Thursday, January 29, 2009

System-wide molecular evidence for phenotypic buffering in Arabidopsis

In this Brief Communication, in a very nice issue of Nature Genetics, the authors profiled several Arabidopsis lines for a system-wide genetical genomics1 study of molecular variation, integrating transcript, protein and metabolite data from a population of recombinant inbred lines2 (RILs) of this model plant.

It appears that most of the genome and transcript variation between the two parental accession used for generating the RILs (and of the RILs themselves), is 'buffered' and does not result on phenotypic variation.
The largest fraction of molecular variants is silent at the phenotypic level and only a few influential 'hot spots' regions cause a mejor phenotypic variation across a range of environmental conditions
Interestingly, and despite the generalized buffering, the authors described six QTL (quantitative trait loci) hotspots,
which seem to correspond to a few molecular 'breakpoints' of an otherwise robust regulatory system
This is somewhat related to an article I posted recently on phenotypic variation buffering in yeast. In general, the idea seems to be that most of the variation in a species remains silent phenotypically, but alterations in certain genes or sequences may unleash the accumulated genetic variation and it can then be manifested at the phenotypic level. In the case of the yeast article, the authors proposed these genes were network hubs.

Although the authors comment that most of the reported hotspots could be linked to well-studied genes, such as CRY2 or HUA2, it must me emphasized that due to the somewhat imperfect resolution of QTL mapping, maybe other genes or regions may be involved in the observed traits.
Buffering and release of variation may be widespread phenomenon; for example, in both Drosophila and Arabidopsis, altered Hsp90 function results in pleiotropic phenotypic effects dependent on the underlying genotype.

I leave you with the final sentence of this article
variation in a multitude of Arabidopsis complex traits can be explained to a considerable extent by only a few QTL hot spots

Here's the abstract and reference:

System-wide molecular evidence for phenotypic buffering in Arabidopsis

Fu J, Keurentjes JJ, Bouwmeester H, America T, Verstappen FW, Ward JL, Beale MH, de Vos RC, Dijkstra M, Scheltema RA, Johannes F, Koornneef M, Vreugdenhil D, Breitling R, Jansen RC.
[1] Groningen Bioinformatics Centre, University of Groningen, 9751NN Haren, The Netherlands. [2] Department of Genetics, University Medical Centre Groningen, University of Groningen, 9700RB Groningen, The Netherlands. [3] These authors contributed equally to this work.

We profiled 162 lines of Arabidopsis for variation in transcript, protein and metabolite abundance using mRNA microarrays, two-dimensional polyacrylamide gel electrophoresis, gas chromatography time-of-flight mass spectrometry, liquid chromatography quadrupole time-of-flight mass spectrometry, and proton nuclear magnetic resonance. We added all publicly available phenotypic data from the same lines and mapped quantitative trait loci (QTL) for 40,580 molecular and 139 phenotypic traits. We found six QTL hot spots with major, system-wide effects, suggesting there are six breakpoints in a system otherwise buffered against many of the 500,000 SNPs.

Jingyuan Fu, Joost J B Keurentjes, Harro Bouwmeester, Twan America, Francel W A Verstappen, Jane L Ward, Michael H Beale, Ric C H de Vos, Martijn Dijkstra, Richard A Scheltema, Frank Johannes, Maarten Koornneef, Dick Vreugdenhil, Rainer Breitling, Ritsert C Jansen (2009). System-wide molecular evidence for phenotypic buffering in Arabidopsis Nature Genetics, 41 (2), 166-167 DOI: 10.1038/ng.308

1 I know this may be a new concept for many of you, and instead of explaining it myself, and give a possibly complex definition, I'd rather direct you to an article on Trends in Genetics (2001) 17:388-391.
2See Broman KW. Genetics. 2005 Feb;169(2):1133-46.

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Wednesday, January 28, 2009

Are you tired of pippeting?

A friend of mine recently pointed me to this hilarious ad by the people at Eppendorf.
It's a music video promoting a new system called epMotion.
Here's a pic of the 'boy band' performing the main song and I also attach part of the lyrics...

Pipetting all those well-plates, baby, sends your thumbs into overdrive
And spending long nights in the lab makes it hard for your love to thrive
What you need is automation, girl, something easy as 1 2 3
So put down that pipette, honey, I got something that will set you free

Makes you remember the commercial by BioRad...

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Sunday, January 25, 2009

Darwin year... or gear?

s come up with a whole line of Darwin-related gear considering (for those who still don't know) that 2009 marks the 200th anniversary of the birth of Charles Darwin and the 150th anniversary of the publication of "On the Origin of Species".
There are lots of cool stuff for sale, so I invite you to take a look at the store at or the main website

For example, you can buy a nice t-shirt with the following logo on it:

So, check it out and buy something: 50% of the earnings go directly to conservation charities, and the other 50% will be invested in developing other evolution-related websites. A gift from this site could get you on your PI's best side ;-)

Now, getting a little more 'scholar' about it, in case you haven't noticed, Nature published a document entitled '15 Evolutionary Gems' which "summarizes 15 lines of evidence from papers published in Nature over the past 10 years" on evidence for evolution by natural selection.
This document has been made freely available so there's no excuse not to check it out and read a little about the 'incontrovertible evidence' on evolution by natural selection.
[It will make a good 'beach reading' for those on their summer vacation (in the southern hemisphere)]

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Friday, January 23, 2009

On replying to referees

I've recently posted a paper on how to reply to referees' comments when submitting a paper for publication.

While waiting for my gel to solidify, I came across with a comic of the graduate student comic strip Piled Higher & Deeper, or PhD comics, which seemed appropriate...

While neither of the ways presented on the comic are the right ways to do it, I thought it was funny and wanted to share it with you ;-)
If you are a grad student and you've never heard of PhD comics before, I strongly encourage you to visit its site, but be warned that it will definitely take a lot of time out of your research....

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Wednesday, January 21, 2009

RNA silencing

I think it was about time Nature published a new Insight on RNA silencing (there was one on RNA interference in 2004). As I mentioned on a recent post, small RNAs have revolutionized molecular biology and are now considered as important regulators of gene expression and also genome integrity.
Since the pioneering work of Victor Ambros and Gary Ruvkun in animals (describing the first miRNA and its target) and David Baulcombe in plants (describing a "little thing" called 'co-supression'), great advances have been made and these small RNAs have been found to participate on a vast array of biological processes on both plants and animals.
This Insight has just been published online today, so as soon as I get my paper issue of Nature, I'll take a deeper look at it (I just breezed through the articles at the lab).
It's a Free Access document, so I invite all of you to take a look at it, and post your comments here.

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Monday, January 19, 2009

Plant Biology Video Contest is organizing a contest for the best new videos illustrating different aspects of plant life (from the molecular and cellular aspects of plant biology to the whole plant and ecosystem levels). You can enter the contest simply by uploading your video to Youtube and filling an entry form at the organizer’s site. They must be, however, intended for the general public.
For those thinking ‘why in earth would I enter such a contest?” you may find it interesting to know that there are up to $8,000 US in prizes:
Grand Prize is $1,000; multiple categories will be eligible for 1st Prizes of $500; 2nd Prizes of $250; and Honorable Mentions.

Check the rules and more details at Chlorofilms’ website.

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Saturday, January 17, 2009

A new education site in genetics by NPG

I was pleased to read in my January 1st issue of Nature that NPG (Nature Publishing Group) has launched an 'online teaching tool for undergraduate biology and genetics'. This site is called Scitable and hosts a number of articles in all areas of genetics, from molecular to evolutionary genetics. The site describes itself as a 'free educational resource for faculty who want to help their students develop a deeper comprehension and appreciation for science'. This is a very laudable initiative and I'm glad that NPG supported such an endeavor.

An interesting thing is that as an educator, you can upload items to the site (presentations, etc). I don't know, though, how they are reviewed (or if they are indeed reviewed, for that matter).
In general, this is a very good idea, although I'm less convinced about the fact that faculty will indeed post their presentations there or even take the time to review the articles. Time will tell.

The thing I didn't like, though, is that you cannot comment (or at least not publicly) on the articles posted. You can, however, start a discussion, but I got the feeling that the 'discussions' section was created not to post feedback on the articles, but to reply to general questions/topics posted by the Section editor.
If this is an educational site, we should make sure that the facts are accurate, and if any mistake shall appear there, we (the site visitors/users) should be able to point them out directly.

What errors could there be in a site created by the publisher of Nature, you may ask. When asked about his opinion of the site, Laurence Moran (Professor in the Department of Biochemistry at the University of Toronto and the author of the fantastic blog, Sandwalk), pointed out:

"It's better than a lot of other sites but it suffers from some of the same flaws, namely an overemphasis on "new" discoveries. This distracts from the core material".
Regarding specific errors, he mentioned:

"It discusses random genetic drift under "Neutral Theory." While the author does point out that beneficial alleles can be eliminated and detrimental alleles can be fixed, he doesn't seem to grasp the implications. He also makes the fundamental error of implying that drift only works in small populations".
Another thing Larry mentioned, is something I also noticed the exact second I started browsing around the site: Scitable gets the 'central dogma of molecular biology' wrong. This is a widely misinterpreted concept and considering that the one and only Francis Crick published a paper on Nature itself to re-explain what the dogma actually means (Crick, Nature 19701, after his original proposal of the concept in 19582), this is unacceptable. I won't elaborate on the concept here, mainly because it gets way off the purpose of this post (although I may address this issue in a later one), but for a nice discussion on what the concept really means (and what it definitely does not), you can check Larry's clarification [Basic Concepts: The Central Dogma of Molecular Biology]

Take this into consideration as well (taken from Crick's 1970 paper):
"It (the central dogma) is not the same, as is commonly assumed, as the sequence hypothesis, which was clearly distinguished from it in the same article (Crick, 1958). In particular, the sequence hypothesis was a positive statement, saying that the (overall) transfer nucleic acid → protein did exist, whereas the central dogma was a negative statement saying that transfers from protein did not exist".
Anyway, there are a series of interesting tools in the site, like 'create a classroom' or 'student q&a room'. Further, all topics have sections with titles such as
"What do we know?", "How do we know it?" and "Why do we care?".

I invite you all to check it out and then come back here with your comments.

UPDATE March18 2009:
Ryan Gregory has pointed out some other factual errors he have found in Scitable. Check his comments here [Scitable again].

1 Crick, F. (1970) Central Dogma of Molecular Biology. Nature 227, 561-563.
2 Crick, F.H.C. (1958) On protein synthesis. Symp. Soc. Exp. Biol. XII:138-163

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Friday, January 16, 2009

Small silencing RNAs: an expanding universe

Ghildiyal M, Zamore PD.

University of Massachusetts Medical School, Worcester, MA 01605-2324, USA.

Since the discovery in 1993 of the first small silencing RNA, a dizzying number of small RNA classes have been identified, including microRNAs (miRNAs), small interfering RNAs (siRNAs) and Piwi-interacting RNAs (piRNAs). These classes differ in their biogenesis, their modes of target regulation and in the biological pathways they regulate. There is a growing realization that, despite their differences, these distinct small RNA pathways are interconnected, and that small RNA pathways compete and collaborate as they regulate genes and protect the genome from external and internal threats.

Nature Reviews Genetics 10, 94 (2009). doi:10.1038/nrg2504

It's always a pleasure to read Phil Zamore's reviews. He writes very clearly and to the point, a characteristic that I think is missing from the majority of scientists nowadays. Although efforts have been made in some grad programs to teach young scientists to write, this is not often the case.
This is a bigger problem for non-native English speakers; I can't think of anything more annoying that having a paper rejected for poor language. I've taken my precautions and trained myself in scientific writing; I even took an internship at 'Science Editor', the periodical of the Council of Science Editors, so I hope that never happens to me.

Well, this is not at all the point I wanted to make by posting this paper. I posted this nice review mainly because of the great impact these riboregulators have had on the way we perceive gene expression regulation. Although there are some other great reviews on the subject (by David Bartel or Tom Tuschl, just to name two important researchers in the field) , I highlighted this one, mainly because it's one of the best that has been published since this blog is up and running. Although this review is mainly focused on siRNAs, it also mentions miRNAs and the most-recently-discovered piRNAs. It also discusses on how their pathways interact with one another. This review does a nice job classifying these small RNAs based on their biogenesis, which appears to be the best way to do this if you ask me.

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Thursday, January 15, 2009

Self-Sustained Replication of an RNA Enzyme

Lincoln TA, Joyce GF.

Departments of Chemistry and Molecular Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

An RNA enzyme that catalyzes the RNA-templated joining of RNA was converted to a format whereby two enzymes catalyze each other's synthesis from a total of four oligonucleotide substrates. These cross-replicating RNA enzymes undergo self-sustained exponential amplification in the absence of proteins or other biological materials. Amplification occurs with a doubling time of about one hour, and can be continued indefinitely. Populations of various cross-replicating enzymes were constructed and allowed to compete for a common pool of substrates, during which recombinant replicators arose and grew to dominate the population. These replicating RNA enzymes can serve as an experimental model of a genetic system. Many such model systems could be constructed, allowing different selective outcomes to be related to the underlying properties of the genetic system.

Science. 2009 (Published Online January 8, 2009)

This provocative paper was suggested by Roberto Munita, a grad student at P. Universidad Católica de Chile. All of those who crave articles with evolutionary implications on the emergence of life, may find this article interesting.

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Two novel GPCR-type G proteins are abscisic acid receptors in Arabidopsis

Pandey S, Nelson DC, Assmann SM.

Biology Department, 208 Mueller Laboratory, Penn State University, University Park, PA 16802, USA.

In plants, G proteins modulate signaling by the stress hormone, abscisic acid (ABA). We identify and characterize two novel Arabidopsis proteins that show homology to an orphan vertebrate GPCR (GPR89) and interact with the sole Arabidopsis G protein alpha subunit, GPA1, but also have intrinsic GTP-binding and GTPase activity. We have named these proteins GPCR-type G proteins (GTG1 and GTG2). Arabidopsis mutants lacking both GTG1 and GTG2 exhibit ABA hyposensitivity. GTG1 and GTG2 bind ABA specifically. The GDP-bound form of the GTGs exhibits greater ABA binding than the GTP-bound form, the GTPase activity of the GTGs is inhibited by GPA1, and gpa1 null mutants exhibit ABA-hypersensitive phenotypes. These results predict that, unusually, it is the GDP-bound, not the GTP-bound, form of the GTGs that actively relays the signal. We propose that GTG proteins function both as a new type of G protein and as a class of membrane-localized ABA receptors.

Cell. 2009 Jan 9;136(1):136-48.

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Wednesday, January 14, 2009

Dynamics of DNA replication loops reveal temporal control of lagging-strand synthesis

Hamdan SM, Loparo JJ, Takahashi M, Richardson CC, van Oijen AM.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA.

In all organisms, the protein machinery responsible for the replication of DNA, the replisome, is faced with a directionality problem. The antiparallel nature of duplex DNA permits the leading-strand polymerase to advance in a continuous fashion, but forces the lagging-strand polymerase to synthesize in the opposite direction. By extending RNA primers, the lagging-strand polymerase restarts at short intervals and produces Okazaki fragments. At least in prokaryotic systems, this directionality problem is solved by the formation of a loop in the lagging strand of the replication fork to reorient the lagging-strand DNA polymerase so that it advances in parallel with the leading-strand polymerase. The replication loop grows and shrinks during each cycle of Okazaki fragment synthesis. Here we use single-molecule techniques to visualize, in real time, the formation and release of replication loops by individual replisomes of bacteriophage T7 supporting coordinated DNA replication. Analysis of the distributions of loop sizes and lag times between loops reveals that initiation of primer synthesis and the completion of an Okazaki fragment each serve as a trigger for loop release. The presence of two triggers may represent a fail-safe mechanism ensuring the timely reset of the replisome after the synthesis of every Okazaki fragment.

Nature 457, 336-339 (15 January 2009) | Published online 23 November 2008

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Tuesday, January 13, 2009

So what exactly is this blog about?

I usually spend a lot of time surfing through email alerts and RSS feeds from my Google reader, from a series of scientific journals. Every time I found an article I thought a colleague/friend might find interesting/useful, I used to forward it to them. After sending a whole lot of papers to my colleagues, they suggested that I created a blog where I could compile all of these articles instead of sending them and filling their email accounts. I considered this to be very useful, as they could subscribe to the blog, and not only read what I thought would be interesting to them, but all that I thought of as being interesting altogether. So, this blog was initially created in order to highlight some research articles/websites/news and commentaries in the life sciences (mainly molecular biology).

Later, we decided it was better to comment and discuss many of the papers rather than only posting links to them. Posts that feature only links are not very useful. We joined ResearchBlogging and frequently submit our discussions to that aggregator. But what about all those paper that we don't discuss, but that may be interesting to many other molecular biologists? That's why we created "Around the Journals", in which we highlight selected molbio articles from a hand-picked list of journals directly from our Google Reader account

We noticed that there are not many websites and blogs dedicated specifically to molecular biology, and the few that are, don't generally give detailed, analytical and/or comprehensive descriptions of the reported papers, nor are they generally reviewed by biologists.

We consider this site to be an interesting contribution in this matter and our aim is to group, analyze and discuss, in just one place, a series of papers,news,websites and tools in molecular biology in a way to help fellow researchers and also to create a community where discussion, one of the basis of science, can take place.

It is noteworthy that we cannot (due the ever growing amount of papers and journals) be comprehensive here and several articles that people might think of as 'MUST-HIGHLIGHT articles' may not be here. This may be for several reasons. As mentioned, our search for articles is not comprehensive. Second, the articles may be biased towards our fields of research. One way we would like to approach this limitation is by inviting fellow scientists working in different areas in molecular biology to contribute to the blog by suggesting papers to be highlighted here or even by writing their own reviews of the articles. Those will be reviewed by the Editor before publication in the blog. As we are part of, these articles may have a wide dissemination.

OK. Enough with the seriousness. In this blog we will also talk about life as a scientist, things we consider interesting or noteworthy and we may also use it to rant a little, so bare with us.

Please feel free to comment on any of the posted articles and to suggest article,websites, etc. to be highlighted here, at aemonten (at)

A special invitation to participate is extended to grad students from schools everywhere. This will lead to interesting discussion, which are the basis of science.


Alejandro Montenegro-Montero (Editor)
Francisco Barriga

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The replisome uses mRNA as a primer after colliding with RNA polymerase

Pomerantz RT, O'Donnell M.

The Rockefeller University, Howard Hughes Medical Institute, 1230 York Avenue, New York, New York 10021, USA.

Replication forks are impeded by DNA damage and protein-nucleic acid complexes such as transcribing RNA polymerase. For example, head-on collision of the replisome with RNA polymerase results in replication fork arrest. However, co-directional collision of the replisome with RNA polymerase has little or no effect on fork progression. Here we examine co-directional collisions between a replisome and RNA polymerase in vitro. We show that the Escherichia coli replisome uses the RNA transcript as a primer to continue leading-strand synthesis after the collision with RNA polymerase that is displaced from the DNA. This action results in a discontinuity in the leading strand, yet the replisome remains intact and bound to DNA during the entire process. These findings underscore the notable plasticity by which the replisome operates to circumvent obstacles in its path and may explain why the leading strand is synthesized discontinuously in vivo.

Another paper by Mike O'Donnell  highlighting the complexities of the DNA replication machinery and suggesting an exciting explanation to an 'ancient' observation regarding the discontinuous synthesis not only of the lagging strand (which is explained by the antiparallel disposition of the DNA strands that must be replicated by a single advancing holoenzyme), but also of the leading strand in vivo. Indeed, Okazaki, in his original work, observed this discontinuity in vivo and has been demonstrated by a number of in vivo studies since then. 

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Monday, January 12, 2009

Negative feedback that improves information transmission in yeast signalling

Yu RC, Pesce CG, Colman-Lerner A, Lok L, Pincus D, Serra E, Holl M, Benjamin K, Gordon A, Brent R.

Molecular Sciences Institute, 2168 Shattuck Avenue, Berkeley, California 94704, USA.

Haploid Saccharomyces cerevisiae yeast cells use a prototypic cell signalling system to transmit information about the extracellular concentration of mating pheromone secreted by potential mating partners. The ability of cells to respond distinguishably to different pheromone concentrations depends on how much information about pheromone concentration the system can transmit. Here we show that the mitogen-activated protein kinase Fus3 mediates fast-acting negative feedback that adjusts the dose response of the downstream system response to match the dose response of receptor-ligand binding. This 'dose-response alignment', defined by a linear relationship between receptor occupancy and downstream response, can improve the fidelity of information transmission by making downstream responses corresponding to different receptor occupancies more distinguishable and reducing amplification of stochastic noise during signal transmission. We also show that one target of the feedback is a previously uncharacterized signal-promoting function of the regulator of G-protein signalling protein Sst2. Our work suggests that negative feedback is a general mechanism used in signalling systems to align dose responses and thereby increase the fidelity of information transmission.

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Friday, January 9, 2009

MAPK target networks in Arabidopsis thaliana revealed using functional protein microarrays

Popescu SC, Popescu GV, Bachan S, Zhang Z, Gerstein M, Snyder M, Dinesh-Kumar SP.

Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA.

Signaling through mitogen-activated protein kinases (MPKs) cascades is a complex and fundamental process in eukaryotes, requiring MPK-activating kinases (MKKs) and MKK-activating kinases (MKKKs). However, to date only a limited number of MKK-MPK interactions and MPK phosphorylation substrates have been revealed. We determined which Arabidopsis thaliana MKKs preferentially activate 10 different MPKs in vivo and used the activated MPKs to probe high-density protein microarrays to determine their phosphorylation targets. Our analyses revealed known and novel signaling modules encompassing 570 MPK phosphorylation substrates; these substrates were enriched in transcription factors involved in the regulation of development, defense, and stress responses. Selected MPK substrates were validated by in planta reconstitution experiments. A subset of activated and wild-type MKKs induced cell death, indicating a possible role for these MKKs in the regulation of cell death. Interestingly, MKK7- and MKK9-induced death requires Sgt1, a known regulator of cell death induced during plant innate immunity. Our predicted MKK-MPK phosphorylation network constitutes a valuable resource to understand the function and specificity of MPK signaling systems.

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Drosophila Stem Cells Share a Common Requirement for the Histone H2B Ubiquitin Protease Scrawny

Buszczak M, Paterno S, Spradling AC.

Present address: UT Southwestern Medical Center, Department of Molecular Biology, Dallas, TX 75390, USA.; Howard Hughes Medical Institute Research Laboratories, Department of Embryology, Carnegie Institution of Washington, Baltimore, MD 21218, USA.

Stem cells within diverse tissues share the need for a chromatin configuration that promotes self-renewal, yet few chromatin proteins are known to regulate multiple types of stem cells. We describe a Drosophila gene, scrawny (scny), encoding a ubiquitin protease, which is required in germline, epithelial, and intestinal stem cells. Like its yeast relative UBP10, Scrawny deubiquitylates histone H2B and functions in gene silencing. Consistent with previous studies of this conserved pathway of chromatin regulation, scny mutant cells have elevated levels of ubiquitinylated H2B and trimethylated H3K4. Our findings suggest that inhibiting H2B ubiquitylation via scny represents a common mechanism within stem cells that is used to repress the premature expression of key differentiation genes, including Notch target genes.

As commented in Science: "Ubiquitination of one of the histones, H2B, has consequences for modifications such as methylation of other histones. These interactions cascade down to control the general activity of the genes bound up with these histones. Buszczak et al. show that in Drosophila, a ubiquitin protease, scrawny, helps keep genes silent. Scrawny's functions seem particularly important for stem cells in the germline, in epithelia, and in the intestine. In various types of stem cells, the balance between stem and differentiated fates might be tipped by a common chromatin modification route".

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Thursday, January 8, 2009

Dear editor - a note from any author in response to any referee

Kelly BD.

Department of Adult Psychiatry, University College Dublin, Mater Misericordiae University Hospital, 62/63 Eccles Street, Dublin 7, Ireland.

A hilarious satire of some less-than-helpful referees. 

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How to reply to referees' comments when submitting manuscripts for publication

Williams HC.

Centre of Evidence Based Dermatology, Queen's Medical Centre, United Kingdom.

BACKGROUND: The publication of articles in peer-reviewed scientific journals is a fairly complex and step-wise process that involves responding to referees' comments. Little guidance is available in the biomedical literature on how to deal with such comments. OBJECTIVE: The objective of this article is to provide guidance to novice writers on dealing with peer review comments in a way that maximizes the chance of subsequent acceptance. METHODS: This will be a literature review and review of the author's experience as a writer and referee. RESULTS: Where possible, the author should consider revising and resubmitting rather than sending an article elsewhere. A structured layout for responding to referees' comments is suggested that includes the 3 golden rules: (1) respond completely; (2) respond politely; and (3) respond with evidence. CONCLUSION: Responding to referees' comments requires the writer to overcome any feelings of personal attack, and to instead concentrate on addressing referees' concerns in a courteous, objective, and evidence-based way.

I think this is a useful article, particularly for young researchers submitting their first articles.
In general, it is important to learn how to cope with peer commentaries early on, specially the ones from referees and to get the best out of them. A rejection letter can lead to suggestions that can greatly improve the article and can even result in acceptance in a better-ranked journal(1)

(1) Jefferson T et al., Effects of editorial peer review: a systematic review. JAMA 2002; 287:2784-6.

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Tuesday, January 6, 2009

Eleven golden rules of quantitative RT-PCR

Udvardi MK, Czechowski T, Scheible WR.

This is an important paper for plant biologists, considering that "the use of the term ‘semi-quantitative’ (and hence, semi-quantitative assays from which quantitative conclusions are to be made) are not acceptable in The Plant Cell; instead, assays must be shown to be sufficiently quantitative to support a conclusion of changes in levels" (thus, you should use qPCR)

In this sense, the following paper should also be taken into account: 
Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis. Czechowski T et al. Plant Physiol. 2005 Sep;139(1):5-17

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The lysine demethylase LSD1 (KDM1) is required for maintenance of global DNA methylation

Wang J, Hevi S, Kurash JK, Lei H, Gay F, Bajko J, Su H, Sun W, Chang H, Xu G, Gaudet F, Li E, Chen T.

Epigenetics Program, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA.

Histone methylation and DNA methylation cooperatively regulate chromatin structure and gene activity. How these two systems coordinate with each other remains unclear. Here we study the biological function of lysine-specific demethylase 1 (LSD1, also known as KDM1 and AOF2), which has been shown to demethylate histone H3 on lysine 4 (H3K4) and lysine 9 (H3K9). We show that LSD1 is required for gastrulation during mouse embryogenesis. Notably, targeted deletion of the gene encoding LSD1 (namely, Aof2) in embryonic stem (ES) cells induces progressive loss of DNA methylation. This loss correlates with a decrease in DNA methyltransferase 1 (Dnmt1) protein, as a result of reduced Dnmt1 stability. Dnmt1 protein is methylated in vivo, and its methylation is enhanced in the absence of LSD1. Furthermore, Dnmt1 can be methylated by Set7/9 (also known as KMT7) and demethylated by LSD1 in vitro. Our findings suggest that LSD1 demethylates and stabilizes Dnmt1, thus providing a previously unknown mechanistic link between the histone and DNA methylation systems.

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Monday, January 5, 2009

Network hubs buffer environmental variation in Saccharomyces cerevisiae

Levy SF, Siegal ML.

Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA.

Regulatory and developmental systems produce phenotypes that are robust to environmental and genetic variation. A gene product that normally contributes to this robustness is termed a phenotypic capacitor. When a phenotypic capacitor fails, for example when challenged by a harsh environment or mutation, the system becomes less robust and thus produces greater phenotypic variation. A functional phenotypic capacitor provides a mechanism by which hidden polymorphism can accumulate, whereas its failure provides a mechanism by which evolutionary change might be promoted. The primary example to date of a phenotypic capacitor is Hsp90, a molecular chaperone that targets a large set of signal transduction proteins. In both Drosophila and Arabidopsis, compromised Hsp90 function results in pleiotropic phenotypic effects dependent on the underlying genotype. For some traits, Hsp90 also appears to buffer stochastic variation, yet the relationship between environmental and genetic buffering remains an important unresolved question. We previously used simulations of knockout mutations in transcriptional networks to predict that many gene products would act as phenotypic capacitors. To test this prediction, we use high-throughput morphological phenotyping of individual yeast cells from single-gene deletion strains to identify gene products that buffer environmental variation in Saccharomyces cerevisiae. We find more than 300 gene products that, when absent, increase morphological variation. Overrepresented among these capacitors are gene products that control chromosome organization and DNA integrity, RNA elongation, protein modification, cell cycle, and response to stimuli such as stress. Capacitors have a high number of synthetic-lethal interactions but knockouts of these genes do not tend to cause severe decreases in growth rate. Each capacitor can be classified based on whether or not it is encoded by a gene with a paralog in the genome. Capacitors with a duplicate are highly connected in the protein-protein interaction network and show considerable divergence in expression from their paralogs. In contrast, capacitors encoded by singleton genes are part of highly interconnected protein clusters whose other members also tend to affect phenotypic variability or fitness. These results suggest that buffering and release of variation is a widespread phenomenon that is caused by incomplete functional redundancy at multiple levels in the genetic architecture.

This is an interesting paper describing a series of genes in yeast (~300) that may act as 'phenotypic capacitors' and as such, may be important in maitining phenotypic robustness (robustness, in the sense that even though most species maintain abundant genetic variation and experience a wide range of environmental conditions, the phenotypic variation between individuals is relatively low). The authors identified these putative capacitors by using morphological phenotyping of individual yeast cells from single-gene deletion strains. 

Capacitor: gene product that causes high variance in multiple nonredundant phenotypes when deleted. 

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Why peer discussion improves student performance on in-class concept questions

Smith MK, Wood WB, Adams WK, Wieman C, Knight JK, Guild N, Su TT.

Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA.

When students answer an in-class conceptual question individually using clickers, discuss it with their neighbors, and then revote on the same question, the percentage of correct answers typically increases. This outcome could result from gains in understanding during discussion, or simply from peer influence of knowledgeable students on their neighbors. To distinguish between these alternatives in an undergraduate genetics course, we followed the above exercise with a second, similar (isomorphic) question on the same concept that students answered individually. Our results indicate that peer discussion enhances understanding, even when none of the students in a discussion group originally knows the correct answer.

This study suggests that discussion among students in a class can have an important effect on the understanding of difficult concepts, even when no one in the discussion group initially knows the answer. In fact, around half of the students participating in the study reported that having someone in the group who knows the correct answer is unnecessary for the discussion to be productive. 

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Sunday, January 4, 2009

The importance of stupidity in scientific research

Schwartz MA.

Department of Microbiology, UVA Health System, University of Virginia, Charlottesville, VA 22908, USA.

J Cell Sci. 2008 Jun 1;121(Pt 11):1771


This paper was published around May, 2008. I'm not really sure how it escaped my attention to post it earlier (maybe because of the accumulating piles of papers on my desk).

I think this is a nice paper to make new grad students read.

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Non-Coding RNA Prediction and Verification in Saccharomyces cerevisiae

Kavanaugh LA, Dietrich FS.

Department of Molecular Genetics and Microbiology, Institute for Genome Sciences and Policy, Duke University Medical Center, Durham, North Carolina, United States of America.

Non-coding RNA (ncRNA) play an important and varied role in cellular function. A significant amount of research has been devoted to computational prediction of these genes from genomic sequence, but the ability to do so has remained elusive due to a lack of apparent genomic features. In this work, thermodynamic stability of ncRNA structural elements, as summarized in a Z-score, is used to predict ncRNA in the yeast Saccharomyces cerevisiae. This analysis was coupled with comparative genomics to search for ncRNA genes on chromosome six of S. cerevisiae and S. bayanus. Sets of positive and negative control genes were evaluated to determine the efficacy of thermodynamic stability for discriminating ncRNA from background sequence. The effect of window sizes and step sizes on the sensitivity of ncRNA identification was also explored. Non-coding RNA gene candidates, common to both S. cerevisiae and S. bayanus, were verified using northern blot analysis, rapid amplification of cDNA ends (RACE), and publicly available cDNA library data. Four ncRNA transcripts are well supported by experimental data (RUF10, RUF11, RUF12, RUF13), while one additional putative ncRNA transcript is well supported but the data are not entirely conclusive. Six candidates appear to be structural elements in 5' or 3' untranslated regions of annotated protein-coding genes. This work shows that thermodynamic stability, coupled with comparative genomics, can be used to predict ncRNA with significant structural elements.

(Note from AMM: Please DO take advantage of PLoS's 'commentaries' tool available for each article -labeled as 'View and Join Ongoing Discussions'- 

If you find this article interesting, please make sure you read Donald Forsdyke's comments on the aforementioned section.)

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Friday, January 2, 2009

How to succeed in science: a concise guide for young biomedical scientists. Part II: making discoveries.

Yewdell JW.

Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland 20892, USA.

Making discoveries is the most important part of being a scientist, and also the most fun. Young scientists need to develop the experimental and mental skill sets that enable them to make discoveries, including how to recognize and exploit serendipity when it strikes. Here, I provide practical advice to young scientists on choosing a research topic, designing, performing and interpreting experiments and, last but not least, on maintaining your sanity in the process.

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How to succeed in science: a concise guide for young biomedical scientists. Part I: taking the plunge.

Yewdell JW.

Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland 20892, USA.

Biomedical research has never been more intellectually exciting or practically important to society. Ironically, pursuing a career as a biomedical scientist has never been more difficult. Here I provide unvarnished advice for young biomedical scientists on the difficulties that lie ahead and on how to find the right laboratories for training in the skills that you will need to succeed. Although my advice is geared towards succeeding in the United States, many aspects apply to other countries.

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Seeding and propagation of untransformed mouse mammary cells in the lung.

Podsypanina K, Du YC, Jechlinger M, Beverly LJ, Hambardzumyan D, Varmus H.

Program in Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA.

The acquisition of metastatic ability by tumor cells is considered a late event in the evolution of malignant tumors. We report that untransformed mouse mammary cells that have been engineered to express the inducible oncogenic transgenes MYC and Kras(D12), or polyoma middle T, and introduced into the systemic circulation of a mouse can bypass transformation at the primary site and develop into metastatic pulmonary lesions upon immediate or delayed oncogene induction. Therefore, previously untransformed mammary cells may establish residence in the lung once they have entered the bloodstream and may assume malignant growth upon oncogene activation. Mammary cells lacking oncogenic transgenes displayed a similar capacity for long-term residence in the lungs but did not form ectopic tumors.

Science. 2008 Sep 26;321(5897):1841-4.

(This article has been recommended by F. Barriga, a grad student at IRB Barcelona (Institute for Research in Biomedicine) and has been labelled as such.

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Efficient tumour formation by single human melanoma cells.

Quintana E, Shackleton M, Sabel MS, Fullen DR, Johnson TM, Morrison SJ.

Howard Hughes Medical Institute, Life Sciences Institute, Department of Internal Medicine, and Center for Stem Cell Biology, University of Michigan, Ann Arbor, Michigan 48109-2216, USA.

A fundamental question in cancer biology is whether cells with tumorigenic potential are common or rare within human cancers. Studies on diverse cancers, including melanoma, have indicated that only rare human cancer cells (0.1-0.0001%) form tumours when transplanted into non-obese diabetic/severe combined immunodeficiency (NOD/SCID) mice. However, the extent to which NOD/SCID mice underestimate the frequency of tumorigenic human cancer cells has been uncertain. Here we show that modified xenotransplantation assay conditions, including the use of more highly immunocompromised NOD/SCID interleukin-2 receptor gamma chain null (Il2rg(-/-)) mice, can increase the detection of tumorigenic melanoma cells by several orders of magnitude. In limiting dilution assays, approximately 25% of unselected melanoma cells from 12 different patients, including cells from primary and metastatic melanomas obtained directly from patients, formed tumours under these more permissive conditions. In single-cell transplants, an average of 27% of unselected melanoma cells from four different patients formed tumours. Modifications to xenotransplantation assays can therefore dramatically increase the detectable frequency of tumorigenic cells, demonstrating that they are common in some human cancers.

Nature. 2008 Dec 4;456(7222):593-8

(This article has been recommended by F. Barriga, a grad student at IRB Barcelona (Institute for Research in Biomedicine) and has been labelled as such.

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