Thursday, August 27, 2009

Bacterial freeloaders, early metastasis and more in my picks of the week from RB

Another week has gone by and some very interesting blog posts have been aggregated into Every week [see my opening post on the matter], I'll select some blog posts I consider particularly interesting in the field of molecular biology [see here to get a sense of the criteria that will be used] and list them here for you to check out.

This week, I've selected four posts:

1) Iddo Friedberg highlights some interesting research being done on quorum sensing, a form of bacterial intercellular communication.

Under certain conditions, bacteria can cooperate as a population to create biofilms, a "tangled matrix of polymeric substances that includes proteins, DNA and polysaccharides which can serve as tough physical barriers that are immune to attacks by many antibiotics and other bacteriocidal agents".

In most natural environments, association with a surface in a structure known as a biofilm is the prevailing microbial lifestyle. Surface association is an efficient means of lingering in a favorable microenvironment rather than being swept away by the current (Watnick & Colter, 2000).
Iddo discusses a couple of articles on how bacterial “freeloaders” (organisms which do not contribute to the formation of these biofilms but benefit from it) do in these systems.

2) Next up is a nice post from Skeptic Wonder on a fascinating endosymbiotic relationship between an amoebae and a kinetoplastid called Perkinsela. Interestingly, this interaction appears to be "mutualistic as the host and the endosymbiont both die without each other" and it could have arisen from parasitizing off the same host.
The question remains: is Perkinsela now an 'organelle'?

3) Tissue invasion and metastasis are hallmarks of cancer. Cells from primary tumor masses can travel and colonize the same or different organ sites leading to the formation of secondary tumors. Importantly, these “metastases” are the cause of 90% of human cancer-related deaths (Nguyen et al., 2009). In general, metastasis is considered a late event in cancer progression, but Varun Sreenivasan over at Wissenschaft discusses recent evidence on the systemic dissemination of tumor cells even before the full establishment of the primary tumor, using a mouse model of breast cancer.

4) Mystery Rays from Outer Space directs our attention to a few cases of "transmissible tumors": “cases where tumors actually spread from their original host, to other individuals”. Vertically transmitted tumors (maternal–fetal transmission) are the main focus of this post.

In case you don’t find this noteworthy, keep in mind that:
“Tumors aren’t supposed to be able to spread in this way (i.e should not be transmissible), because they’re essentially foreign transplants — they should be rapidly rejected, as if they were, say, a skin graft between two random people.”

That's it for this week. Stay tuned for more MolBio Research Highlights!

Some of the articles discussed in this week's selected posts:

Diggle, S., Griffin, A., Campbell, G., & West, S. (2007). Cooperation and conflict in quorum-sensing bacterial populations Nature, 450 (7168), 411-414 DOI: 10.1038/nature06279

Czárán T, & Hoekstra RF (2009). Microbial communication, cooperation and cheating: quorum sensing drives the evolution of cooperation in bacteria. PloS one, 4 (8) PMID: 19684853

DYKOVA, I., FIALA, I., & PECKOVA, H. (2008). Neoparamoeba spp. and their eukaryotic endosymbionts similar to Perkinsela amoebae (Hollande, 1980): Coevolution demonstrated by SSU rRNA gene phylogenies European Journal of Protistology, 44 (4), 269-277 DOI: 10.1016/j.ejop.2008.01.004

Hüsemann, Y., Geigl, J., Schubert, F., Musiani, P., Meyer, M., Burghart, E., Forni, G., Eils, R., Fehm, T., & Riethmüller, G. (2008). Systemic Spread Is an Early Step in Breast Cancer Cancer Cell, 13 (1), 58-68 DOI: 10.1016/j.ccr.2007.12.003

Tolar J, & Neglia JP (2003). Transplacental and other routes of cancer transmission between individuals. Journal of pediatric hematology/oncology : official journal of the American Society of Pediatric Hematology/Oncology, 25 (6), 430-4 PMID: 12794519

References used in this post:

Watnick P, Kolter R (2000) Biofilm, city of microbes. J Bacteriol. 182(10):2675-9
Nguyen DX, Bos PD, Massagué J (2009). Metastasis: from dissemination to organ-specific colonization. Nature Reviews Cancer 9, 274-284

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Sunday, August 23, 2009

RNA and it's regulatory role: Video

Here's a nice, simple (broad audience-oriented) and short video from AAAS where John Mattick (who visited our university a few months ago [see Long overdue post on John Mattick's visit]), Stephen Buratowski, and Science editor Guy Riddihough "discuss the new and increasing understanding of how RNA regulates DNA (...)".

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Thursday, August 20, 2009

My weekly picks from Researchblogging #2

Another week has gone by and some very interesting blog posts have been aggregated into Researchblogging. Every week [see my opening post on the matter], I'll select some blog posts I consider particularly interesting in the field of molecular biology [see here to get a sense of the criteria that will be used] and list them here for you to check out.

This week four blog posts made the cut. Let's get down to business:

1) Charles Daney over at Science and Reason nicely (and in very simple terms, which is always appreciated) discusses a recent article on an interesting link between inflammation and cancer (lymphoma) through cytokine-regulated miRNA expression. Charles describes that the authors reported that SHIP1, a phosphatase that has been described as a tumor suppressor, is a target of a miRNA previously associated with cancer. This effect is somehow regulated by the cytokine TNF alpha.
What is not clear is exactly what mechanism connects inflammation with cancer. There's undoubtedly a variety of mechanisms, given how complicated cellular processes turn out to be when you get down to the finer details. (This article) illustrates one such mechanism, in a single type of cancer.
There is just one phrase in his post I don’t quite agree with, but I’m just splitting hairs:
However, non-coding DNA is certainly less critical to cell function than the DNA of actual genes.
With “actual genes”, I’m assuming he refers to protein-coding genes, however it should be noted that independent genes coding for miRNAs or other ncRNAs such as snoRNAs are also “genes”. Further, there is plenty of evidence supporting important roles for non-coding RNAs in different systems, but that’s something to discuss on another time.

Anyway, this is a nice post discussing a very interesting article, so you should check it out.

2) Next up is Joseph Boyle at the Y.O.R.F. discussing part of his research on the “reannotation and analysis of the Carsonella ruddii genome and sequence-based functional analysis of its metabolic enzymes”. C. ruddii, an endosymbiotic bacteria, it’s a fascinating organism as it has the smallest bacterial genome. Although not a discussion of a particular article per se, Joseph presents some nice data modeling metabolic pathways in C. ruddii.

3) Considering how we now explore “through what seems to be never ending stretches of genetic code from several different species” in our computers, Daniel Ocampo-Daza over at Ego Sum Daniel has put forward an interesting idea: are we “naturalists in the new world of genomes?"

4) Do healthy old people (>85 years old), which have never been diagnosed with cancer, cardiovascular disease, Alzheimer’s, pulmonary disease, or diabetes, harbor specific and characteristic genetic variants responsible for their well-being? Dan Koboldt from MassGenomics discusses a recent article published in PLoS ONE in which the authors go after the genetic basis of longevity

That's it for this week. I'll be back in 7 days to highlight posts in molecular biology aggregated at

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Thursday, August 13, 2009

My weekly picks from ResearchBlogging #1

As many of you may already know, (RB) has created “Editor’s selections” in which “experts who are also accomplished bloggers” serve as editors in each of the four major content areas at RB: Biology, Health/Clinical Research, Psychology/Neuroscience, and everything else. Their task is to select posts they find interesting in their respective areas and post links to them at RB [See Dave Munger’s explanation: Editor’s Selections — a new way to find your favorite posts].

I posted the following comment over at Dave’s post (edited):
This is a great idea. Nevertheless, having just one editor for “Biology” may not be enough. If the selected scientist/blogger is someone working on evolution, he will undoubtedly be more interested, and then highlight, articles in that area more frequently than in some other areas. Maybe with the rise of new bloggers this could be fixed over time.
Dave sent me an email explaining that indeed he felt the same way and was looking for a second biology editor. I was among the potential candidates to fill the position (which was an honor!) but in the end Vincent Racaniello was selected to join Jarrett Byrnes in the “Biology” field, as the second biology editor. I'm sure both Vincent and Travis will do an excellent job. You can check their picks every week over at ResearchBlogging News.

As I mentioned at Dave’s post, I considered “Editor’s selections” to be a great idea and even though I wasn’t selected, I decided I wanted to serve as a sort of “independent”1 Biology editor, highlighting posts on molecular biology aggregated at RB and posting them here at MolBio Research Highlights for other readers to enjoy.

Once a week, I will be selecting and sharing the posts on molecular biology I consider appealing, under the following criteria:

1. The “interest” of the article being discussed. As you can imagine, this reflects my personal bias on what I consider of interest. To get a sense of my interests, check “Around the journals” where I highlight articles directly from by Google Reader, from a wide selection of journals, and share them with you. In general, gene expression (transcription, RNA processing, translation) and its regulation, and both genetics and genomics are the main focus.

2. The analysis of the article discussed and clarity of the post. The ideal post is a critical one, which also puts the article into context and explains why the blogger considered the article to be important (enough to blog about).

Note I will only consider posts aggregated under "Biology" at RB.

This week, I selected a nice and critical post by Daniel MacArthur over at Genetic Future discussing a Nature Biotechnology article reporting “yet another "complete" individual genome sequence”. Here’s the kick, though: this is the first genome to be sequenced using single molecule sequencing technology. The technology in question is Heliscope, by Helicos BioSciences.

Daniel nicely discusses the pros and cons of this new technology in light of the data reported and compares it with the performance of other competitors, namely Illumina. You should definitely check it out.

That wraps it up for the week.
I’ll post my picks every Thursday here at MolBio Research Highlights so stay tuned!

1 Independent in the sense that I’m not doing this for RB.

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Tuesday, August 11, 2009

BMC 4th Annual Research Awards

In order to "celebrate the best published research across medical and biological science within any of BioMed Central's open access journals", BMC created the BioMed Central Annual Research Awards, now on its 4th edition.

If you publish in one of BioMed Central's 199 journals before the end of 2009 (December 31st) you'll be eligible for nomination from other readers, reviewers or editors (you can't nominate yourself), in the categories of "Biology" or "Medicine" for "best published research".

The winners, who will get $5,000, will be chosen by a panel of BioMed Central's editorial team members (Peter Newmark and Michaela Torkar for the Biology Award) and invited external experts.

Last year's Biology award, was given to Basil Honegger at The University of Zürich, for his article "Imp-L2, a putative homolog of vertebrate IGF-binding protein 7, counteracts insulin signaling in Drosophila and is essential for starvation resistance" published in the top-tier Journal of Biology.

You can start nominating articles here. If you nominate an article, let us know, or even better, write a post explaining why you chose that article and get it published here at MolBio Research Highlights!

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Sunday, August 9, 2009

On geeks, nerds and dorks

A friend of mine keeps calling me a "nerd" because I continuously talk about science with my colleagues and friends, even at parties and bars. Also, because I work in a lab, I watch the Discovery channel on a regular basis and because I'm computationally savvy. Further, having a copy of Nature in my backpack "doesn't help", according to her. I always knew this description to be technically wrong and that there must be another adjective for these "set of skills and characteristics".

While reading the "About us" section over at I found what I was looking for to prove her wrong:

According to the Online Urban Dictionary, a Geek is defined as being in possession of both technical knowledge and social skills, which sets us apart from nerds (who have only the former) and dorks (who have neither, poor souls). Geeks are savvy and passionate about the world of technology and some of us have super powers.

Geeks are basically, the clever switched-on people who aren’t ashamed to admit to cyber capabilities not unlike the Terminator. Sociable fun loving types with a passion for tech and an ear to the world.
I knew I was a geek and not a nerd (the latter having a bad connotation) for a long time, but I couldn't quite explain it to her, so this definition comes in handy: it's clear and makes the distinction evident. I'm a social person and my friends are not only the people in my lab or my contacts in twitter or friendfeed .

Regrettably, though, there isn't a direct translation of "geek" into Spanish for me to teach her.
Also, after I showed her my findings she mentioned:

(...) You taking the time to find out the distinction over the Internet, just proves me right, rather that helping your case.


Anyway, for those who watch Big Bang Theory, the distinction may become clearer by remembering the "The Bath Item Gift Hypothesis" episode:

The guy in the middle (David Underhill, a MacArthur Genius Grant recipient and Caltech experimental physicist) is a geek, and Leonard, well... he is a nerd.


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Tuesday, August 4, 2009

The Method of the year

Is that time of the year again. The time to vote for the "Method of the year", a recognition given by Nature Methods since '07. Every once in a while a method is developed with the potential to greatly advance our knowledge in a particular field, allowing us to ask new questions or to refine our answers to long-standing problems in the life sciences. The idea is to "select a methodology with a demonstrated potential to strongly influence the pace and direction of scientific inquiry".

In 07, Nature Methods nominated "next-generation" sequencing for the award (although the name is far from useful, see Post-apres-next generation sequencing), and "super-resolution fluorescence microscopy" was their choice in 08.

You can now participate by nominating and voting for methodological developments to be considered for the recognition at 1
You may nominate any recent method or class of methods, published anywhere in the scientific literature, that you believe is likely to have a profound impact on future biological research. You are welcome to nominate a method that you yourself developed, but please acknowledge your connection to it. 2
After reading the editorial in Nature Methods I was left with the impression that even though they are hosting an open poll for choosing the Method of the Year, ultimately, they'll have the final saying in deciding, even if it doesn't match the most voted one:
We will take the results of the popular vote into consideration when choosing the Method of the Year 2009, and the votes will also serve as inspiration for picking the Methods to Watch that accompany it.2
Anyway, it's a good chance to log in and nominate your favorite technique!

1 You'll need a Nature account to participate.
2 Nature Methods 6, 547 (2009)

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Monday, August 3, 2009

The most-cited institutions and Journals has released a ranking of the top 20 institutions (out of over 4,000) which have attracted the highest total citations to their papers published in Thomson Reuters-indexed journals over 22 fields. This has been done using the data from Essential Science Indicators since January 1, 1999 to April 30, 2009 [The Most-Cited Institutions Overall, 1999-2009].

This includes the "Molecular Biology & Genetics" field, so we checked it out and bring it to you.

The top 20 institutions over all fields include 14 US-based universities, 3 UK-based universities, and one each in Canada, Japan, and Germany.

Considering all 22 fields, the 20 most-cited institutions are:

14 UCL
17 MIT

Interestingly, Harvard leads in 9 of the 22 fields, including "Molecular Biology & Genetics".
Harvard's citation strengths lie in biological and health sciences: the top five fields in their the citation record are Clinical Medicine, Molecular Biology & Genetics, Biology & Biochemistry, Neuroscience & Behavior, and Immunology.
The Max Planck Society ranks #2 overall and #2 in the "Molecular Biology & Genetics" and also in the "Biology & Biochemistry" sub-categories.

And on a personal note... Wisconsin rules!

Now, regarding journals, the top 10 most-cited (during the same period, 1999-2009) in all fields are:

1 Journal of Biological Chemistry
2 Proc. Natl. Acad. Sci. USA (PNAS)
3 Nature
4 Science
5 Physical Review Letters
6 J. American Chemical Society
7 Physical Review B
8 Astrophysical Journal
9 New England Journal of Medicine
10 Applied Physics Letters

[Source: Top Ten Most-Cited Journals (All Fields), 1999-2009]

Note that this has not been normalized in any way, and just reflects the total number of citations.

If you divide the total number of citations by the number of articles published in those journals, you get the following ranking:

01. New England Journal of Medicine
02. Science
03. Nature
04. PNAS
05. JBC
06. J. American Chemical Society
07. Physical Review Letters
08. Astrophysical Journal
09. Applied Physics Letters
10. Physical Review B

[Image credit: The NAD group]

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