones out there … so if people have comments or suggestions please post.

Plus see below for an example of some of the Mendeley embed widgets one can make

http://www.mendeley.com/profiles/jonathan-eisen/widget/7207/2627036690/e619ef77f9cdf2ab2139da5ecf1c19e9a25e6be7/

Jonathan Eisen is a member of Biological Sciences on Mendeley.

http://www.mendeley.com/groups/1147121/_/widget/29/3/

Microbial Forensics is a group in Biological Sciences, Law on Mendeley.

http://www.mendeley.com/groups/844031/_/widget/31/3/

Microbiology of the Built Environment is a group in Biological Sciences, Environmental Sciences, Materials Science on Mendeley.

What is in a name? A case study of genomic epidemiology w/ Bacillus cereus and Bacillus anthracis

There is a very interesting new paper that just came online in the Archives of Pathology: Rapidly Progressive, Fatal, Inhalation Anthrax-Like Infection in a Human: Case Report, Pathogen Genome Sequencing, Pathology, and Coordinated Response

I was alerted to the paper by Eileen Choffnes of the National Academy of Sciences Institute of Medicine Forum on Microbial Threats (which I am a member of). In the paper, James Musser, Angela Wright and colleagues, the authors discuss the use of genome sequencing in the characterization of a fatal infection with a bacterium that appeared to be a species of Bacillus. Their summary is below and pretty much sums it up:

Context.—Ten years ago a bioterrorism event involving Bacillus anthracis spores captured the nation’s interest, stimulated extensive new research on this pathogen, and heightened concern about illegitimate release of infectious agents. Sporadic reports have described rare, fulminant, and sometimes fatal cases of pneumonia in humans and nonhuman primates caused by strains of Bacillus cereus, a species closely related to Bacillus anthracis.

Objectives.—To describe and investigate a case of rapidly progressive, fatal, anthrax-like pneumonia and the overwhelming infection caused by a Bacillus species of uncertain provenance in a patient residing in rural Texas.

Design.—We characterized the genome of the causative strain within days of its recovery from antemortem cul- tures using next-generation sequencing and performed immunohistochemistry on tissues obtained at autopsy with antibodies directed against virulence proteins of B. anthracis and B. cereus.

Results.—We discovered that the infection was caused by a previously unknown strain of B. cereus that was closely related to, but genetically distinct from, B. anthracis. The strain contains a plasmid similar to pXO1, a genetic element encoding anthrax toxin and other known virulence factors. Immunohistochemistry demonstrated that several homologs of B. anthracis virulence proteins were made in infected tissues, likely contributing to the patient’s death.

Conclusions.—Rapid genome sequence analysis permit- ted us to genetically define this strain, rule out the like- lihood of bioterrorism, and contribute effectively to the institutional response to this event. Our experience strongly reinforced the critical value of deploying a well- integrated, anatomic, clinical, and genomic strategy to respond rapidly to a potential emerging, infectious threat to public health.

The part in which I am interested, not surprisingly, is the genomic-evolution part. This is of interest since Bacillus anthracis is in a way a subspecies of a larger clade of bacterial types that includes Bacillus cereus and Bacillus thuringensis. These two generally do not cause fatal disease in humans, though I believe there are prior cases (see for example, Anthrax, but not Bacillus anthracis?). Also, I note, B. thuringensis is also known as Bt and is used extensively in agriculture to kill pests. Anyway, though Bt abd Bc are known to occasionally cause humans trouble, without a doubt, if you say you have found a case of Bacillus anthracis in people, some serious freaking out will occur at some level. People will want to know things – like is this a natural occurrence or a purposeful attack? And in the end, there is a lot associated with the name since of course “anthrax” scares people.

So the authors here basically sequenced the genome of this isolate and then did some detailed phylogenomic analysis to place it in the Bacillus cereus/thuringensis/anthracis group. See below:

And it turns out, this strain is not in the anthrax portion of the tree. It is in the Bacillus cereus part. The key thing here is that this strain is clearly, phylogenetically, in the Bacillus cereus/thuringensis part of this clade. Not so sure if the genomics was necessary here. I think some detailed MLST and/or phylogenetics of other variable markers might have done the same trick. But still, the resolution one gets from the phylogenomics is pretty good. This is of course nothing really new. There have been some nice genomic epidemiological studies done in the last year or two such as in the German E. coli and in some other cases (see for example, Prospective Genomic Characterization of the German Enterohemorrhagic Escherichia coli O104:H4 Outbreak by Rapid Next Generation Sequencing Technology and Origins of the E. coli Strain Causing an Outbreak of Hemolytic-Uremic Syndrome in Germany and The 2011 Shiga toxin-producing Escherichia coli O104:H4 German outbreak: a lesson in genomic plasticity and Open-Source Genomic Analysis of Shiga-Toxin-Producing E. coli O104:H4 and Pathogens: Genes and Genomes).

Though this is not per se new, this paper focuses a bit more on the pathology part of the story and even ends by linking to a new paper from one of the authors on how this type of work changes how we should conceive of pathology training:

One of us recently proposed the inception of a third, training track in pathology termed genomic pathology, designed to complement the traditional anatomic and clinical pathology tracks. As the introgression of genome- scale analyses proceeds rapidly and inexorably into con- temporary patient care and pathology practice, the career opportunities for this new type of trainee will increase considerably, and new patient-care niches will be created. We believe cases such as this highlight the need for, and potential utility of, a cadre of pathologists trained and facile in genomic pathology.

The paper on Genomic Pathology (thank goodness they did not invent a new omics word) can be found here. There is no doubt we are in a new era. Genomic sequencing is certainly going to be used in more and more cases like this and we definitely need to change the training paradigm if we want more people to use and understand it.

Some other reading worth checking out:

Some videos of interest

Reference:
Wright AM, Beres SB, Consamus EN, Long SW, Flores AR, Barrios R, Richter GS, Oh SY, Garufi G, Maier H, Drews AL, Stockbauer KE, Cernoch P, Schneewind O, Olsen RJ, & Musser JM (2011). Rapidly Progressive, Fatal, Inhalation Anthraxlike Infection in a Human: Case Report, Pathogen Genome Sequencing, Pathology, and Coordinated Response. Archives of pathology & laboratory medicine PMID: 21827220

Finally updated my blog template after, oh, five years

Well, after breaking the html behind my blog template many times with all sorts of hacked code for widgets and trackers and other things. I have decided to clean up my act. And just revert to a standardized Blogger template for now. If some things are missing, maybe I will revert. The colors I am going to play with – not sure if I want something new or to go back to the old ones. But for now, there will be a bit of a new look here.

Open Parkinson’s – need for more progress on Open Access for papers on Parkinson’s

I have a new aspect of open science I am concerned about. It is research on Parkinson’s. This comes from having a family member with Parkinson’s who is not doing so well. And I am getting frustrated with trying to read up on some Parkinson’s related research but hitting a paywall for much of it. Uggh. This is so incredibly annoying and, in many ways, immoral. If we want to speed up the work towards cures, treatments and prevention strategies, we need to share more broadly everything we know about this disease. Yes, I know – publishing costs money. And yes, I know, open access and open science does not in any way solve all the problems associated with scientific and medical discovery and research. But I do know that openness can accelerate the pace of progress.

If you look at “openness” in relation to Parkinson’s studies it is pretty disappointing. For example, of 60,400 publications that come up in Pubmed with a simple search for “Parkinson’s” 9053 have free full text available. That’s is just not enough. One thing that is interesting (and disconcerting) is what it looks like over time:

In some ways, there is good news here. The percentage of free text papers goes up over time from 2000-2009. But there is much bad news too. First – even in the best year, more than 70% of papers are not freely available. But perhaps more disconcerting, the percentage of freely available papers drops in 2010 and 2011. Why is this? I think most likely it comes from the delays in deposition to Pubmed Central that happen at many journals. So, it is good that some material gets out there, and apparently a higher fraction is getting out over time. But there is a big delay in the release of much of this material and the max percentage is still low. That is really unfortunate as the best way to catalyze scientific discovery to me is via rapid, open sharing. Imagine, for example, if Twitter posts were only available after 6 months. Useful? I don’t think so. What about weather information? Wait six months for a forecast? Sure, some aspects of scientific research do not need any input from others. But if papers are not important, then, why do we all fuss over them so much? That is because they contain knowledge, techniques, data, ideas, theories, and more. And it would be really better for all if everyone could have access to the full text of all such papers immediately.

Now mind you, I have only focused here on availability of free full text. There is another major issue in “open access” which is, well, openness. Openness of papers involves the rules on use, distribution and reuse. Many of the “free full text” papers in Pubmed Central have restrictions on how those papers can be used. The ideal to me is for the papers to be fully open such that anyone can redistribute them, repost them, take material from them, and use it in any way (with attribution). Why is this important? Well, it would allow anyone to create a Parkinson’s papers database, for example, with interesting search and discovery features. Or anyone could use a paper as part of a course, without having to worry about permissions. Or anyone could use material from a paper as part of a news story or blog post without getting into fights about fair use.

Now – there are some Parkinson’s related papers available out there outside of Pubmed, in institutional repositories and such. But these are not easy to find at this time. So in a way they don’t count for much.

I will be writing more about Open Science issues and Parkinson’s in the future. But for now I have a request. Anyone out there working on Parkinson’s please find a way to make your discoveries more freely and openly and rapidly available. I realize many/most of you are very passionate about this disease. I realize many of you work your tails off. And openness may be the last thing on your mind when working, struggling to get grants and make discoveries and deal with all your other job requirements and life issues. But even if you for some reason choose not to publish in an open access manner, at least post your papers on a website. Deposit them into repositories. Create a Mendeley account and post your papers there. Try and find a way to get them into Pubmed Central. Try to find ways to get your papers picked up by Google Scholar. Do something to increase the probability that your work will have an impact.

I will be writing more about open science and Parkinson’s in the future. Stay tuned.

Fun with marketing #numerology

Just got an email marketing a new book on numerology. I have a feeling, just a slight one, the marketer does not know much about me. But I thought I would share so everyone can ponder numerology. In order to spare people if they are not interested I have put everything below the “jump break”

Dear Jonathan Eisen:
Glynis McCants has studied Numerology for over 21 years and her accuracy at predicting events has earned her repeat appearances on The Tyra Banks Show, The Today Show, The View and many others. When she does live, quick Numerology readings on air, SHE DOES NOT MISS! In fact, the producers of Jim Carrey’s movie Number 23 hired her as their expert as did the producers of Dancing with the Stars. Upon its release, her latest book Love by the Numbers became the best-selling Numerology book in the country. Love by the Numbers has received rave reviews for its accuracy in helping single people find lasting love, and giving people in a relationship the tools they need to re ignite the passionate love they once had.

In a radio interview at the beginning of this year, Glynis said that in the month of August, there would be a lot of political upheaval and serious issues with the economy. The recent downgrade of The United States Credit Rating is a great example of this, and Glynis can give more insights on this subject.

Please read the following press release and let me know if I may book an informative, as well as entertaining interview for you with Glynis McCants. Thank you.
Please view Glynis in television appearances at: http://vids.myspace.com/index.cfm?fuseaction=vids.individual&VideoID=23012149

Rick Stevens
Ascot Media Group
Post Office Box 133032
The Woodlands, TX 77393
Office: (281) 333-3507
pr@ascotmediagroup.com
http://www.ascotmedia.com

FOR IMMEDIATE RELEASE
Welcome To Glynis McCants’ World – The World Of Accurately Predicting Romantic Love!
San Marino, CA, August 10, 2011 – Glynis McCants is an internationally-known celebrity Numerologist, whose latest book Love by the Numbers (Sourcebooks Publishing), was written for anyone looking for a healthy love relationship, or wanting to improve the one they already have. With a background in comedy, McCants is an in-demand motivational speaker on relationships and in her quick, live on-air readings – she does not miss!
Knowledge is power, and by researching Numerology for over 21 years and using the 2,500 year-old Pythagoras Number System, Glynis tells us that when you have someone’s name and date of birth, you can discover who they really are. Celebrity couples are one of Glynis’ specialties. She predicted that Reese Witherspoon/Ryan Phillippe, Halle Berry/Eric Benet, Ryan Reynolds/Scarlett Johansson’s marriages would not go the distance. Not only did Glynis know Jennifer Lopez was not going to walk down the aisle with Ben Affleck, but she was certain that Jennifer’s marriage with Marc Anthony would be a very difficult one, and that they would not be living “happily ever after.” Glynis makes it clear that Numerology is in everything– people, our home, business, and even the city and state in which we live.
Naming your baby by the Numbers really does make a difference. In the news, Pink, Jewel, Ivanka Trump, Kate Hudson, and Victoria Beckham have all recently given birth, and Glynis teaches that giving the baby the right name can ensure compatibility with child and parents. As your guest, she can explain how that works.
Glynis’ book Love by the Numbers is incredibly accurate, informative and entertaining! For many years, Glynis was a Numerology Counselor who taught others how to find healthy love relationships. One day, after a period of dating disappointments, she realized that she needed to follow her own advice and apply the science to finding her own compatible relationship. She used the power of Numerology to find her husband Charlie. They have been together for nine years, and are still madly in love, and feel as if they are on an extended honeymoon.
While other books make it complicated, the author has defined each number in a simple, understandable process. Its 25 exciting chapters teach readers how to find the Six Numbers that make up their Numerology Blueprint, and how to do a chart comparison. You can also discover what turns your partner on- or- off in love. Love by the Numbers will also show you how to pick the perfect wedding date to avoid a wedding day disaster! There are instances where taking the husband’s surname can actually harm the relationship—this book lets you know if that is the case for you.
Glynis McCants has made repeat TV appearances on The Tyra Banks Show, The Today Show, The Other Half, The Leeza Show, The View and Entertainment Tonight. She was the Numerology expert on Dancing with the Stars and for Jim Carrey’s film, Number 23. Glynis has been featured in top magazines and is a recurring guest on George Noory’s Coast to Coast Radio. She is also heard weekly on The Leeza At Night radio show. Glynis was voted Favorite Guest on PBR for three years running.
Please visit the Glynis McCants website at: http://www.numberslady.com for more information.
###
TIP SHEET:
Olympia Dukakis: “What impresses me most about Glynis is her boundless hope and optimism about the world we live in today. She uses the ancient science of Numerology as her guide, but her insight and wisdom are invaluable. Glynis believes that you can achieve all of your dreams, and by the time you finish reading this book, you will too.”
Leeza Gibbons, Talk Show Host: “I’ve seen Glynis work her Numerology magic dozens of times…always with the same result; empowering people to create the best version of themselves by really knowing and understanding who they are.”
Caroline Rhea: “Glynis knows so much about numbers, she makes the Yellow Pages seem obsolete.”
L.A. Confidential magazine: “To put it simply, if cupid and a clairvoyant were to have an affair, Glynis McCants would very much look like their offspring.”
John Edward, Psychic Medium: “When I think about Numerology I think about two people: Pythagoras and his modern day equivalent, Glynis McCants, The Numbers Lady. Glynis has taken a historic metaphysical science and transformed it into an easy to understand, organized and quite honestly entertaining field of study. To sum it up, she’s GOT your number – now it’s time for you to get it.”

Hydrogen as a fuel? No this is not about cars, this is about animals and their symbionts in the deep sea

As many of you know, I generally avoid writing about non open access publications here. But occasionally I make exceptions. And I am making one today. There is a wicked cool paper out in Nature today. Entitled “Hydrogen is an energy source for hydrothermal vent symbioses” comes from Nicole Dubilier, Jillian Petersen and others. It is about my favorite ecosystem(s) on the planet – hydrothermal vents. I became interested in these vents in 1989 when I met Colleen Cavanaugh who at the time was a Junior Fellow at Harvard. She told me about her work on bacteria that live inside tubeworms, clams and other creatures in the deep sea that are key to the lives of these animals. The bacteria are chemosynthetic (i.e., they use the energy of chemicals to drive carbon fixation). The animals have either no digestive systems or very degenerate ones and the bacteria function much like chloroplasts do for plants. The bacteria basically make everything for their hosts while the hosts collect energy (chemicals in this case) and oxygen and CO2 for the microbes.

After hearing Colleen tell me about her work on these symbioses and how at the time nobody knew much about the symbionts, I joined her new lab at Harvard (she was just appointed as a junior professor) and worked in her lab in my Senior year and after graduating (and ended up publishing my first paper on symbionts of a clam Solemya velum). I have been captivated by symbioses ever since. So much so that many years later I worked with Colleen, Irene Netwon, Tanya Woyke, Dongying Wu and others to sequence and analyze the first genome of any of the chemosynthetic symbiotic bacteria.

Anyway – enough about me. Prior to this new work, all of the symbioses in the deep sea had been found to involve either H2S (or related S compounds) or methane as energy sources. What is completely fascinating about the new work is that they show here that H2 can also serve as an energy source for chemosynthetic symbioses. From the abstract:

The discovery of deep-sea hydrothermal vents in 1977 revolutionized our understanding of the energy sources that fuel primary productivity on Earth. Hydrothermal vent ecosystems are dominated by animals that live in symbiosis with chemosynthetic bacteria. So far, only two energy sources have been shown to power chemosynthetic symbioses: reduced sulphur compounds and methane. Using metagenome sequencing, single-gene fluorescence in situ hybridization, immunohistochemistry, shipboard incubations and in situ mass spectrometry, we show here that the symbionts of the hydrothermal vent mussel Bathymodiolus from the Mid-Atlantic Ridge use hydrogen to power primary production. In addition, we show that the symbionts of Bathymodiolus mussels from Pacific vents have hupL, the key gene for hydrogen oxidation. Furthermore, the symbionts of other vent animals such as the tubeworm Riftia pachyptila and the shrimp Rimicaris exoculata also have hupL. We propose that the ability to use hydrogen as an energy source is widespread in hydrothermal vent symbioses, particularly at sites where hydrogen is abundant.

I am personally hoping that the authors post PDFs of the paper somewhere for everyone to read. I will post a link if they do.

I note – there is also a very accessible News and Views written about this paper. The News and Views is written by Victoria Orphan and Tori Hoehler and is entitled “Hydrogen for dinner.” I particularly like the last paragraph:

Petersen and colleagues’ work exemplifies the technology-driven revolution that is occur- ring in the biological sciences. The continuous development of ever more powerful and spe- cific molecular tools allows taxonomic identity and gene content to be linked to metabolic potential and activity, and to be visualized in context. As these techniques converge with new instrumentation that allows the in situ characterization of physicochemical parameters — even in environments as remote and extreme as hydrothermal vents — biologists are freed from their reliance on model organisms in artificial surroundings. Now, more than ever, our understanding of biology can be placed in the correct environmental and ecological context, enabling the discovery of previously unknown activities that support life.

Petersen JM, Zielinski FU, Pape T, Seifert R, Moraru C, Amann R, Hourdez S, Girguis PR, Wankel SD, Barbe V, Pelletier E, Fink D, Borowski C, Bach W, & Dubilier N (2011). Hydrogen is an energy source for hydrothermal vent symbioses. Nature, 476 (7359), 176-80 PMID: 21833083

Organic farming and antibiotic resistant bacteria:

Well, this news story is certainly going to get some publicity and almost certainly some responses. The Washington Post and Baltimore Sun are reporting on a new paper: Lower Prevalence of Antibiotic-resistant Enterococci On U.S. Conventional Poultry Farms That Transitioned to Organic Practices. The paper is from Environmental Health Perspectives – an open access journal so anyone out there can check it out. However, you might want to start with the news stories:

Organic farming reduces resistance of bacteria to antibiotics, study finds – The Checkup – The Washington Post

Organic farms harbor less antibiotic-resistant bacteria (Baltimore Sun)

In summary – the researchers cultured microbes from poultry farms – including conventional ones as well as ones that recently switched from conventional to organic practices. And though potentially unpleasant types of microbes were found everywhere, the percentage of those microbes that were resistant to antibiotics was much higher at the conventional farms than the newly organic ones. Not surprising to me or to many others. But at least someone is studying it. In general (from other word), it seems like we desperately need to reduce antibiotic usage on farms — to limit the potential selection for and spread of antibiotic resistance. But general recommendations are less useful than specific studies. Hopefully this study is sound and will get a lot of press.

Uggh: "Barcoding" researchers keep ignoring microbes and history #antimicrobiites #annoying

Barcoding is a technique in which researchers sequence a small region of the genome of an organism and use this sequence information as a “tag” to identify species/types. The term barcoding is most commonly associated with sequencing a small portion of the mitochondrial genome of a multicellular eukaryote. There is a new paper in PLoS One discussing barcoding: Neotropical Bats: Estimating Species Diversity with DNA Barcodes. The paper seems potentially interesting. But I could not get past the part where they write “To the best of our knowledge, it is one of the largest molecular surveys of biodiversity.”

Let’s examine this statement a bit. In the study here the authors did a heroic task – they did barcoding for some 9000 individuals. It is impressive, in many ways. But one can only call it a large molecular survey of biodiversity if one thinks biodiversity = plants and animals. If however you include microbes, as of course you should, then this new study is not even remotely the “largest molecular survey of biodiversity.” In fact, one could argue that 100s if not 1000s of studies of biodiversity of microbes are “larger” in many ways than this study. In microbial studies 9000 “individuals” are characterized routinely in most studies via the use of collecting DNA from environmental samples and sequencing genes from 100s -1000s to even billions of individual cells in a sample. This is done routinely in both metagenomic work (where one collects DNA from the environment and randomly sequences it) or ribosomal RNA PCR surveys where one collects DNA and then sequences rRNA genes from the sample. Overall, hundreds of microbial studies cover more biodiversity than this one – more species – wider phylogenetic diversity – more samples even.

So – could it be that the authors of the current paper are not aware of the microbial work? I don’t know – for they do not even mention it in this paper. This is amazing / startling / annoying / disappointing. After all, molecular studies of biodiversity were first done in microbial studies in the mid 1980s – pioneered by people like Norm Pace and colleagues surveying ribosomal RNA from mixed communities like Yellowstone hotsprings (e.g., see here and here). And in the 80s and 90s microbial work covered incredibly diverse ecosystems with many studies determining 100s-1000s of sequences. As sequencing got cheaper and cheaper, molecular studies of microbial biodiversity expanded to go beyond just single genes to studies of “metagenomes” from the environment. And in single gene studies, researchers now routinely sequence millions to billions of representatives of single genes using rRNA PCR and Illumina sequencing, for example.

Should these authors here be discussing microbes? I think so. After all, not only would this give their paper historical context. But it would almost certainly give it scientific context and value since there are hundreds of papers on microbes looking at species richness, biodiversity metrics, and such ((a simple pubmed search found 1357 papers using rRNA PCR and diversity as the query, for example). And since the work here is on mitochondrial DNA there may be even more parallels to microbes than one might think at first blush.

I note – this is not the first time Paul Hebert, the senior author on this study has gotten on my nerves about barcoding in terms of not mentioning microbes. I even posted a “dissent” regarding one of his earlier papers on Faculty of 1000 (which I used to contribute to before they become non open access). I am not sure what the explanation is, but the lack of referencing the historical work on using DNA to study diversity is disappointing (though I note in at least one of the first papers by Hebert, there was more brief mention of microbes). Not mentioning the 25 years of work on molecular studies of biodiversity in microbes gives the impression that Hebert invented using DNA to study biodiversity. And that is not needed. Barcoding has some nice features and uses. No need to purposefully or accidentally make it seem like it is something new.

Are microbial studies the same as the barcoding studies being done? No. Many barcoding studies have things like individual voucher specimens and museum collections. And microbial studies frequently have mixed samples like soil or water and DNA. So what. The general point of many of these studies is the same – using molecular data to infer information about species richness, beta diversity, phylogenetic patterns, etc. And for this, studies of microbes long preceded the barcoding approach. And there is a lot of useful literature out there as well as tools, methods and concepts. I for one peruse the barcoding papers to see if there is anything useful there for my work. It would almost certainly be good for the barcoding researchers to check out the microbial literature. And if the leaders in the barcoding arena continue to not mention microbes, well that would be unfortunate.

New paper from my lab (& the Facciotti lab): Mauve Assembly Metrics #Halophiles #Genomics

Just a quick post here. A new paper from my lab has come out in Bioinformatics. The paper is relatively simple. Titled “Mauve Assembly Metrics” it reports work of Aaron Darling and Andrew Tritt (with some minor contributions from me and Marc Facciotti). Aaron wrote the program Mauve when he was a student in Nicole Perna’s lab at Wisconsin: Mauve: multiple alignment of conserved genomic sequence with rearrangements. Over the years he (and others) have continued to develop the program and written a few papers too including for example, the development of progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. This new paper reports basically a system/scripts to measure assembly quality. Here is the abstract:

High throughput DNA sequencing technologies have spurred the development of numerous novel methods for genome assembly. With few exceptions, these algorithms are heuristic and require one or more parameters to be manually set by the user. One approach to parameter tuning involves assembling data from an organism with an available high quality reference genome, and measuring assembly accuracy using some metrics. We developed a system to measure assembly quality under several scoring metrics, and to compare assembly quality across a variety of assemblers, sequence data types, and parameter choices. When used in conjunction with training data such as a high quality reference genome and sequence reads from the same organism, our program can be used to manually identify an optimal sequencing and assembly strategy for de novo sequencing of related organisms.

Check out the paper: Mauve Assembly Metrics. Download the scripts/code http://ngopt.googlecode.com and Mauve and play around and let me know what you think.

Note this paper was supported by a grant from the National Science Foundation (ER 0949453). That grant is focused on comparative genomics (sequencing and analysis) of halophlic archaea. Stay tuned for more on that project as we are writing up a series of papers ….

Some related links:

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