Grasping The (extracellular) Matrix, Location, location, location! and more in my picks of the week from RB

Another week has gone by and some very interesting molbio blog posts have been aggregated to Researchblogging.org. 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], briefly describe them and list them here for you to check out.

Note that I'm only taking into consideration the molbio-related blog posts aggregated under "Biology".

Congratulations to everyone who got their post selected.

1) Not too often do we have the chance to read a blog post discussing a research article, written by the first author himself. Nick Anthis at The Scientific Activist comments on his first first-author paper exploring the “important biological process of integrin activation”.

Integrins are transmembrane cell-adhesion molecules that mediate communication between the inside and the outside of the cell. Integrins are instrumental in anchoring cells to the extracellular matrix, and this is ultimately regulated from “within the cell” by direct binding of regulatory proteins, like talin, to the cytoplasmic domains of integrins.
The study reports the “the first structure of talin bound to an authentic full-length beta integrin tail” which leads to a new model of integrin activation.

2) Regulatory T –cells (TReg cells) help control immune responses, playing a key role in immune homeostasis. Interestingly, it has been proposed that these cells facilitate tumors' escape from immune monitoring. Among the various origins of TReg cells, they have been reported to arise in the CD8+ population of T-cells:

“At least some of the CD8 suppressor T cells can arise from apparently-conventional CD8 T cells. That is, you can pull CD8 T cells out of a normal mouse’s spleen, and depending on what those cells see and are exposed to, they could progress to being conventional CTL — killing tumor cells, producing interferon and other cytokines, generally being a destructive force — or they could become suppressor CD8 T cells, and actively prevent that destruction from happening”

Ian York at Mystery Rays of Outer Space discusses a recent article reporting the fascinating finding that “one of the forces that can drive a CD8 T cell into being a suppressor T cell is a tumor”.

3) Several studies have reported that a gene’s position within the nucleus can have a profound impact on its transcriptional activity. Some nuclear neighborhoods appear to harbor active genes, while others are associated with transcriptional repression.
Lucas Brouwers at Thoughtomics discusses an important article from early 2008 describing one of the latter: the nuclear lamina. Through the use of the DNA adenine methyltransferase identification technique, the authors found well-defined lamina-associated domains. Interestingly, these domains are characterized by low levels of transcription. Together with previous evidence, it supports the view of the nuclear lamina as a transcriptionally repressive compartment.

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

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

Anthis NJ, Wegener KL, Ye F, Kim C, Goult BT, Lowe ED, Vakonakis I, Bate N, Critchley DR, Ginsberg MH, & Campbell ID (2009). The structure of an integrin/talin complex reveals the basis of inside-out signal transduction. The EMBO journal PMID: 19798053

Shafer-Weaver, K., Anderson, M., Stagliano, K., Malyguine, A., Greenberg, N., & Hurwitz, A. (2009). Cutting Edge: Tumor-Specific CD8+ T Cells Infiltrating Prostatic Tumors Are Induced to Become Suppressor Cells The Journal of Immunology, 183 (8), 4848-4852 DOI: 10.4049/jimmunol.0900848

Guelen, L., Pagie, L., Brasset, E., Meuleman, W., Faza, M., Talhout, W., Eussen, B., de Klein, A., Wessels, L., de Laat, W., & van Steensel, B. (2008). Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions Nature, 453 (7197), 948-951 DOI: 10.1038/nature06947

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Eukaryotic genomes as RNA machines

Eukaryotic genomes appear to be "RNA machines" ¹, in the sense that they are almost entirely transcribed, generating a large number of non coding RNAs. Interestingly, some (a yet unknown percentage) perform important regulatory functions and have been shown to exhibit cell type-specific expression, localization to subcellular compartments, and association with human diseases, suggesting that these transcripts may not just represent "transcriptional noise". As only a minority of the myriad of transcripts originating from eukaryotic genomes have been characterized, the extent of their functional relevance (i.e how many of these transcripts serve a role) is currently unknown.

While reading for a class I have to give next week, I came across with a nice way to describe this fascinating finding about eukaryotic genomes:

"If RNA types were to have their own color, each eukaryotic genome would continuously be emitting a riot of hues, with some regions radiating across the entire spectrum as, for example, development unfolds" ²

What a beautiful way to put it...

[Image credit: Ru Tover]

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¹Amaral PP, Dinger ME, Mercer TR, Mattick JS (2008) The eukaryotic genome as an RNA machine. Science 319(5871):1787-9.

²Ponting CP, Oliver PL, Reik W (2009) Evolution and functions of long noncoding RNAs. Cell 136(4):629-41.

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Quotes from the science blogosphere 2

Williamson's hypothesis that caterpillars arose from an accidental mating between butterflies and velvet worms "is the most stupid thing that has ever been proposed"

-Gonzalo Giribet (in a interview for Nature)

The alluded article is a controversial one published in PNAS, a few months ago. This article raised a lot of questions regarding the soon-to-be defunct Track I submission route in this journal (See Good bye track I papers: PNAS)

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Houdini viruses and probing the 3D architecture of the human genome, in my picks of the week from RB

Another week has gone by and some very interesting molbio blog posts have been aggregated to Researchblogging.org. 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], briefly describe them and list them here for you to check out.

Note that I'm only taking into consideration the molbio-related blog posts aggregated under "Biology".

Congratulations to everyone who got their posts selected.

This week, two blog posts made the cut:

1) Lab safety procedures are of utmost importance, particularly in labs that work with human pathogens. A few cases of “lab escapees” have been reported in the virus literature: the last case of smallpox and the 2007 outbreak of foot and mouth disease in the UK where probably the result of escaped lab strains. Ian York from Mystery Rays from Outer Space discusses a recent article reporting a Brazilian isolate of a particular Dengue virus strain, which appears to be closely related to one isolated in Asia more than two decades ago.

(As) dengue viruses mutate and evolve fairly rapidly, this kind of stability (35-fold lower than expected) would be extraordinary in a virus that’s been circulating for two decades.

One possible explanation (among others) for this is that the reported strain is a lab escapee.

2. For the past 40 years, chromatin structure has been the matter of intensive research. With the development of new methodologies, we’ve been able to study beyond the structure of the nucleosome filament into the fascinating, yet still incompletely understood, world of higher-order chromatin folding.
Techniques like the widely applied chromosome conformation capture technology (3C, and its derivations) have allowed us to “analyze the folding of chromatin in the native cellular state at a resolution beyond that provided by current microscopy techniques”^a.

Greg Fish from Weird Things discusses a recent article in Science reporting the development of a new of such techniques called Hi-C which “adapts the above approach (that is, 3C) to enable purification of ligation products followed by massively parallel sequencing”.

Simply put, by using their method, the authors probed the “three-dimensional architecture of the human genome by coupling proximity-based ligation with massively parallel sequencing”.

The thing which sets this technique apart, is that Hi-C allows unbiased identification of chromatin interactions across an entire genome.
Greg comments on two fascinating discoveries arising from this study concerning chromatin conformation and genome organization. You should definitely check both this post and the article out!


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

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

Aquino, V., Amarilla, A., Alfonso, H., Batista, W., & Figueiredo, L. (2009). New Genotype of Dengue Type 3 Virus Circulating in Brazil and Colombia Showed a Close Relationship to Old Asian Viruses PLoS ONE, 4 (10) DOI: 10.1371/journal.pone.0007299

Lieberman-Aiden, E., van Berkum, N., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B., Sabo, P., Dorschner, M., Sandstrom, R., Bernstein, B., Bender, M., Groudine, M., Gnirke, A., Stamatoyannopoulos, J., Mirny, L., Lander, E., & Dekker, J. (2009). Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome Science, 326 (5950), 289-293 DOI: 10.1126/science.1181369


References used in post:
^a Nature Methods - 4, 895 - 901 (2007)

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Celebrate Open Access Week

Last year, the first ever Open Access Day took place, and due to its success, this year events will be schedule for a whole week, starting today!

More here.

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Quotes from the science blogosphere

I read a lot of blogs and I love it. Most (all) of them are of a scientific nature, although their orientation varies: some discuss primary research literature and science in general and a few others are funny rants about life as a scientist. They are all part of the fantastic science blogosphere experience I've been living since last January, and I value them deeply. During lab downtime , I can just sit down and browse through my Google Reader to see what's new on my favorite blogs.

Every so often, I come across with a funny quote that I usually then share through my Facebook status or my Gmail nickname. Last night, while preparing my "Picks of the Week", I read a comment on one of the posts that made me crack up, and immediately shared it through the channels mentioned. It then occur to me that I could also share them through my blog for others to enjoy.

So here I am, sharing just two of the most recent ones, but I will be sharing more as I find them:

(...) cell signalling is the most boring subject in cell biology. There are of course exceptions, but if you've spent your entire PhD studying ONE residue of a X-kinase-kinase-kinase doing in-vitro auto-phosphorylation assays and cloned 92 different point mutations, I feel bad for you.

-Anonymous Coward, as a comment on this post at Bayblab.

It is my solid faith that the intelligent designer took a few hits of LSD on the 7th day, and created the protists. True story.

-Psi Wavefunction, as a comment on this post at Lab Rat.


I then remembered that a few weeks ago, I actually shared a quote from a fellow blogger here at my blog [Rant by fellow blogger: manuscript reviewing]

(...) I must admit it was difficult not to laugh while trying to find a diplomatic way of saying that the manuscript was the scientific equivalent of vomit and that it appeared to have been conceived, executed and written by a turnip.

-Professor in Training (blog post, here).


I promise to keep them coming. I will label these posts under "blog quotes".

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Coming soon at MRH: Cancer Research Blog Carnival

As some of you may already know, MolBio Research Highlights will host the 27th issue of the Cancer Research Blog Carnival, a "monthly roundup of posts from the cancer blogosphere".

A few blog posts from our blog have been featured in previous issues of the Carnival. You can check them out here and here.

The Carnival is open to submissions in a variety of cancer-related topics, such as cancer biology, cancer genetics, therapeutics and diagnosis, just to name a few. Considering that we will be hosting the next issue and then we have full editorial control on what gets to be featured, it's important to notice that, in agreement with the spirit of this blog, we will favor blog posts with a molecular biology orientation, although posts of a different nature or focus, may also make the cut.

The carnival will be posted on November 6th, so there's plenty of time for you to get down to writing.

There have been lots of fascinating publications on cancer genetics and molecular biology during the last month, so there's a lot to work with.

We look forward to your submissions! If you have written a blog post on a cancer-related topic and you want it featured in the next issue of the Cancer Research Blog Carnival, use the submission form available here.

To get a sense of the topics discussed on this Carnival, you can check out the collection of past carnivals here.

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Nature Communications: a new journal from NPG

Nature Communications, a new online-only journal from NPG is now open for business:

Nature Communications is an online-only, multidisciplinary journal dedicated to publishing high-quality research in all areas of the biological, physical and chemical sciences. Papers published by the journal represent important advances of significance to specialists within each field.

Noteworthy is the fact that:

(...) papers published in Nature Communications will be of high quality, without necessarily having the scientific reach of papers published in Nature and the Nature research journals.

The journal will be launched in Spring 2010, but is now accepting submissions.

Learn more at the Journal's home page.

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Omics-dominated issue! Genomics, metagenomics, reactomics and more, in my picks of the week from RB

Another week has gone by and some very interesting molbio blog posts have been aggregated to Researchblogging.org. 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], briefly describe them and list them here for you to check out.

Note that I'm only taking into consideration the molbio-related blog posts aggregated under "Biology".

As previously stated (see here), "Picks of the week" will now be posted on Mondays, so here we are, and with a fascinating "Omics-dominated" issue.

Congratulations to everyone who got their posts selected.

This week, 4 (actually 5) blog posts are highlighted:

1) Iddo Friedberg brings us a fantastically written post on microbial diversity. The driving force behind his post? A recent article reporting that due to sequencing errors, metagenomics studies may be overestimating the number of reported operational taxonomic units, by as much as two orders of magnitude! Although he doesn’t get into the paper’s details, I considered this article to be so enticing, that I had to highlight it for you to check out.

2) Thoughtomics blogs about a recent article which reports a fascinating finding: it appears that there is a striking negative correlation of genomically encoded tyrosine content and biological complexity (as measured by the number of cell types in each organism). That is, the more complex the organism, the less tyrosines in its proteins.

Further, a correlation was also found regarding tyrosine kinases in the metazoan lineage, although of a reverse nature: the more tyrosine kinases you have, the less tyrosine your proteins have! A provocative explanation to all this, in the context of the evolution of signaling networks in multicellular animals, is presented, as discussed by the authors.

3) Keith Robison from Omics! Omics! discusses an interesting new article published in Science describing “a sensitive metabolite array for genome sequence–independent functional analysis of metabolic phenotypes and networks, the reactomes, of cell populations and communities.”

The authors synthesized an array consisting of over a thousand substrate compounds ("collectively representing central metabolic pathways of all forms of life") immobilized to a glass slide. By applying cell extracts to this array, the authors effectively performed a high-throughput screening of enzyme activities: "Productive catalytic action of an enzyme on a substrate of the array, gave a fluorescent signal". Further, the protein remained linked to the nanoparticle, from which it could then be cleaved, trypsinized and identified by mass spectrometry.

"Proof of principle was shown by reconstruction of the metabolic maps of model bacteria. Utility of the array for unsequenced organisms was demonstrated by reconstruction of the global metabolisms of three microbial communities derived from acidic volcanic pool, deep-sea brine lake, and hydrocarbon-polluted seawater".

4) Finally, Dan Koboldt and Keith Robison at MassGenomics and Omics! Omics! respectively, both discuss a recent article on the topic of cancer genomics. Through the use of Illumina technology, a Canadian group sequenced both the genome and transcriptome of an oestrogen-receptor-alpha-positive metastatic lobular breast cancer and compared it to a primary tumor sample from the same patient, from 9 years earlier.

The authors found 32 somatic non-synonymous coding mutations in the metastasis and measured the frequency of these somatic mutations in DNA from the primary tumour sample: most of these mutations were absent from the primary tumor. Interesting questions arising from this result are discussed on these posts.

Also, as the authors performed mRNA-Seq to assess the transcriptome, they were able to validate two instances of high-frequency, protein-altering RNA editing events, and they found that the “ADAR RNA-editing enzyme was one of the most highly expressed genes in the metastasis”.

From the article:

Taken together, our data show that single nucleotide mutational heterogeneity can be a property of low or intermediate grade primary breast cancers and that significant evolution can occur with disease progression.

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

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


Quince, C., Lanzén, A., Curtis, T., Davenport, R., Hall, N., Head, I., Read, L., & Sloan, W. (2009). Accurate determination of microbial diversity from 454 pyrosequencing data Nature Methods, 6 (9), 639-641 DOI: 10.1038/nmeth.1361

Tan CS, Pasculescu A, Lim WA, Pawson T, Bader GD, & Linding R (2009). Positive selection of tyrosine loss in metazoan evolution. Science (New York, N.Y.), 325 (5948), 1686-8 PMID: 19589966

Beloqui, A., Guazzaroni, M., Pazos, F., Vieites, J., Godoy, M., Golyshina, O., Chernikova, T., Waliczek, A., Silva-Rocha, R., Al-ramahi, Y., La Cono, V., Mendez, C., Salas, J., Solano, R., Yakimov, M., Timmis, K., Golyshin, P., & Ferrer, M. (2009). Reactome Array: Forging a Link Between Metabolome and Genome Science, 326 (5950), 252-257 DOI: 10.1126/science.1174094

Shah, S., Morin, R., Khattra, J., Prentice, L., Pugh, T., Burleigh, A., Delaney, A., Gelmon, K., Guliany, R., Senz, J., Steidl, C., Holt, R., Jones, S., Sun, M., Leung, G., Moore, R., Severson, T., Taylor, G., Teschendorff, A., Tse, K., Turashvili, G., Varhol, R., Warren, R., Watson, P., Zhao, Y., Caldas, C., Huntsman, D., Hirst, M., Marra, M., & Aparicio, S. (2009). Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution Nature, 461 (7265), 809-813 DOI: 10.1038/nature08489

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"Picks of the week" will now be published on Mondays

A huge headache and lots of accumulated lab work have finally pushed me into making a decision I`ve been considering for a while now.

I will move my "Picks of the Week" [see this post if you don´t know what that is. Also, see here] from Thursdays to Mondays: this allows me to start preparing these posts on the weekends, which doesn`t disturb my "lab time" as much.

I´ll have more time to read, analyze and discuss insightful and provocative posts aggregated to Researchblogging.org, and then highlight them here for you. I think this works for the best.

I´ll be back on Monday with my Picks of the Week of molbio blog posts aggregated to ResearchBlogging.org.

Stay tuned!

(Image Credit: Wheaton College)

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Quick post: World University Rankings 2009

The Times Higher Education-QS World University Rankings have recently been released.
No many surprises on the Top-10, still pretty much US-dominated. You can check the Top 200 Universities here.

Now, onto what's relevant to us: The Top Universities for life sciences & biomedicine (They too are US-dominated)

Here's the top 10:

Harvard University
University of Cambridge
University of Oxford
Stanford University
University of California, Berkeley
Johns Hopkins University
University of Tokyo
Massachusetts Institute of Technology
Yale University
McGill University

You can check the whole ranking, here.

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Excellent!!: Nobel Prize for structure and function of the ribosome

It has been on everyone's list for number of years now, and this year it finally came true:

The 2009 Nobel Prize in Chemistry was given to Venkatraman Ramakrishnan, Thomas A. Steitz and Ada E. Yonath "for studies of the structure and function of the ribosome".

Congratulations!!

Here's a pic I took in a meeting in Bariloche, Argentina in '07, at a Gene Expression and RNA Processing meeting.

You can see two Nobel prize recipients here: Tom Cech (1989) and Tom Steitz (2009), both in Chemistry.

From left to right: Tom Cech, Tom Steitz, Joan Steitz

More info here: http://nobelprize.org/nobel_prizes/chemistry/laureates/2009/index.html

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Silence: a journal of RNA regulation

I was browsing around BioMed Central's website, surfing through different BMC journals when I came across with Silence.

"Silence? What the heck is this?" I thought to myself. So I clicked on it and there it was:

Silence is an online, peer-reviewed open access journal that covers all aspects of genetic and epigenetic control that are mediated by RNA.

Although Silence is presently accepting submissions, it's yet to be launched by BioMed Central.

David Baulcombe and Phil Zamore (Editors in chief) lead a FANTASTIC editorial board:

Victor Ambros (United States)
Rumiana Bakalova (Japan)
David Bartel (United States)
James Carrington (United States)
Richard Carthew (United States)
Xuemei Chen (United States)
Mark E Davis (United States)
Witold Filipowicz (Switzerland)
Klaus Giese (Germany)
Scott Hammond (United States)
Gregory Hannon (United States)
Craig P Hunter (United States)
Elisa Izaurralde (Germany)
Steve Jacobsen (United States)
Richard A Jorgensen (United States)
Mark A Kay (United States)
Anastasia Khvorova (United States)
V Narry Kim (Korea, Republic Of)
Judy Lieberman (United States)
John Mattick (Australia)
Marjori Matzke (Austria)
Peter Mouritzen (Denmark)
Norbert Perrimon (United States)
Nikolaus Rajewsky (Germany)
John J Rossi (United States)
Mikiko C Siomi (Japan)
Frank J Slack (United States)
Erik Sontheimer (United States)
Markus Stoffel (Switzerland)
Thomas Tuschl (United States)
Peter Waterhouse (Australia)

So many great scientists! So many people I'd like to invite to my University! I got to invite John Mattick here last April [see Long overdue post on John Mattick's visit] and now I'm pushing for David Bartel, but most of these scientists were on the same list Mattick was when we decided on him, so we'll just have to see.

Anyway, the journal seems timely and I look forward to its first issue.
Check it out: it's Open Access

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The almighty Fungi

The fungi have a number of characteristics that make them good research organisms, like relatively small genomes and haploid life stages. Further, DNA transformation and gene KOs are routine in some of them.

Current Biology now brings us a Primer on The Fungi! (A primer offers accessible accounts of a broad range of subjects in biology).

The importance of Fungi to medicine, industry, and the biosphere is widely appreciated. In this Primer, Stajich and colleagues summarize the key diversifications that have taken place within this kingdom and describe the modes of nutrition, reproduction, and communication within the various clades.

The magazine highlight is available FREE online.

That's right: FREE. No excuse to miss it.

Check it out here.


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(Image credit: Phycomyces blakesleeanus genome at JGI)

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“Noitulove”, one-Factor iPS cells and more in my picks of the week from RB

Another week has gone by and some very interesting molbio blog posts have been aggregated into Researchblogging.org. 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], briefly describe them and list them here for you to check out.

Note that I'm only taking into consideration the molbio-related blog posts aggregated under "Biology".

Once again, three blog posts were selected this week:

1. Reverse evolution has been defined as the “reacquisition by derived populations of the same character states as those of ancestor populations” ^a

Can evolutionary changes be reversible? One could argue that the longer the “evolutionary path” (longer time span since diversifying from an ancestral state), the harder is to return to that specific ancestral state, due to accumulation of more changes.
Although there are many limitations to the study of reversibility, a recent paper argues that by “studying the reversibility of evolutionary changes in protein structure and function, (some of) these limitations can be overcome”

Keith Robinson at Omics! Omics! discusses this paper which, by means of ancestral gene reconstruction, protein engineering and X-ray crystallography, uses the vertebrate glucocorticoid receptor as a case-study for reverse evolution. It appears that the path that led the ancestral gene to acquire its new functions it’s one that’s very hard to retrace directly. Several mutations which optimized the new specificity of the glucocorticoid receptor also destabilized elements of the protein structure that were required to support the ancestral conformation. So, reversing only the key function-switching mutations yields a non functional protein.

From the article:

Our findings indicate that even if selection for the ancestral function were imposed, direct reversal would be extremely unlikely, suggesting an important role for historical contingency in protein evolution.

Keith states:

[T]his is a well-detailed case where evolutionary change eventually blocked the route back to the start.

^a Teotónío AH & Rose MR (2001)Perspective: reverse evolution. Evolution 55: 653–660

2. A few weeks ago the Albert Lasker Basic Medical Research Award honored John Gurdon and Shinya Yamanaka

for discoveries concerning nuclear reprogramming, the process that instructs specialized adult cells to form early stem cells — creating the potential to become any type of mature cell for experimental or therapeutic purposes.

[See Quick post: Gurdon and Yamanaka win Lasker]

Yamanaka showed that you can generate pluripotent stem cells from mouse embryonic or adult fibroblasts by introducing four transcription factors, Oct3/4, Sox2, c-Myc, and Klf4, under ES cell culture conditions.
The study of these induced pluripotent stem cells (or iPS cells) has grown rapidly over the last few years: several studies have now reported the generation of iPS cells from human cells using the same factors.

Charles Daney over at Science and Reason discusses a recent article in Nature reporting the generation of iPS cells from human fetal neural stem cells using only one transcription factor: OCT4. Interestingly, these cells resemble human embryonic stem cells in global gene expression profiles, epigenetic status, as well as pluripotency in vitro and in vivo.

Charles also comments on potential therapeutic applications of iPS cells and on a few issues that hamper their use at the time.

3. Structural genomics is the large-scale determination of protein structures. Cranial Discomfort discusses a provocative new article in Science reporting a three-dimensional reconstruction of the central metabolic network of the bacterium Thermotoga maritima, through the use of structural genomics and systems biology.
The network encompassed 478 proteins of which the structures of only 120 have been determined experimentally and 358 were predicted and modeled with a variety of computational approaches. This allowed for the generation of a metabolic model of T. maritima.

From the article:

(…) integration of structural data with networks analysis generates insight into the function, mechanism, and evolution of biological networks.

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

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


Bridgham JT, Ortlund EA, & Thornton JW (2009). An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature, 461 (7263), 515-9 PMID: 19779450

Kim, J., Greber, B., Araúzo-Bravo, M., Meyer, J., Park, K., Zaehres, H., & Schöler, H. (2009). Direct reprogramming of human neural stem cells by OCT4 Nature, 461 (7264), 649-643 DOI: 10.1038/nature08436

Zhang Y, Thiele I, Weekes D, Li Z, Jaroszewski L, Ginalski K, Deacon AM, Wooley J, Lesley SA, Wilson IA, Palsson B, Osterman A, & Godzik A (2009). Three-dimensional structural view of the central metabolic network of Thermotoga maritima. Science (New York, N.Y.), 325 (5947), 1544-9 PMID: 19762644

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