Conferences

Prof. David Botstein[wp], the director of the Lewis-Sigler Institute at Princeton is with us at the CRI, 29 and 30 of March.

Two talks on consecutive days are planned that reflect Botstein's excellence both in quantitative biology research and education:

Monday March 29th
9h30- 11h30: "The fruits of the genome for society"
(presentation + open discussion)
Botstein's lab : http://www.princeton.edu/genomics/botstein/

16h00 - 19h00: Informal meeting with AIV & FdV students

Tuesday March 30th
9h30- 11h30 : "Merging education and research-The Lewis-Sigler institute"
(presentation + open discussion).

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The Lewis-Sigler Institute was established to innovate in research and teaching at the interface of modern biology and the more quantitative sciences. It has a quite unique collaborative structure where undergraduate students are integrated within the institute's research endeavors and all faculty, PhD and post-docs take part in the teaching, through interactive courses and lab work.
David Botstein, member of the American Academy of sciences and awardee of numerous prestigious prizes, has made fundamental contributions to modern genetics, including the discovery of many yeast and bacterial genes and the establishment of key techniques that are commonly used today as the method for mapping genes that laid the groundwork for the Human Genome Project.
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Short Biography
David Botstein (born 1942 in Switzerland) is an American biologist who has been the director of the Lewis-Sigler Institute for Integrative Genomics at Princeton University since 2003.
He graduated from Harvard in 1963 and received a Ph.D. from the University of Michigan in 1967. He then taught at the Massachusetts Institute of Technology, where he became a Professor of Genetics. In 1990, he became Chairman of the Department of Genetics at Stanford University. He has also worked for Genentech, as the Vice President - Science. Dr. Botstein was elected to the U.S. National Academy of Sciences in 1981 and to the Institute of Medicine in 1993.
Botstein is the director of the Integrated Science Program at Princeton University. Many of his students have gone on to be very successful in the field of molecular biology.
In 1980, Botstein and his colleagues Ray White, Mark Scolnick, and Ron Davis proposed a method for mapping genes that was used in subsequent years to identify several human disease genes including Huntington's and BRCA1. Variations of this method were used in the mapping efforts that predated and enabled the sequencing phase of the Human Genome Project.
In 1998, Botstein and his postdoctoral fellow Michael Eisen, together with graduate student Paul Spellman and colleague Patrick Brown, developed a statistical method and graphical interface that is widely used to interpret genomic data including microarray data.
Botstein has won the Eli Lilly and Company Award in Microbiology (1978), the Genetics Society of America Medal (1988), the Allen Award of the American Society of Human Genetics (1989) and the Gruber Prize in Genetics (2003).
He is the brother of the conductor Leon Botstein. Both of Botstein's parents were physicians.


David Botstein with Eva Maria Schoetz, Miroslav Radman and François Taddei, CRI conference

Johan Paulsson
Dept of Systems Biology, Harvard Med School

Very Special IF this friday 26/02/2010 at 15:00 !

Quantitative approaches to phenotypic heterogeneity in single cells

Abstract: Life in single cells is dictated by chance: Reactions that involve small numbers of molecules generate spontaneous fluctuations that enslave all dependent processes. Such 'noise' can randomize developmental pathways, disrupt cell cycle control or force metabolites away from their optimal levels. It can also be exploited for advantageous heterogeneity or even for more deterministic control. I will discuss new conceptual frameworks for analyzing such processes, addressing many of the complications and challenges in cellular dynamics in ways that promote intuition and facilitate comparisons with experiments. The principles discussed will be illustrated by homeostatic feedback control, partitioning at cell division, stochastic gene expression, multimerization, and small RNAs.

Links about Johan Paulsson :
http://sysbio.med.harvard.edu/faculty/paulsson/
http://paulsson.med.harvard.edu/Paulsson_Lab.htm

Simon Houriez, director of "Signes de sens"
website : www.signesdesens.org

Very Special IF this friday 26/02/2010 at 17:30 !


SIGNES DE SENS works on accessibility to Knowledge and Arts for deaf people. It has been doing this work for six years ; 10 people are employed by the organization. Our work is based on a simple idea : everyone deserves to be able to educate, whatever communication means they use. Everyone deserves specific learning tools to develop curiosity and to learn.

2 GOALS
- Support deaf community. Help it to enlighten and strengthen itself, while being respected as a inority. We propose and create specific tools to help the deaf community in achieving these goals.
- Encourage deaf and hearing people to mix, on equal level basis. Fight against illiteracy. Offer deaf people the opportunity to get access knowledge by reading.

3 ACTIVITIES
- Cultural activities : Propose bilingual cultural activities (French / French Sign language) : theater shows, workshops, exhibition. Make cultural and art places accessible to deaf people : museum, theaters, libraries. We work in France and abroad
- Publishing : Create multimedia tools (books, DVD, the Internet) using mime, sign language, video and pictures. Learn, discover and dream. For everyone : deaf or hearing people. Conte sur tes doigts publishing
- Web : Use the Internet (social networks, web 2.0, video...) for deaf people' access to Knowledge. Use the Internet to learn, meet people, get information...

Few words from Simon to present his background and activities :
"I was studying since a long time and I was quite successful but there was always this question about the meaning of things, the use of learning and searching, as i wanted to become a researcher in physical chemistry. Why do we learn so many things?I think nobody never asked me during my scholar path about this "why?" or "what for?" and often the answer is about getting a good job, a job that firstly allow you to earn enough money to live and secondly an interesting job. About the first part of course you have to think of it but for the second one.. what does that mean "interesting" ? To me, after some personal problems that made me think about "life", this question of interst was central, and i quited my studies to start something else, something "out of the books"and "interesting". I met a deaf guy and I discovered deafness and all the problematic. It was amazing and I started to think about this question, I had an idea an then an other.. I tryed.. I asked someone to help me and an other one.. I developped this project .. as a researcher I suppose. Then the organisation "Signes de sens" was born and it is still running an developing projects about accessibility to knowledges and culture for deaf people. Everything I will explain soon !"

French links :
http://www.youtube.com/watch?v=Eh79hezDK80
http://www.ashoka.org/shouriez

A Neurobiology & Optics club event !

We are pleased to announce the club's first talk of the year 2010 :
On Wednesday February 24th at 18h30, Peter Dalko will give us a talk on "Chemistry for Optical Imaging".

The seminar will take place, as usual, at the Centre for Research and Interdisciplinarity (CRI), Medicine Faculty, site Cochin Port-Royal, Paris Descartes University, 24 rue du Faubourg Saint Jacques, 75014 Paris, and we'll meet at the seminar room 2006, on the second floor.

Peter Dalko with the CRI students :

Conférence introductive du premier Symposium Interdisciplinaire de Doctorants à Paris
animée par Denis Guedj

Evelyn Fox Keller presents : "Climate Science, Truth, and Democracy"

Very Special IF this friday 27/11/2009 at 17:00 !



An impasse of credibility currently prevails in the US around the issues of climate change that threatens to paralyze citizens and experts alike. Much of the internet, radio talk shows, and popular television is flooded with challenges to the credibility and trustworthiness of climate scientists, and even the prestige press (e.g., NY Times and NYRB) has, in an effort to adhere to their traditional ethic of "balance," has contributed to the widespread misimpression that climate scientists are deeply divided about both the extent of the dangers we face and the relevance of human activity. Not knowing who or what to believe, not knowing how to assess the costs of inaction, the natural response for most people is to do nothing. Meanwhile, the evidence of the seriousness of the problem continues to mount. Most climate scientists, even though extremely concerned, have been reluctant to weigh in on these (often acrimonious) public debates, instead seeking recourse in the particular authority granted them by "peer review," and fearing that going outside, beyond the reach of peer review, might undermine their credibility. The effect is that the debate that rages in the public domain remains unchecked for intellectual or scientific reliability. The situation is dire, for, given that we live in a democratic state, the possibility of any effective action depends absolutely on the consent of a properly informed public. The questions I want to pose are therefore of two kinds: The first concerns the role of expertise in a democratic society, the ways in which lay citizens can responsibly participate in policy decisions, and the question of how a lay reader is to decide who and what to believe. The second concerns the nature and limits of the climate scientist's particular responsibility in this political and social situation.

Dr. Etienne Couturier presents "Fold and leaf shape" 6/11/09 at the CRI

by (newly promoted) Dr. Etienne Couturier
Laboratoire Matières et Systèmes Complexes, UMR CNRS 7057-Université Paris Diderot

We have noticed an original analogy between the leaf configuration in the bud and the paper dolls. If you fold a paper sheet and cut it with scissors, each fold will give either a sinus either a lobe when you unfold it. A lot of leaves follow this geometry in the bud. The leaf margin is folded on a plane as if it had been cut with scissor For this purely geometric reason, lobes and sinuses of the unfolded leaf exactely correspond to the initial folds. We have called these leaves "kirigami", which means fold and cut.

The purely geometric first part of this thesis shows how much the leaves geometries are constrained by their folded development. We also show that these geometries are very diverse and create very different leaves shapes. The second more biologic part proposes a mecanism for the fold development and a candidate to play the scissor role. We conclude by giving an original insight on leaf shape evolution.



You may have seen Etienne Couturier as he was starting his PhD in the film "Cherche toujours" by Mathias Théry et Etienne Chaillou (2008)... See the end of the story, live !

Misha Gromov (Abel Prize) presents "Biology seen by a great mathematician"

Conference on Friday 23rd 2009 at 17:00
at the CRI, 2nd Floor, Conference room 2006
Faculté de Médecine Paris Descartes
24 rue du Faubourg Saint Jacques 75014 Paris



Don't miss this event !

Mikhail Leonidovich Gromov (Russian, born 23 December 1943) also romanized as Mikhael Gromov or Michael Gromov) is a Franco-Russian mathematician known for important contributions in many different areas of mathematics. He is considered a geometer in a very broad sense of the word.
Misha Gromov, is now permanent professor at the Institut des Hautes Etudes Scientifiques (IHES at Bures sur Yvette, France) and at the New York University.
He has won many scientific prizes and, recently, the 2009 Abel Prize "for his revolutionary contributions to geometry".

Websites :
http://www.ihes.fr/~gromov/
http://as.nyu.edu/object/IO_3199.html

Andrew Murray presents "Friday Night at the Singles Bar : How yeast cells pick a mate"



Conference Friday 16 October 2009 at 17:30
at the CRI, new conference room 2006, 2nd floor
Faculty of Medecine Paris Descartes
24 rue du Faubourg Saint Jacques
75014 Paris

...Come and enjoy !

Andrew Murray is Professor of Molecular and Cellular Biology, Co-Director, Bauer Center for Genomics Research
He is currently on a sabbatical at the Center for Interdsiciplinary Research in Paris and hosted by the Chaire Blaise Pascal.
He gives a course of Systems biology on thursdays mornings (starting 15/10/2009).

Websites :
http://www.mcb.harvard.edu/Faculty/faculty_profile.php?f=andrew-murray-w
http://www.mcb.harvard.edu/murray/index.html
List of Publications (Pub med)

Don't miss Valentin Nägerl at the CRI on wednesday 1st July 2009, special guest of Neurobiology & Optics club.


Valentin Nägerl, PhD

Nanoscale imaging of living synapses by STED microscopy

Synapses are physical sites of intercellular contact that transmit and transform information in a very rapid and flexible way. They represent incredibly complex and dynamic networks of signaling proteins aggregated in a tiny space (<1µm3), making it a huge experimental challenge to study them in situ. As a result, a lot of our understanding of the properties of single synapses is derived from electron microscopy of fixed tissue samples, which is by definition not well suited for understanding the dynamic processes of synapses.
We are studying the dynamics of living synapses with a new laser-scanning fluorescence microscopy technique, STED imaging, which has vastly improved spatial resolution (at the nanoscale) compared to conventional light microscopy. Expanding our previous research, we are investigating key structural and cell-biological mechanisms of synaptic plasticity, imaging morphology and constituent proteins of synapses in living brain slices on spatial scales relevant to synapse physiology.

Valentin Nägerl
Professor of Neuroscience and Bioimaging
Avenir Group - Synaptic Plasticity and Superresolution Microscopy
Inserm U862/Université Victor Segalen Bordeaux 2
146, rue Léo Saignat
33076 Bordeaux
France
Phone: +33/557571097
Fax: +33/557571684
Email: This e-mail address is being protected from spam bots, you need JavaScript enabled to view it

More info, CV and publications on the next page.

Patrick Berche presents "The history of Bioterrorism", 26/06/2009 at 15:00
at the CRI, new conference room 2006 - 2nd Floor

The dean of our Medicine Faculty, Prof. Patrick Berche, will share with us his rich expertise and knowledge on the "History of Bioterrorism", Friday 26/06/2009 at 15:00

...You are all invited !

Patrick berche on Wikipedia :
http://fr.wikipedia.org/wiki/Patrick_Berche

Patrick berche blog (in french) :
http://blogs.univ-paris5.fr/berchep/weblog/

Book :
Patrick Berche, L'histoire des guerres biologiques secrètes, Robert Laffont, 2009.

17:00 next tuesday 16 June 2009, Agnes Ullmann, special guest of the Genome club !

Seminar on the french school of molecular biology in the sixties.



link to the poster in full size: Poster agnes ullman seminar.jpg

Pr Fritjof Helmchen, Neurobiology and optics club guest

This Friday 12 June 2009 at 18:00 at the CRI, Professor Fritjof Helmchen will be among us.

Professor Fritjof Helmchen is performing his research at the border between Neuroscience and physics. He investigates the dynamics of neuronal activity in the intact brain of anesthetized and awake animals by using innovative optical mesurements methods that allow him to track the spiking activity of hundreds of neurons deep into the (almost) intact cortex of
mammals. He has also been developping miniaturized microscopes allowing him to explore optically the cortical activity in freely moving mice.
The prospect of exploring optically the cortex as a dynamical 3D structure is wildly regarded as key to a full understanding of this complex brain structure. Pr. Helmchen has been a pionner and published a series of milestone articles in this transdisciplinary field. A list of his key articles can be found at the end of this message.

Further description of his precise work can be found at :
http://www.hifo.uzh.ch/research/neurophysiology/helmchen/interest.html

His full Curriculum Vitae can be found at :
http://www.mpimf-heidelberg.mpg.de/departments/cellPhysiology/zpProjects/2pImaging/fritjofHelmchen/fritjofHelmchenCV/index.html

* Engelbrecht CE, Johnston RS, Seibel EJ, Helmchen F (2008) Ultra-compact
fiber-optic two-photon microscope for functional fluorescence imaging in
vivo. Optics Express, 16:5556-5564.
* Göbel W, Kampa BM, Helmchen F (2007) Imaging cellular network dynamics
in three dimensions using fast 3D laser scanning. Nature Methods 4: 73-79.
2006
* Helmchen F, and Denk W (2005) Deep tissue two-photon microscopy. Nature
Methods, 2(12): 932-940.
* Nimmerjahn A, Kirchhoff F, and Helmchen F (2005) Resting microglial
cells are highly dynamic surveillants of brain parenchyma in vivo.
Science, 308:1314-1318.
* Göbel W, Kerr NDJ, Nimmerjahn A, and Helmchen F (2004) Miniaturized
twp-photon microscope based on a flexible coherent fiber bundle and a
gradient-index lens objective. Optics Letters, 29(21) : 2521-2523.
* Nimmerjahn A, Kirchhoff F, Kerr NDJ, and Helmchen F (2004)
Sulforhodamine 101 as a specific marker of astroglia in the neocortex in
vivo. Nature Methods, 1(1) : 31-37.

Tuesday 9 June 2009 , at 18:00, we are honoured to host at the CRI Prof. Eshel Ben Jacob, of the Physics department, Tel-Aviv University, presenting his work on "Learning from bacteria about information processing"

Prof. Ben Jacob is the holder of the Maguy-Glass Chair in Physics of Complex Systems, fellow of the American Physical Society and former President of the Israel Physical Society. Scientific American magazine placed his work on the creation of a type of organic memory chip on its list of the year's 50 most significant scientific discoveries...

Abstract

Bacteria, the first and most fundamental of all organisms, lead rich social life in complex hierarchical communities. Collectively, they gather information from the environment, learn from past experience, and take decisions. Bacteria do not store genetically all the information required for efficient responding to all possible environmental conditions. To solve the new encountered problems (challenges) posed by the environment, they first asses the problem via collective sensing, recall stored information of past experience and then execute distributed information processing of the 109-12 bacteria in the colony thus turning the colony into super-brain. Super-brain, because the billions of bacteria in the colony use sophisticated communication strategies to link the intracellular computation networks of each bacterium (including signaling path ways of billions of molecules) into a network of networks. I will then show illuminating movies of swarming intelligence of live bacteria in which they solve optimization problems that are beyond what we, human being, can solve with our most powerful computers. This will lead me to a discussion about the special nature of bacteria computational principles in comparison to our Turing Algorithm computational principles. If time will permit, I will show that we can learn from the bacteria about our brain. In particular that the crucial role of the neglected other side of the brain - distributed information processing of the astrocytes.

next : recent publications

Not to be missed!

This Friday, 22 May 2009 at 17:00, the Interdisciplinary Fridays will host Prof. John P.A. Ioannidis, MD, PhD. John (see resume below), an MD, is a leader epidemiologist, statistician, an excellent orator...

To have a taste of his works spanning meta-analysis of genomic and medical data to evaluation of research in general and as proof of the direct interest each of us should have in hearing his talk and discussing with him over a glass of wine, have a look at the following article:
Why most published research findings are false.
Ioannidis JP.
PLoS Med. 2005 Aug;2(8):e124. Epub 2005 Aug 30.

Next : Ioannidis profile

This Friday 25 April 2009 at 14:00, we will host Dr. Shai Kaplan (Weizmann Institute, Israel) who will share with us his work on:
Diverse input-functions control bacterial genes

Abstract
Cells respond to environmental signals by adjusting the expression level of their genes. The relation between the level of the input signals and the transcription rate of the gene is called the gene input-function. The input-functions of most genes are currently unknown. Here, we use robotic assay of measurements in living cells to map the input-functions of about 20 E. coli sugar genes at high resolution and accuracy. We find diverse, intricately shaped input-functions, including non-monotonic functions that peak at intermediate signal levels. We find that most of the input-functions show separation of variables, in the sense that they can be described as the product of simple functions that depend only on a single input. This study provides the first broad survey of gene input-functions and can be extended to map the logic of gene regulation in other systems and organisms.

This reflects Shai's PhD work in the labs of Uri Alon and Ehud Shapiro.
You may want to look at some of his PhD papers (below)
Hope you'll all join us for this exciting talk!

The incoherent feed-forward loop can generate non-monotonic input functions for genes.
Kaplan S, Bren A, Dekel E, Alon U.
Mol Syst Biol. 2008;4:203. Epub 2008 Jul 15.
Diverse two-dimensional input functions control bacterial sugar genes.
Kaplan S, Bren A, Zaslaver A, Dekel E, Alon U.
Mol Cell. 2008 Mar 28;29(6):786-92.
De novo DNA synthesis using single molecule PCR.
Ben Yehezkel T, Linshiz G, Buaron H, Kaplan S, Shabi U, Shapiro E.
Nucleic Acids Res. 2008 Oct;36(17):e107. Epub 2008 Jul 30.
Recursive construction of perfect DNA molecules from imperfect oligonucleotides.
Linshiz G, Yehezkel TB, Kaplan S, Gronau I, Ravid S, Adar R, Shapiro E.
Mol Syst Biol. 2008;4:191. Epub 2008 May 6.
PMID: 18463615 [PubMed - indexed for MEDLINE]
A universal mechanism ties genotype to phenotype in trinucleotide diseases.
Kaplan S, Itzkovitz S, Shapiro E.
PLoS Comput Biol. 2007 Nov;3(11):e235. Epub 2007 Oct 16.

For fans of nano applications in Life Sciences,

On Friday 20 March 2009 at 10:00 at the CRI, Dr. Tomaso Zambelli of the ETH, Zurich will give a talk on:

fluidFM: combining AFM and nanofluidics for single cell experiments demonstrated applications include direct injection to neuronal axons without cellular damage (see attached poster), many other applications can be dreamed of and will be discussed in the seminar.

You're all invited to join!

This Friday February 6, 2009 we have the great pleasure to host Prof. Matthew Meselson, Harvard. Matt gained his fame by what is often referred to as 'the most elegant experiment in Biology', describing how DNA replication works in a semi-conservative manner ('the Meselson Stahl experiment'). This was followed by a brilliant career (see below) both in research and in teaching, in true legacy of his PhD supervisor, Linus Pauling. Matt, close to eighty years old, continues relentlessly his bench work (see Science publications in the past year) and has been doing so here in Paris for the last few weeks. He agreed to make a pause to present some of his recent work, as he has enjoyed the interaction with AIV students in the past and plans to visit our program on regular basis ;)
Apart from his scientific endavours, Meselson' has been deeply involved in chemical and biological defense and arms control and has served as a presidential consultant and a key Pugwash actor.
In brief... don't miss !

Ariel Lindner

Read more in the Harvard's Gazette:
http://www.news.harvard.edu/gazette/2004/09.30/01-meselson.html

Pablo Jensen, a physicist from the ENS Lyon, will give us a conference at the CRI on thursday 25th september, 10 AM in the seminar room (2017 - 2nd floor) about :

Science communication, interdisciplinarity and research performance

Pablo is interested in the analysis and modeling of social systems and is also involved in science communication (he already wrote two books) and in teaching (he is launching an interdisciplinary master 2 this year at the frontier between physics, maths & computer sciences).

His last paper published this summer shows that scientists involved in dissemination activities like science mediation or teaching perform better academically, some very good news for most of us!

This work is a beautiful example of the joint power of a simple yet highly socially relevant question and of the availability of extensive data on the web.

Pablo will present this work and the new interdisciplinary master and we will then discuss on these topics.

More about Pablo:
http://perso.ens-lyon.fr/pablo.jensen/

His paper on research performance and dissemination activities:
http://perso.ens-lyon.fr/pablo.jensen/revised.pdf

During the cycle of conferences in Paris of William C. Wimsatt, a philosopher from the university of Chicago, we will host him at the CRI for a colloquium dedicated to evolution of culture.

Evolution of writing : a model for culture evolution ?

Date: Tuesday 17 june 2008

Time: 10:00 - 17:00

Schedule

** Theoretical insights into culture evolution **

10.00 William C. Wimsatt (title to be announced)

Discussion

11.15 To be announced

Discussion

12.30 Lunch

** From theory to experiments : the evolution of writing **

14.00 Marc Smith: "Morphology" and "ductus": visual and mechanical factors in the evolution of latin alphabet

Discussion

15.00 Stanislas Dehaene: Cultural evolution and neuronal recycling : the example of reading

Discussion

16.00 Julien Bénard-Capelle: What can we learm from experimental propagation of symbols ?

Discussion

17.00 Conclusions