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PhD programLaunching

Posted by on March 12th, 2013


WELCOME to the INFORM PhD Program!


The INFORM program (INformation Flow and ORganization at the Membrane) sets up an interdisciplinary consortium at the site of Scientific Park of Luminy in Marseilles, gathering 12 laboratories in Biology, Mathematics and Physics. The objective is to quantitatively understand the biochemical and mechanical basis of cell signaling at different scales from molecular to cellular and tissue levels. The project will allow scientific progress in understanding the dynamics of signaling focusing on a quantitative description of biological mechanisms.

6 PhD fully funded positions will be available for Fall 2013 (aplication deadline May 10th 2013). This PhD program is highly interdisciplinary and based on collaborative projects between partners of the consortium. We encourage graduate students from different backgrounds to apply, biologists but also engineers, physicists and mathematicians.

More details about INFORM project research /technologies and PhD program application procedures can be found on our Website: labexinform.wordpress.com
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Colouring the Mouse Embryo

Posted by on August 13th, 2012


48 anatomical structures of the presented mouse embryo atlas are shown in 3D.

Here is the backdrop for our recent paper in Development, A novel 3D mouse embryo atlas based on micro-CT”.   With the human genome project complete, the sequence and the location of each gene in the genome is understood.  However, the understanding of gene function and the corresponding expressed phenotype for all the genes in the human genome is still in its infancy.  Most of the research aimed to tackle this question will be carried out in the mouse due to the 99% genetic homology between mice and humans and the available techniques to manipulate mice genetically.  Over the last decade, the efforts of a world wide consortium, the International Knockout Mouse Consortium (IKMC, www.knockoutmouse.org), has embarked on a mission to knock out each of the ~23,000 genes in the mouse genome, one at a time, and generate the resultant mice.  With this effort now close to completion another world-wide effort, the International Mouse Phenotyping Consortium (IMPC, www.mousephenotype.org), has been established and the plan on how to phenotype the resultant mice from the IKMC project is being formulated.  What is well understood is that ~30% of the gene knockout mice strains will be embryonic lethal, further accentuating the need for an assay to phenotype mouse embryos throughout development.

If you have two groups of mouse embryos, one wild-type and one mutant, with a single gene knockout, how do you find out what’s different about them?  How do you get clues to the function of the knocked out gene and its role in mouse embryo development?  The most intuitive answer would be to look at the two groups of mouse embryos with a microscope and see if you can find any gross differences in morphology in the mutant group.  You could hypothesize that the organ or structure that shows an aberration in comparison with the wild-type group is an area where that particular gene function is important and carry on with more focused phenotyping assays from there.

This is the exact premise of our recent paper in Development.   Our aim was to eliminate the human bias and time needed to parse through thousands of high-resolution images by developing automated computer methods that could export volume measures of each of the major organ structures within the mature mouse embryo.   We used advanced high-resolution 3D imaging called Micro-CT to image 35 E15.5 C57/Bl6 mouse embryos and developed sophisticated computer software to automatically calculate the mean volumes and standard deviation of 48 structures inside the mouse embryo.  To achieve this, each of the 48 structures within a representative average image of all 35 mouse embryo images were manually painted by one individual, totalling ~400 hours of work.  Through this we acquired baseline volumetric measurements of wild-type mice to determine how tight the variation is among controls.  The resulting labeled data set (the above figure) exists as an E15.5 mouse embryo atlas for which all future mutant strains can be compared with and automatic volume measurements can be executed.  The results presented in this paper, in our opinion, is an important step in demonstrating the feasibility of using 3D imaging as a primary screen in the IMPC pipeline and provides a robust tool that can handle and analyze the large volume of images that will be acquired.

ResearchBlogging.orgWong MD, Dorr AE, Walls JR, Lerch JP, & Henkelman RM (2012). A novel 3D mouse embryo atlas based on micro-CT. Development (Cambridge, England), 139 (17), 3248-56 PMID: 22872090
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Fast times at MBL

Posted by on June 19th, 2012

Sitting down to write this reflection, it struck me that I couldn’t believe it has really been two weeks since I arrived in the quiet town of Woods Hole, MA for the Embryology course at the Marine Biological Laboratory (MBL). Time has become an abstract concept for my fellow students and me; it seems like we just got here and yet have known one another for months. We engage in science almost every hour of every day. There is no work – only play. I was imaging immunostained plankton on a new Nikon A1 confocal microscope at 3am Saturday morning. I would have gone all night except I did not want to miss Nipam Patel’s famous butterfly lecture at 9am the same morning. Again, this isn’t work. I want to be doing this – and so does everyone else here.

I don’t know what generates the enthusiasm and energy at the MBL. In my graduate lab back at the University of Washington I am a hard worker, yet I don’t have the inclination (or ability) to maintain the pace that I have picked up here. It is not uncommon to work in lab until 2 or 3am, and yet we all eagerly attend lectures a few hours later and put in another 15+ hour day, six or seven days a week. Perhaps it’s the access to the best scientific equipment around – the sheer quantity of reagents and quality of microscopes available to us is stunning. However, more likely it’s being removed for six weeks from my regular graduate school environment. There is no pressure to generate actual data during my time here, no PI to disappoint, no lab meetings to prepare, and certainly no time to read current papers (I’ll have a lot of catching up to do in August!). There is only active experimentation. I am encouraged to ask my own questions and take ridiculous risks. I can do what interests me, even if there is no apparent face value for my field. For example, I spent last week honing my antibody staining skills by asking the question, “What is the prettiest combination of antibodies one can use on Drosophila embryos?” At the same time there is enough structure to ensure that I am learning the principles of developmental biology at an alarming pace.

I am a student of molecular biology but fairly new to the field of development, so I initially worried that I would struggle to keep up with students who were already experienced in developmental biology. These worries were unfounded as we all have as varied scientific backgrounds as our countries of origin. As one of five Americans in our class of twenty-four, this experience has allowed me to discover the commonalities in the language of science. Our techniques and questions might be different, but our curiosity and passion is matched. We were told that we would form bonds that will last the rest of our careers here, and two weeks in, I have little doubt that this was the truth.

When we are not actively manipulating embryos, world-renowned scientists distill their experience into our exhausted minds. We absorb as much as we can and then teach them drinking games in the wee hours of the morning. We have learned how to operate multitudes of imaging systems and practiced performing essential experimental techniques on more organisms than most people experience in a lifetime. In just two weeks we have been immersed in the history and current research directions of several models of development, including sea urchin, C. elegans, Drosophila, and many other invertebrates. Each model brings with it new opportunities and excitement, as well as traditions and challenges.

As we make the transition to vertebrate models, I am glad to take this moment to pause and reflect on my experiences so far. Six weeks is a long time to step out of one’s graduate research (and not to mention one’s life). It’s hard to assess what this time will mean to me in the years to come as I continue my own research. But if I were able to continue to engage as fully with the science of life as I have these last two weeks, I would never look back.

 



 

 

 
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Book review: Fast-forward: the fourth dimension in development

Posted by on November 23rd, 2011

Development issue 24 features several book reviews. Over the next few weeks, these book reviews will also appear here on the Node. In this first one, Elaine Dzierzak and Catherine Robin compare developmental biology to Star Trek in their review of “Imaging in Developmental Biology: A Laboratory Manual” (Edited by James Sharp and Rachel O. Wong)
(Originally in Development.)


Book info:
Imaging in Developmental Biology: A Laboratory Manual Edited by James Sharp, Rachel O. Wong Series Editor, Rafael Yuste Cold Spring Harbor Laboratory Press (2011) 883 Pages ISBN 978-0-879699-40-6 (paperback), 978-0-879699-39-0 (hardback) $165 (paperback), $246 (hardback)

Development is a bit like Star Trek, the long-running television series in which ‘space’ is the final frontier. For development, the final frontier is the fourth dimension, ‘time’. Time travel through the embryo, from the zygote to gastrulation, to organogenesis, and birth, has been a subject of fascination and science (fiction?) for centuries. This fascination is reflected in the many historical drawings of developing embryos and by advances in the field of embryology that came with the invention of the microscope. With the aid of microscopy, the field advanced from drawings of embryos to static images of fixed sections, which could be rendered, with some mental effort, into three-dimensional (3D) structures. However, comparisons of embryos at different formative stages could only hint at the patterns of dynamic cell growth and morphological change that occur during development, which recent molecular and genetic analyses have begun to uncover. Importantly, the current advances being made in innovative, real-time imaging technologies and in the computational processing of images have now fast-forwarded the field boldly into the dynamic fourth dimension. These advances are now summarized and explained in a newly published book on imaging, Imaging in Developmental Biology, edited by James Sharp and Rachel O. Wong, both experts in this field.

Imaging in Developmental Biology is an excellent resource from which both novices and experienced researchers can obtain current state-of-the-art embryo-imaging protocols for studying key developmental events, such as cell-fate determination, morphogen gradient formation, cell-cell interactions, cell migration and morphogenesis. The eye-catching cover immediately attracted passing lab members, encouraging them to browse the book, which they did with increasing interest. The first comment often expressed was: “I did not know that we could do so much!” Upon first perusal, this comprehensive book seems almost overwhelming with an impressive 57 chapters and seven appendices. But it does contain just about everything known about imaging embryos. This is not surprising as the volume is based, in part, on the popular and excellent Cold Spring Harbor imaging course. The editors have organized the book into four large sections, which contain chapters that are frequently and conveniently cross-referenced. A particularly helpful table is provided in Chapter 1 that guides the reader to specific protocols of interest in different animal models.

Read the rest of this entry »
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Final Day at The EMBO Meeting – Behaviour and lots of Movies!

Posted by on September 14th, 2011

The famous Richard Axel kicked off the last day in Vienna by presenting new data on how olfactory information is projected from the olfactory bulb to the cortex. After his keynote lecture, the talks in the plenary session continued with a focus on the brain and how it drives behaviour in different circumstances or environments and in different organisms - we watched flies, mice, fish and worms as they (mis)behaved. Especially David Anderson’s movies of aggressive flies and mice had a certain entertainment value!

In the afternoon I found it hard to make a decision which of the five concurrent sessions to go to. I would have liked to attend the RNA session, Asymmetric Cell Division and Quantitative Principles of Morphogenesis, all at the same time! Since I had interviewed Eric Wieschaus and Marcos González-Gaitán at lunchtime, I picked their session on morphogenesis. I’ll be posting their insightful discussion here on The Node soon.

The session turned out to be a very good choice, full of fascinating movies of developing embryos. Eric Wieschaus talked about the mechanisms Drosophila embryos deploy to form two different kinds of folds during gastrulation: transient epithelial folds versus permanent internalisation, the latter ultimately leading to the epithelial-mesenchymal transition. How planar cell polarity is re-oriented during development of the fly wing was the focus of Frank Jülicher’s talk, and Marcos González-Gaitán presented their impressive quantitative analysis and modelling of how growth is regulated by the DPP gradient in the developing fly wing. Benny Shilo continued the fly theme with their analysis of the mechanism that establishes the sharp Dorsal gradient in the early embryo.

The two final speakers represented the growing number of vertebrate researchers addressing questions of morphogenesis in a quantitative manner. Martin Behrndt, a PhD student in Carl-Philipp Heisenberg’s lab, talked about the process of the squamous epithelium spreading over the yolk cell during zebrafish gastrulation, and how they took a biophysical and modelling approach to decipher this mechanism. Alexander Aulehla ended the session by presenting a quantitative live-imaging system to tackle the question of the oscillations of gene expression during somitogenesis in mouse.

All in all, I found the meeting very enjoyable. The evening events made it easy to socialise and network, and the scientific programme was at a very high level. The size of the meeting sometimes made it hard to pick one of the parallel sessions, but I think that’s a good problem, when there are simply too many interesting talks on offer! I’ll definitely try to be there in Nice in 2012.
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Cinematic Highlights at the BSDB Meeting 2011

Posted by on July 5th, 2011

As promised, in this final part of my meeting report on the BSCB-BSDB Spring Conference 2011 I will highlight a couple of talks which came with visual effects - studies involving live imaging. I prefer to watch these movies in seminars rather than downloading them with a paper because getting live explanations can make things clearer and more memorable for me. Drosophila was the main movie star, so this post will cover only fly studies.

Lucy Morris, a postdoc in Allan Spradling’s lab (Carnegie Institution, Baltimore, USA), managed to develop a culture system that keeps the Drosophila germarium (the anterior tip of the ovariole) alive and developing for 14 hours. She used this to follow ovarian follicle generation in real-time: Every 12 hours, a new follicle is generated from a germline stem cell (GSC), which divides and migrates posteriorly, forming a cyst of 16 germline cells. While doing so, the cyst is wrapped by somatic escort cells, which midway through the germarium are replaced by a monolayer of somatic follicle cells. Escort cells have been proposed to arise from an escort stem cell niche at the anterior tip of the germarium and migrate along with the cyst, undergoing apoptosis after being shed. However, in her movies Lucy did not observe high levels of escort cell apoptosis, divisions or net migration! Rather, escort cells stayed still and let germline cysts pass them by using dynamic membrane protrusions to help them along. Lucy also found that escort cells do undergo rare divisions, but do so only to maintain a constant ratio of germ cells to escort cells.

After shedding the escort cells, the cyst is coated by a monolayer of follicle cells, which continue to encase the egg chamber until the egg is formed. This follicular epithelium carries integrins on its basal surface, which connect to the cytoskeleton and thereby mediate follicle cell migration over the extracellular matrix. Nick Brown (Gurdon Institute, Cambridge, UK) and his group imaged the movement and morphology of wild-type and mutant follicle cells to gain insight into the functions of specific integrin-associated proteins during this process. They identified a complex of proteins downstream of integrins that regulates actin stress fibres during a specific time point in development, leading to a sudden switch in the distribution of dynamic actin protrusions and a subsequent stop in migration - an observation that would have been impossible to make using fixed specimens only.

Arno Müller’s (University of Dundee, UK) lab is interested in the mechanism of mesoderm layer formation and he presented movies in which they monitored the dynamic changes in morphology that the cells undergo during these tissue rearrangements. They found that the mesoderm cells change their migrational behaviour and morphologies during the process, with the consecutive phases having different requirements for the two FGF ligands, Pyramus and Thisbe.

Finally, germ-band extension was featured in more movies from the embryo, presented by Bénédicte Sanson (University of Cambridge, UK). During this process, the embryonic trunk elongates in the antero-posterior axis and narrows dorsal-ventrally. Bénédicte’s lab imaged the surface of wild-type and mutant embryos and automatically tracked cell movements and shapes to explain which cell behaviours lead to the net tissue deformation. These movies provided them with the data to conclude that both cell intercalation and cell shape changes contribute to the deformation in the fast phase of germ-band extension, whereas in the subsequent slower phase only cell intercalations are required. Polarised cell intercalation is directed by antero-posterior patterning, an intrinsic “force”. The changes in cell shape however can be explained by the invaginating mesoderm acting as an extrinsic force. Bénédicte therefore proposed that a balance between these two forces is essential for axis extension.

I learned from these and other talks that if you would like to know how cells behave in a tissue you will have to try to image them. Not only does this frequently result in spectacular movies, it also provides a lot of information in a very short time. Of course the imaging protocol first has to be established, a task that admittedly can present a whole PhD or postdoc project on its own - but more often than not, it seems to be worth the effort.

ResearchBlogging.org

Morris LX, & Spradling AC (2011). Long-term live imaging provides new insight into stem cell regulation and germline-soma coordination in the Drosophila ovary. Development (Cambridge, England), 138 (11), 2207-15 PMID: 21558370

Clark IB, Muha V, Klingseisen A, Leptin M, & Müller HA (2011). Fibroblast growth factor signalling controls successive cell behaviours during mesoderm layer formation in Drosophila. Development (Cambridge, England), 138 (13), 2705-15 PMID: 21613323

Butler LC, Blanchard GB, Kabla AJ, Lawrence NJ, Welchman DP, Mahadevan L, Adams RJ, & Sanson B (2009). Cell shape changes indicate a role for extrinsic tensile forces in Drosophila germ-band extension. Nature cell biology, 11 (7), 859-64 PMID: 19503074
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Digital fly embryo

Posted by on July 5th, 2010

Using light microscopy to study developmental processes in situ is a bit tricky if your samples are not transparent. In that aspect, early zebrafish development is a walk in the park compared to studying non-transparent fly embryos, or even fish in a later stage of development.

But research published in Nature Methods this week comes with a solution. Thanks to Philipp Keller and his colleagues, it’s now possible to take very clear images of non-transparent samples, such as Drosophila embryos, or to monitor zebrafish development much longer - up to three days. This has produced a database of detailed images and movies of Drosophila embryo development.

A few years ago, the group developed a technique called digital scanned laser light sheet fluorescence microscopy (DSLM), in which a laser beam illuminates a slice of the sample, and a detector records fluorescence of just that slice. But that produced a very noisy signal in the presence of many refractive cell membranes - in other words, with non-transparent samples. To solve this problem, they changed the laser beam properties: Instead of a continuous beam of light, the signal was pulsed. By combining multiple pulsed images of the same section, the signal and noise were easier to distinguish, which led to a much clearer image.

How clear exactly? To test the new system (DSLM-SI), Keller monitored zebrafish development up to three days. Compared to studies done with traditional methods, he could see far more detail, including eye and midbrain development. When using DSLM-SI, they were also able to collect very detailed information of cell positions over time in a Drosophila embryo, and combined this information into a dataset with 1.5 nucleus data entries. You can see the resulting dataset, images, and movies on the digital embryo website.

Fore more information, see the EMBL press release, or the original paper.

(image via EMBL, courtesy of Philipp Keller and EMBL.)


(Read an interesting paper about developmental biology lately? Let us know on the Node!)
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