Sunday, August 29, 2010

Top 25 articles in Biochemistry, Genetics and Molecular Biology

Yesterday, I twittered about Sciverse, a new "Elsevier platform that combines ScienceDirect (fulltext journal articles) and Scopus (abstract and citation database of peer-reviewed literature)" (more about it here, in @mfenner's blog).

While browsing around the ScienceDirect site, I found a new service: "Top-25 hottest articles".

Basically, Top 25 "allows you to see which articles have been downloaded the most, either from any of the 24 subject areas and/or from any of the 2,500 journals on ScienceDirect".

These reports are published quarterly and so reflect usage behavior from the prior three months.

So, which articles have been the most downloaded ones in the period between April and June 2010, in the field of "Biochemistry, Genetics and Molecular Biology"?

1. The Hallmarks of Cancer
Cell, Volume 100, Issue 1, January 2000, Pages 57-70
Hanahan, D.; Weinberg, R.A.

2. Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP Cell, Volume 141, Issue 1, April 2010, Pages 129-141
Hafner, M.; Landthaler, M.; Burger, L.; Khorshid, M.; Hausser, J.; Berninger, P.; Rothballer, A.; Ascano, M.; Jungkamp, A.C.; Munschauer, M.; Ulrich, A.; Wardle, G.S.; Dewell, S.; Zavolan, M.; Tuschl, T.

3. A Chromatin-Mediated Reversible Drug-Tolerant State in Cancer Cell Subpopulations
Cell, Volume 141, Issue 1, April 2010, Pages 69-80
Sharma, S.V.; Lee, D.Y.; Li, B.; Quinlan, M.P.; Takahashi, F.; Maheswaran, S.; McDermott, U.; Azizian, N.; Zou, L.; Fischbach, M.A.; Wong, K.K.; Brandstetter, K.; Wittner, B.; Ramaswamy, S.; Classon, M.; Settleman, J.

4. Immunity, Inflammation, and Cancer
Cell, Volume 140, Issue 6, March 2010, Pages 883-899
Grivennikov, S.I.; Greten, F.R.; Karin, M.

5. Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors
Cell, Volume 126, Issue 4, August 2006, Pages 663-676
Takahashi, K.; Yamanaka, S.

6. The Inflammasomes Cell, Volume 140, Issue 6, March 2010, Pages 821-832
Schroder, K.; Tschopp, J.

7. Mitochondria Supply Membranes for Autophagosome Biogenesis during Starvation
Cell, Volume 141, Issue 4, May 2010, Pages 656-667
Hailey, D.W.; Rambold, A.S.; Satpute-Krishnan, P.; Mitra, K.; Sougrat, R.; Kim, P.K.; Lippincott-Schwartz, J.

8. Pattern Recognition Receptors and Inflammation
Cell, Volume 140, Issue 6, March 2010, Pages 805-820
Takeuchi, O.; Akira, S.

9. Reconstitution of the RIG-I Pathway Reveals a Signaling Role of Unanchored Polyubiquitin Chains in Innate Immunity
Cell, Volume 141, Issue 2, April 2010, Pages 315-330
Zeng, W.; Sun, L.; Jiang, X.; Chen, X.; Hou, F.; Adhikari, A.; Xu, M.; Chen, Z.J.

10. Ragulator-Rag Complex Targets mTORC1 to the Lysosomal Surface and Is Necessary for Its Activation by Amino Acids
Cell, Volume 141, Issue 2, April 2010, Pages 290-303
Sancak, Y.; Bar-Peled, L.; Zoncu, R.; Markhard, A.L.; Nada, S.; Sabatini, D.M.

11. A Transcriptional Signature and Common Gene Networks Link Cancer with Lipid Metabolism and Diverse Human Diseases
Cancer Cell, Volume 17, Issue 4, April 2010, Pages 348-361
Hirsch, H.A.; Iliopoulos, D.; Joshi, A.; Zhang, Y.; Jaeger, S.A.; Bulyk, M.; Tsichlis, P.N.; Shirley Liu, X.; Struhl, K.

12. NLRC5 Negatively Regulates the NF-@kB and Type I Interferon Signaling Pathways Cell, Volume 141, Issue 3, April 2010, Pages 483-496
Cui, J.; Zhu, L.; Xia, X.; Wang, H.Y.; Legras, X.; Hong, J.; Ji, J.; Shen, P.; Zheng, S.; Chen, Z.J.; Wang, R.F.

13. A Temporarily Distinct Subpopulation of Slow-Cycling Melanoma Cells Is Required for Continuous Tumor Growth
Cell, Volume 141, Issue 4, May 2010, Pages 583-594
Roesch, A.; Fukunaga-Kalabis, M.; Schmidt, E.C.; Zabierowski, S.E.; Brafford, P.A.; Vultur, A.; Basu, D.; Gimotty, P.; Vogt, T.; Herlyn, M.

14. Endoplasmic Reticulum Stress and the Inflammatory Basis of Metabolic Disease
Cell, Volume 140, Issue 6, March 2010, Pages 900-917
Hotamisligil, G.S.

15. 53BP1 Inhibits Homologous Recombination in Brca1-Deficient Cells by Blocking Resection of DNA Breaks Cell, Volume 141, Issue 2, April 2010, Pages 243-254
Bunting, S.F.; Callen, E.; Wong, N.; Chen, H.T.; Polato, F.; Gunn, A.; Bothmer, A.; Feldhahn, N.; Fernandez-Capetillo, O.; Cao, L.; Xu, X.; Deng, C.X.; Finkel, T.; Nussenzweig, M.; Stark, J.M.; Nussenzweig, A.

16. Molecular and Cellular Approaches for Diversifying and Extending Optogenetics Cell, Volume 141, Issue 1, April 2010, Pages 154-165
Gradinaru, V.; Zhang, F.; Ramakrishnan, C.; Mattis, J.; Prakash, R.; Diester, I.; Goshen, I.; Thompson, K.R.; Deisseroth, K.

17. Identification of the Switch in Early-to-Late Endosome Transition
Cell, Volume 141, Issue 3, April 2010, Pages 497-508
Poteryaev, D.; Datta, S.; Ackema, K.; Zerial, M.; Spang, A.

18. Matrix Metalloproteinases: Regulators of the Tumor Microenvironment
Cell, Volume 141, Issue 1, April 2010, Pages 52-67
Kessenbrock, K.; Plaks, V.; Werb, Z.

19. An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation Cell, Volume 141, Issue 2, April 2010, Pages 344-354
Tuller, T.; Carmi, A.; Vestsigian, K.; Navon, S.; Dorfan, Y.; Zaborske, J.; Pan, T.; Dahan, O.; Furman, I.; Pilpel, Y.

20. 3.3 A Cryo-EM Structure of a Nonenveloped Virus Reveals a Priming Mechanism for Cell Entry
Cell, Volume 141, Issue 3, April 2010, Pages 472-482
Zhang, X.; Jin, L.; Fang, Q.; Hui, W.H.; Zhou, Z.H.

21. A Hierarchy of Self-Renewing Tumor-Initiating Cell Types in Glioblastoma
Cancer Cell, Volume 17, Issue 4, April 2010, Pages 362-375
Chen, R.; Nishimura, M.C.; Bumbaca, S.M.; Kharbanda, S.; Forrest, W.F.; Kasman, I.M.; Greve, J.M.; Soriano, R.H.; Gilmour, L.L.; Rivers, C.S.; Modrusan, Z.; Nacu, S.; Guerrero, S.; Edgar, K.A.; Wallin, J.J.; Lamszus, K.; Westphal, M.; Heim, S.; James, C.D

22. Peroxisomes Are Signaling Platforms for Antiviral Innate Immunity
Cell, Volume 141, Issue 4, May 2010, Pages 668-681
Dixit, E.; Boulant, S.; Zhang, Y.; Lee, A.S.Y.; Odendall, C.; Shum, B.; Hacohen, N.; Chen, Z.J.; Whelan, S.P.; Fransen, M.; Nibert, M.L.; Superti-Furga, G.; Kagan, J.C.

23. Th17 and Regulatory T Cells in Mediating and Restraining Inflammation
Cell, Volume 140, Issue 6, March 2010, Pages 845-858
Littman, D.R.; Rudensky, A.Y.

24. Transmembrane Receptor DCC Associates with Protein Synthesis Machinery and Regulates Translation
Cell, Volume 141, Issue 4, May 2010, Pages 632-644
Tcherkezian, J.; Brittis, P.A.; Thomas, F.; Roux, P.P.; Flanagan, J.G.

25. Persistent Telomere Damage Induces Bypass of Mitosis and Tetraploidy
Cell, Volume 141, Issue 1, April 2010, Pages 81-93
Davoli, T.; Denchi, E.L.; de Lange, T.

Well that's a very "cancer & immunology"-oriented list!

Let's take a closer look at these stats:

23 out of the 25 articles are from Cell. The other two, from Cancer Cell.
17 are review articles.
The article "The hallmarks of cancer" (2000) has been cited in 7602 documents! 

You can subscribe to the Top25 list by RSS here.

Just as a comparison, let's take a look at what the "Essential Science Indicators" tool from Web of Science has to say regarding "highly cited articles" in the field of "Molecular Biology and Genetics". This list has been updated as of July 1, 2010 to cover a ~10-year period (January 1st, 2000 to April 30th, 2010).


CELL 100 (1): 57-70 JAN 7 2000

NATURE 409 (6822): 860-921 FEB 15 2001

SCIENCE 291 (5507): 1304-+ FEB 16 2001

GENETICS 155 (2): 945-959 JUN 2000

SCIENCE 293 (5532): 1074-1080 AUG 10 2001

CELL 116 (2): 281-297 JAN 23 2004

SCIENCE 287 (5461): 2185-2195 MAR 24 2000

NATURE 403 (6765): 41-45 JAN 6 2000

NATURE 420 (6915): 520-562 DEC 5 2002

AMER J HUM GENET 68 (4): 978-989 APR 2001


Read More......

Saturday, August 28, 2010

Quotes from the science blogosphere

"In terms of grammar, English is possibly one of the least logical and most puzzling languages there is. This is the result of its hybrid origins. Modern English is basically a mixture of a Teutonic language (Old English) and a Romance language (Norman French). These come from entirely different sub-groups of Indo-European. To be sure, this fusion even happened almost a thousand years ago, but we’ve never gotten over it."

Henry Gee (Senior editor at Nature), as a reply to a question at the "Ask the Nature Editor" forum.

(Image credit)


Read More......

Saturday, August 21, 2010

The 2nd issue of the MolBio Carnival is coming

This is just to remind you that a new issue of The MolBio Carnival is coming and it will be hosted by Lucas Brouwers at Thoughtomics. It will go live on Sept 6th, so there's still plenty of time to submit your best molbio posts to this great carnival.

More info on submission guidelines and how to submit your posts here.


Read More......

Monday, August 2, 2010

The MolBio Carnival: the first edition

I’m pleased to host the very first edition of the MolBio Carnival, your monthly roundup of interesting posts in molecular biology from the science blogosphere. There has been a great response to this initiative and I had a great time reviewing submissions and writing this post.

You can read all about this Carnival here (submission guidelines, scope, etc), but right now, let’s get down to business, as we have a very exciting first edition:

1) Leucocite recruitment to injured tissue is an important feature of the inflammatory response. The mechanism mediating this recruitment, however, is largely unknown. Becky Ward at It Takes 30, highlights an interesting Science paper describing that in zebrafish, a hydrogen peroxide (H2O2) concentration gradient is produced at the wound margin and it appears to act as a signal for rapid leukocyte recruitment.

2) On a second submission, Becky discusses a provocative article addressing the molecular basis of the association of a particular HLA allele, HLA-B57, with HIV “elite controllers” (HIV-infected individuals that maintain very low levels of HIV RNA without therapy and that generally do not progress to AIDS). Briefly, the peptide-binding characteristics of HLA-B57 molecules appears to affect thymic development in a way that it leads to a more cross reactive B57-restricted T cell repertoire.
"The bottom line is that any HIV peptide that binds to HLA-B57 (…) is going to have a much harder time finding a mutation that will evade the immune response. And this would explain why people who are lucky enough to have HLA-B57 among their class I MHC molecules would be better at controlling HIV infection"
3) Stem cells divide asymmetrically which allows preserving stem cell number while generating differentiated cells. Kat at Science Update blog, from Cancer Research UK, discusses a fascinating article in which the authors show that mouse intestinal stem cells appear to have a characteristic mitotic spindle orientation. Notably, this orientation appears to correlate with the asymmetric distribution of labeled DNA, supporting the idea that Cairns’ “immortal strand” hypothesis could be applied to stem cells of the gut epithelium. Further, the authors provide evidence for an important role of adenomatous polyposis coli tumor suppressor (Apc) in this process.

Figure from Kat's post highlighting the importance of APC in the asymmetric division of stem cells

4) Methods that allow us to calculate the affinity of a small molecule with a protein can be of great importance to the discovery of new drugs and biological probes, and for chemical genomics. Nir London at the Macromolecular Modeling Blog, reviews in an expert-level fashion, a number of different methods to answer the following question: Can we predict small-molecules binding affinities?

5) Circadian clocks control a large number of daily processes in most organisms. These endogenous cellular timekeepers regulate rhythms in gene expression, physiology and behaviour and enable organisms to anticipate predictable environmental variations. Despite the wealth of knowledge concerning the functioning of central oscillators, little is known about the mechanisms that allow them to temporally control gene expression and the activity of different clock targets. Here at MolBio Research Highlights, I discuss an article in which the authors use a clever genetic strategy to characterize circadian output pathways using the model organism Neurospora crassa.

6) Caloric restriction has been shown to increase lifespan and protect against metabolic disease. Michelle over at C6H12O6 comments on an interesting paper in which the authors develop a mouse model of glioblastoma multiforme, one of the “most aggressive and invasive forms of primary human brain cancer”, and tested the efficacy of caloric restriction for its ability to reduce tumour size and invasion.

From her post:
“As it seems, caloric restriction decreases tumor spread and angiogenesis in a malignant brain cancer mouse model. This is strong evidence that cancer cells have difficulty proliferating under metabolic stress, even when healthy cells are functioning normally”
7) Igor Ulitsky, at You'd Prefer An Argonaute, discusses a nice recent article in PLoS Biology reporting that in contrast to what has been suggested by earlier studies, the proportion of 'dark matter' transcription in mammalian genomes appears to be much lower than previously thought. The authors conclude that tiling array approaches to surveying the transcriptome are prone to false positives, and by performing RNA-Seq, they show that many of the tags that fall outside the annotated regions of the genome appear to be somehow associated with known genes, or as Igor puts it:
“(..) about 80% of those reads fall within 10kb of known genes and are likely to represent either unannotated parts of those genes, or transcripts whose biogenesis function is related to the gene adjacent to them, as their expression is generally highly correlated with their neighbors"
8) Iddo Friedberg at Byte Size Biology discusses a Nature paper describing the fascinating functional relationship between the mRNAs produced by the PTEN tumour suppressor gene and its pseudogene PTENP1, and the consequences of this interaction. Briefly, the 3’ UTR of PTEN and PTENP1 are very similar and have conserved seed sequences for interacting with several miRNAs. Notably, the authors show that PTENP1 3′ UTR can act as a decoy of PTEN-targeting miRNAs, thereby enhancing the levels of this tumour suppressor.

9) I have previously stated in my blog that the different steps in gene expression are stochastic biochemical events and that this randomness can lead to substantial cell-to-cell variability in RNA and protein levels that can have phenotypic consequences even within a clonal population of cells. On a fascinating and provocative post, Pablo Astudillo at Astu’s Science Blog, discusses biological heterogeneity, noise and buffering, in the context of developmental biology, reviewing several interesting articles.

Noise control in a theoretical embryo (From Pablo's post)

10) Bacteria in the phylum Planctomycetes have fascinating and unsual properties, including budding reproduction, sterol biosynthesis, absence of cell wall peptidoglycan, and notably, intracellular membrane-bounded compartments. It is also noteworthy that planctomycetes appear to have genes coding for proteins that are similar to “membrane coat proteins”, central players in the eukaryotic-specific process of endocytosis.

Lucas Brouwers at Thoughtomics (who will host the next edition of the MolBio Carnival), comments on a recent PNAS paper reporting the interesting discovery of an endocytic process in the planctomycete Gemmata obscuriglobus which appears to be similar to eukaryotic clathrin-mediated endocytosis. This may have important implications for our understanding of eukaryotic evolution.
“So where does that leave us? Endocytosis, comparmentalization and membrane sorting are no longer exclusive to eukaryotes.”
Gemmata obsuriglobus is capable of endocytosis!

11) From her new home at Field of Science, LabRat highlights a paper characterizing the mechanism herpes simplex virus uses to move around the cell in order to achieve efficient replication and pathogenesis. It appears that a number of viral proteins interact with cellular microtubule motors such as the inbound motor dynein and the outbound motor kinesin-1, which ultimately helps the virus get a free ride across the microtubule network.
“They found that several of the capsid proteins could bind to important transporter molecules, and furthermore that several different transporter molecules could sometimes bind to the same capsid protein”
12) To finish up the 1st issue of the MolBio Carnival, Bosco at Trapped in the U.S.A. tells us the story behind Amgen’s erythropoietin (EPO) patent, which includes corporate espionage and a Japanese scientist that must have gotten a pretty big check.

That's it for this month's edition of The MolBio Carnival. You can check future hosts and past editions at the Carnival’s index page. Be sure to subscribe to its RSS feed to receive notifications and summaries when new editions of the Carnival are posted.
Also, be sure to submit your best molbio blog articles,  using our carnival submission form, to the next edition of The Molbio Carnival, which will be hosted by Lucas Brouwers over at Thoughtomics. More info here.

ResearchBlogging.orgHere are some of the articles discussed in the posts featured in this edition of The MolBio Carnival:

Niethammer, P., Grabher, C., Look, A., & Mitchison, T. (2009). A tissue-scale gradient of hydrogen peroxide mediates rapid wound detection in zebrafish Nature, 459 (7249), 996-999 DOI: 10.1038/nature08119

Quyn, A., Appleton, P., Carey, F., Steele, R., Barker, N., Clevers, H., Ridgway, R., Sansom, O., & Näthke, I. (2010). Spindle Orientation Bias in Gut Epithelial Stem Cell Compartments Is Lost in Precancerous Tissue Cell Stem Cell, 6 (2), 175-181 DOI: 10.1016/j.stem.2009.12.007

van Bakel H, Nislow C, Blencowe BJ, & Hughes TR (2010). Most "dark matter" transcripts are associated with known genes. PLoS biology, 8 (5) PMID: 20502517

Altschuler, S., & Wu, L. (2010). Cellular Heterogeneity: Do Differences Make a Difference? Cell, 141 (4), 559-563 DOI: 10.1016/j.cell.2010.04.033


Read More......