Well, am on Winter Break here at Davis and am going to be taking at least a few weeks off of blogging/twitter/etc. And trying to ignore email too. I know – probably some irony in posting about taking a break, but whatever … am really taking a break.
Best wishes to all out there and see you next year ….
I have many thoughts about the recent NASA – arsenic – microbe story.
Quick summary
I was recently interviewed for a story in the Scientist by Bob Grant about blogging and related activities (see his story “You Aren’t Blogging Yet here). As preparation for this interview I made a top 10 list of ways that blogging had been beneficial to me. And I thought I would post my list here. I note, I made this list in about 10 minutes so I am sure there are other things I could add, but it was REALLY easy to make the list so I think w/o a doubt there have been many many benefits ….
10 ways blogging/microblogging has been beneficial to my career:
Anyway – just a little post about ways that blogging and tweeting have been helpful for my career. Other examples/areas that blogging and tweeting have helped people’s careers in science would be welcome here …
Very cool news from UC Berkeley. Jill Banfield, one of the greats of environmental microbiology, is going to receive both the Benjamin Franklin Medal in Earth and Environmental Science and the L’Oreal-UNESCO “for women in science” award.
I am very happy to see this. Jill has done some amazing work in multiple areas of environmental microbiology and continues to push frontiers in technology and science. And since I am always on an Open Access crusade here, here are some links to some of her recent papers that are free in Pubmed Central:
Well, I have been inspired recently by some of my interactions with people in the humanities. In general I think that there need to be more professional interactions between scientists and people in the humanities. So here is a simple suggestion, that could be taken up by scientists.
When you go to give a talk at another place, and your hosts ask who you want to meet with, include someone from outside the sciences. Either find someone yourself or asks your hosts to do it. I am going to do this for all my future visits to other campuses. Not only might it help in terms of interactions across fields, but I know my brain hurts after a full day of meeting with only scientists, so this has got to be better …
The Uniqueome: A mappability resource for short-tag sequencing — Bioinformatics
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From “The Uniqueome: A mappability resource for short-tag sequencing
Ryan Koehler, Hadar Issac , Nicole Cloonan,*, and Sean M. Grimmond.” Bioinformatics (2010) doi: 10.1093/bioinformatics
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Just a quick post here about a paper that came out about a month or so ago: PLoS Biology: Genomic Fossils Calibrate the Long-Term Evolution of Hepadnaviruses
This paper, by Clément Gilbert, Cédric Feschotte is quite cool. In it they describe their work on “Paleovirology” where they look for viruses than have “endogenized” by inserting into the genome of some host species. This endogenization is important in particular when the endogenous form becomes inactive and thus, in essence, trapped in the genome. This in turn is important because many viruses evolve so rapidly when they are “free” that it is very hard to reconstruct their ancient history through comparative analysis. But the endogenized viruses serve in essence as a molecular “fossil record” that aids in the comparison and phylogenetic analysis of various families of viruses. As we get more and more genomes, this searching for and analysis of endogenous viruses will get much better.
Anyway, in the paper they report on endogenous viruses in the Zebra Finch genome that are in the Hepadnaviridae family. Here is their summary:
Paleovirology is the study of ancient viruses and the way they have shaped the innate immune system of their hosts over millions of years. One way to reconstruct the deep evolution of viruses is to search for viral sequences “fossilized” at different evolutionary time points in the genome of their hosts. Besides retroviruses, few virus families are known to have deposited molecular relics in their host’s genomes. Here we report on the discovery of multiple fragments of viruses belonging to the Hepadnaviridae family (which includes the human hepatitis B viruses) fossilized in the genome of the zebra finch. We show that some of these fragments infiltrated the germline genome of passerine birds more than 19 million years ago, which implies that hepadnaviruses are much older than previously thought. Based on this age, we can infer a long-term avian hepadnavirus substitution rate, which is a 1,000-fold slower than all short-term substitution rates calculated based on extant hepadnavirus sequences. These results call for a reevaluation of the long-term evolution of Hepadnaviridae, and indicate that some exogenous hepadnaviruses may still be circulating today in various passerine birds.
| Figure 4. Summary of the evolutionary scenario inferred in this study. |
It is an interesting paper and worth a look if for those who have any interest in viral evolution. And I am becoming more and more fascinated by “Paleovirology” these days so I thought I would just post about this article here. And I guess I am not alone in this opinion that the article is interesting (though I am late). Here is some coverage of their paper:
Gilbert, C., & Feschotte, C. (2010). Genomic Fossils Calibrate the Long-Term Evolution of Hepadnaviruses PLoS Biology, 8 (9) DOI: 10.1371/journal.pbio.1000495
The resulting drug-target interaction network for all structurally characterized approved drugs bound to putative M.tb receptors, we refer to as the ‘TB-drugome’
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Figure 2. A protein-drug interaction network to illustrate similarities between the binding sites of M.tb proteins (blue), and binding sites containing approved drugs (red). From Kinnings SL, Xie L, Fung KH, Jackson RM, Xie L, et al. (2010) The Mycobacterium tuberculosis Drugome and Its Polypharmacological Implications. PLoS Comput Biol 6(11): e1000976. doi:10.1371/journal.pcbi.1000976
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Just saw this interesting paper arguing that open access to literature is critical for the field of aquaculture. The paper argues that open access to literature has accelerate innovation by promoting more partnerships with hobbyists and with others who might normally be outside the “inner circle.” Definitely worth a read and it fits under my “YARFOA” category – Yet Another Reason For Open Access.
The paper is “The importance of open access in technology transfer for marine ornamental aquaculture: The case of hobbyist-led breeding initiatives” from the Journal Aquaculture, Aquarium, Conservation & Legislation International Journal of the Bioflux Society.
It is is by Andrew Rhyne who is connected with the New England Aquarium and also at Roger Williams University.
I love the concluding paragraph by the way:
Opening the door to an open process. I would hope that others would join me in supporting the free flow of information by publishing their work in open access journals, and encouraging societies like the World Aquaculture Society, the American Fisheries Society, and European Aquaculture Society to go to an open access format. We should fully applaud blogging or posting on discussion forums in real time about efforts to rear new species or develop new live feeds. The dialog that occurs on MOFIB and other online forums can spark innovation that is not possible through traditional formats. I believe that open access is the key to faster breakthroughs, and to better translation between academia, hobbyists, and commercial industry. The Aquaculture field has an opportunity to become an exemplary model for all applied science fields: let’s seize it.
As many of you know, I spend a lot of time bashing #badomics words. Some have asked if I just hate all omics words. And the answer is no. First, I am only annoyed by words that use “omics” or “ome” in the sense of “genomics” or “genome”. Thus words that use the “ome” suffix in the sense of a cellular complex (e.g., ribosome, proteosome, etc) are not on my radar. And words that use “omics” in the sense of “economics” (e.g., Obamanomics”) are not my concern either. My problem is those that in essence are latching onto “genomics” excessively.
And on twitter as well as in my blog I have bashed many such #badomics words including vaccinomics, waveomics, adversomics, bibliome, epitheliome, nutriome, transactome, N-terminome, miRNAome, modomics, tRNomics, variome, Speechome, connectome, negatome, material degradomics, and many more. I even give out two types of awards here in this regard: Worst New Omics Word Award and bad omics word of the day. And alas, I am sure I will give out more.
But today I thought it might be useful to be positive. And thus I am going to discuss what I view as a good omics word. Not great mind you. But pretty good. And this is “transcriptomics” and its relative “transcriptome”. Both of these are pretty good words.
From Wikipedia here is the definition of transcriptome
The transcriptome is the set of all RNA molecules, including mRNA, rRNA, tRNA, and other non-coding RNA produced in one or a population of cells. The term can be applied to the total set of transcripts in a given organism, or to the specific subset of transcripts present in a particular cell type.
This seems to be a perfectly reasonable and useful use of the “ome” suffix. It is genomic in scale (i.e., all RNA in the cell – not like many badomics words which are too specific). And it is broad in that it can be used to refer to all the RNA in an organism or cell or such. The first use I have found is from this paper on yeast in 1997. But there may be earlier examples.
Anyway – trying to be positive today. And transcriptome to me is a good omics word.
Jonathan Eisen's Lab 