#jesuisCharlie #CharlieHebdo

 je ne suis pas d’accord avec ce que vous dites, mais je me battrai jusqu’au bout pour que vous puissiez le dire

I disapprove of what you say, but I will defend to the death your right to say it – Evelyn Beatrice Hall

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On Randomness, Determinism, False Dichotomies and Cancer

Exploreable

Before I start – a short summary

[1] A recent paper attributed a large proportion of variation in incidence of cancers across different tissues to the number of stem cell divisions in them, and
stochastic errors in cell division.

[2] The paper grouped tumour types with known external causes as “deterministic” and those without as “stochastic”

[3] I have seen people being hostile to the notion of stochasticity in cancer who’ve postulated other deterministic factors, with the implicit assumption that what is stochastic is really deterministic processes with as-of-now undiscovered causes.

[4] Here I explain why processes with known causes are still stochastic, leading to my gripe with both the misunderstanding that has permeated discussion of the paper as well as the iffy notion of grouping tumours into stochastic and deterministic ones in the paper. My assertion is that even those cancers strongly driven by external carcinogens involve randomness/stochasticity.

Background

View original post 1,649 more words

CRISPR/Cas9 : Emmanuelle Charpentier futur prix Nobel ?

 sbi_precisionx_cas9_schema505-420(source image : ici)

CRISPR. Le mot (enfin l’acronyme) est lâché. Si, en tant que biologiste, vous n’en n’avez jamais entendu parler, c’est que vous hibernez depuis 2 ans ou que vous êtes sur le terrain au fin fond de l’Amazonie à récolter des échantillons pour votre prochain papier.

Derrière cet acronyme un peu barbare (CRISPR pour ‘Clustured Regularly Interspaced Short Palindromic Repeats’) se cache l’une des plus importantes révolutions technologiques que la biologie moléculaire a connu ces 40 dernières années, au même titre que le clonage ou la PCR.

Le principe : programmer une endonucléase bactérienne (protéine qui coupe l’ADN) appelée Cas9 avec des petits ARN non codants (qui agissent comme guide) pour permettre le clivage de manière spécifique à l’endroit désiré du génome. Grâce à ce nouvel outil de génie génétique, cibler n’importe quel gène dans une cellule pour le modifier devient presque un jeu d’enfant. Eteindre ou allumer l’expression d’un gène, le modifier, le réparer, l’enlever; tout est aujourd’hui possible.

 

Un bref historique

Et pourtant, la découverte initiale aurait pu rester totalement anecdotique. Mais elle est devenue un exemple formidable de ‘détournement’ d’une découverte scientifique dans un domaine (microbiologie) au profit d’un autre domaine (l’édition et la modification des génomes), avec des applications aujourd’hui presque illimitées.

Cette histoire commence donc en 1987 par une simple observation qui est restée longtemps confidentielle : la présence d’une région inhabituelle de 5 répétitions partiellement palindromiques dans le génome d’E. Coli à l’extrémité du gène de l’isozyme alkaline phosphatase (si vous ne savez pas à quoi sert cette enzyme, moi non plus !). Il faudra ensuite attendre 2002  pour que l’équipe de Léo Shouls aux Pays-Bas mette en évidence la présence de ces séquences dans la plupart des génomes bactériens. Et c’est aussi en 2002 que l’acronyme CRISPR deviendra définitif.

Mais à quoi peuvent bien servir ces séquences répétées me direz-vous ? Et bien les premiers éléments de réponse arrivent en 2005 et ce fut plutôt une surprise. Ces séquences des génomes bactériens étaient tout bonnement identiques à des séquences des génomes de bactériophages ! (Les bactériophages sont des virus qui n’infectent que les bactéries). Et de manière remarquable, les bactéries contenant ces séquences de phage étaient résistantes à ce même phage. En d’autres termes, en intégrant des fragments d’ADN étranger au sein de son propre chromosome, la bactérie acquiert une résistance à ce phage.

Comment ? Et bien une partie de la réponse a été apportée en 2007 par une équipe française travaillant pour Danisco, une société de l’industrie laitière qui cherchait à protéger la bactérie lactique Streptococcus thermophilus des attaques de bactériophages. Pour simplifier, quand le phage réinfecte la bactérie : (1) il est reconnu, (2) la bactérie exprime sous forme d’ARN ces séquences répétées CRISPR qui correspondent à des fragments du génome du phage, (3) ces crRNAs forment un complexe avec les protéines Cas (endonucléase) et (4) s’apparient avec l’ADN de phage pour le détruire. Une sorte de système immunitaire qui utilise l’ADN étranger et non pas le couple antigène/anticorps pour se défendre.

Femmes, Science et Cocorico !

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Tout explose en 2012 avec ce papier publié dans Science par les équipes de Jennifer Doudna et Emmanuelle Charpentier. Ces 2 femmes aujourd’hui internationalement reconnues et lauréates de nombreux prix ont donc été les premières à démontrer que ce système immunitaire bactérien pouvait être reprogrammé à façon pour modifier n’importe quel gène de n’importe quel organisme.

Alors le mot est lancé : prix Nobel ! Oui je pense sincèrement que Jennifer Doudna et Emmanuelle Charpentier seront un jour récompensées du prix Nobel pour cette découverte.

Et pour la petite histoire Emmanuelle Charpentier est française !!! Expatriée depuis bien longtemps d’abord en Suède puis maintenant titulaire de l’une des plus prestigieuses chaires d’Allemagne,  Emmanuelle est une microbiologiste française.

Femme, française, prix Nobel. Ces mots vont plutôt bien ensemble vous ne trouvez pas ?

Pour en savoir plus (en français)

CRISPR Wikipedia

Article dans Le Monde

Article dans Le Figaro

Diapositives de Tuan Nguyen, INSERM : 1ère partie & 2ème partie

If you have nothing to hide, you have nothing to fear

Academic publishing in general and the peer-review process in particular, if not broken, are seriously under strain. We all remember Arsenic life or the more recent STAP cells fiasco. Pre-publication peer-review is unfortunately not always getting the job done as a filter.

Many publishers have already embarked on experiments/alternatives/developments with respect to improving transparency and efficiency. Unfortunately, each journal has its own version of peer review. This blog post deals with these currently available alternatives, hoping (dreaming) that one day those ‘new’ policies may becoming the norm for all the publishers societies.

Referee cross-commenting

As a reviewer I would love to be able to see the final decision and other Reviewer’s comments. But it not always the case. I have probably reviewed about 20-25 papers since the beginning of my career. Only a couple of time I was informed of the final decision and in only one recent reviewing, the editor send me a message to let me know of other reviewer’s comments.

So for me, to have access to the comments provided by the other reviewers should be compulsory. EMBO press employs this review format and I think it’s great and very useful. It is partly designed to minimize contradictory statements.

The full Monty- Uncropped scans of Western blots included in supplemental figures.

If you have nothing to hide, you have nothing to fear. We all do want to show pretty and clean data but you don’t have to make results look better than reality. With regards to ‘representative data’, a lot of journals such as Nature Cell Biology now require to send all the unedited, uncropped scans of Western blots with your manuscript. Peer review should be a gatekeeper for possible doctored images and doing the ‘full Monty’ appears to me to be going in the right direction. Systematic image screening similar to those made at EMBO press should also become a standard for all publishers.

Transparent review

Transparency is one of the fundamental guiding principles in science. Would the publication of referee reports and editorial decision benefits the debate? EMBO press certainly thinks so (an example here), so do I. One direct benefit is to know to what extent a paper has been improved during the peer review process.

Pre-Print servers

An invite approach that has worked well for the physics community is the use of the pre-print server arXiv. Seeing the emergence of several preprint servers to biology (fighare, BioRxiv, peerj and F1000Research) is certainly a good sign. It is an effective way to share and get a collegial feedback not restricted to 2-3 reviewers. Other advantages include rapid dissemination and immediate visibility. We are constantly answering questions about our work at meetings, seminars, conferences and with our publications. But you usually answer to a couple of people. By sharing your work openly you can answer 100, 1000! The more feedback you receive, the better your work will be. Unfortunately not all academic journals submission policies allow pre-prints and its very regrettable.

That’s it for today. Please feel free to comment and give your thoughts/feedback.

Further reading

https://flipboard.com/section/science-communication-central–bSQ2TN

http://scholarone.com/media/pdf/peerreviewwhitepaper.pdf

http://www.labtimes.org/labtimes/issues/lt2012/lt02/lt_2012_02_41_41.pdf

http://publicationethics.org/files/u7140/Peer%20review%20guidelines.pdf

http://www.nature.com/nmat/journal/v10/n2/full/nmat2952.html

http://wowter.net/2013/12/24/towards-five-stars-transparent-pre-publication-peer-review/

http://www.nature.com/nature/journal/v468/n7320/full/468029a.html

http://www.plosbiology.org/article/info:doi%2F10.1371%2Fjournal.pbio.1001563#s4

http://www.nature.com/news/research-integrity-cell-induced-stress-1.15507

http://www.sciencedirect.com/science/article/pii/S0896627314002888

http://violentmetaphors.com/2013/12/13/how-to-become-good-at-peer-review-a-guide-for-young-scientists/

 

My reviewer oath

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Rule 1: Avoid conflict of interest. I will disqualify myself from review if I feel unable for any reason to provide an unbiased assessment.

 

Rule 2: Ask yourself honestly whether the paper falls within the scope of your expertise. If I don’t fell qualified for the paper, I will decline to do the review.

 

Rule 3: Punctuality is a virtue of kings. I will return my review within the specified deadline. There are many sources of unnecessary time loss in the publication process. Everyone loses out if some do not play by the rules.

 

Rule 4: Review unto others as you would have them review unto you. I will not propose a bunch of new experiments, especially the ones that I do not perform for my own work.

 

Rule 5: Leave it to the future to judge a manuscript’s impact. I will only evaluate the evidence for the claims. Impact is unpredictable. Peer review is only a process of ‘pre-filtering’. Readers are the ‘post-filter’, in other words = peer validation.

 

Rule 6: It is their papers, not yours. I will not try to turn author’s paper into a paper I would have written.

 

Rule 7: Review the work, not the authors.  Whether the author is a Nobel laureate or a graduate student, I will judge the paper the same.

 

Rule 8: Don’t hide behind a cloak of anonymity, sign your review. I will have the courage to stand by my reviews, including negative reviews.

Bonjour, Welcome, Palya

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I am a senior academic researcher (CR1) at the CNRS. I am working at the Interdisciplinary Research Institute (IRI, Villeneuve d’Ascq, France), a research center designed to foster synergy between biologists, mathematicians, physicists & chemists to unravel the basics of biology.

Our group is interested in understanding how transcriptional regulation of gene expression controls cellular development and how the breakdown of this regulation leads to disease. My research focuses on protein structure & function with a special interest in transcription factors & their cofactors.

Inspired by Steve Royle, Alfonso Arias, David Stephens and Sylvain Deville, among others, I have finally decided to take the plunge : I am starting a blog (kind of) !

This blog will be mainly about comments on published papers and a little about me.

In French or in English, according to my inspiration.

The Topsy-Turvy Mediator complex

Wang et al. (Cell research 2014) and Tsai et al. (Cell 2014) recently describe a substantially improved cryo-EM of the Mediator Complex which permitted an unambiguous and topsy-turvy assignment of the Head, Middle and Tail modules.

Mediator is a gigantic evolutionarily conserved multi-protein complex comprising over 25 different subunits (~ 1.2 MDa) that plays major roles in both basal and activated transcription (Malik and Roeder, 2010; Poss et al., 2013; Yin and Wang, 2014). Its sheer size, low abundance and conformational variability have prevented the high-resolution structural determination of the entire complex and thus the exact Mediator architecture is still a matter of debate (Larivière et al., 2012). To date, high-resolution structures of the 7-subunit Mediator head module (Imasaki et al., 2011; Larivière et al., 2012; Robinson et al., 2012) and several single subunits or domains are available (Baumli et al., 2005; Bontems et al., 2011; Hoeppner et al., 2005; Larivière et al., 2006; Larivière et al., 2008; Milbradt et al., 2011; Schneider et al., 2011; Thakur et al., 2009; Vojnic et al., 2011; Yang et al., 2006).

In addition, structural information of full Mediator at low resolution have come from cryo-EM studies (Asturias et al., 1999; Bernecky et al., 2011; Bernecky and Taatjes, 2012; Cai et al., 2009; Davis et al., 2002; Elmlund et al., 2006; Knuesel et al., 2009; Näär et al., 2002; Taatjes et al., 2002; Taatjes et al., 2004; Tsai et al., 2013; Wang et al., 2013).

A major point of agreement that emerges from these extensive biochemical studies is that Mediator subunits are organized into three core modules (Head, Middle, Tail) and a dissociable CDK8 kinase module. However, information about subunit localization and boundaries of the three core modules has remained rather elusive, even contradictory. For example a recent cryo-EM of yeast Mediator at 28 Å resolution identified a previously additional independent module referred to as the arm domain (Cai et al., 2009).

In two recent reports, the Cai (Wang et al., 2014) and Asturias (Tsai et al., 2014) labs describe a cryo-EM analysis that completely redefine the modular organization of the core Mediator. In particular the head module was previously assigned to one end of the Mediator structure with the middle and tail modules folded back on one another to from the upper portion of Mediator (Chadick and Asturias, 2005).

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Using either tagged or deleted individual subunits combined with unequivocal docking of the X-ray structure of the Head module, the authors arrive at an impressive improved cryo-EM reconstruction of Mediator at a resolution of ~ 18 Å. And in a dramatic topsy-turvy twist, the Head and Middle modules form now the upper portion while the dense domain at the base corresponds to the Tail. As a consequence of the enhanced resolution, previously unassigned metazoan-specific subunits are now clearly localized. For example, MED27, MED28, MED29 and MED30 make extensive contacts with the Head module while MED26 associates with the Middle module.

Does this completely new pattern of modules rearrangement provide a more concrete view of the conformational changes that these modules undergo upon interaction with the RNA polymerase II ? Previously, the most prominent change resulted from the relative rotation and translation of the Middle and Tail modules that leads to a complete repositioning of the Middle module (Cai et al., 2009). These module movements triggered by formation of the holoenzyme are still carried on but from now on that is the Head and the Middle modules that undergo a coordinated rotation.

These observations directly challenge the previous holoenzyme model in which the reported RNA pol II binding site was located near the Head module. Astonishingly, the entire interaction surface of the Head module is now highly exposed and extensive Mediator/RNA pol II contacts are mediated through the Middle and Tail modules.

In the future, with the cryo-EM resolution revolution (Kühlbrandt 2014), the near-atomic resolution of full Mediator and even of the full transcription pre-initiation complex (PIC) may soon become a reality.