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This month on the Node- August 2014

Posted by , on 1 September 2014

Here are last month’s highlights! Don’t forget to check our jobs page too.

 

morphometricsResearch:

– Gary wrote about his visit to a particle accelerator to image Xenopus embry0s using X-rays.

– Thomas discussed his  paper in Development on the evolution of the development underlying the complex cerebellum found in amniotes.

– Milos introduced his blog ‘Creative Morphometrics’, where he addresses problems in cell shape analysis and proposes solutions using R and python code.

– and Christele discussed a Cell Stem Cell paper challenging the dogma that haematopoietic stem cells keep their DNA intact to ensure a healthy lifelong function.

 

Discussion:

– We reposted an opinion piece published in Development considering the role of morpholinos in the context of new genome editing techniques. Join the discussion!

– What should the future of research be like? Join other graduate students and postdocs in the discussion by participating in the Future of Research symposium!

 

Also on the Node:

Chile2– The latest post in our outreach series is by Kathleen, who launched the project ‘Ciencia Al Tiro‘, which brings science to underprivileged children in Chile.

– We reposted an obituary on the life and research of Yoshiki Sasai.

– The interview chain continues, with an interview with the winner of the SDB poster prize Niteace Whittington

– And Cat reported from the European Evo-Devo meeting, which took place in Vienna last month.

 

 

Happy reading!

 

 

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Advocating FOR grads and postdocs: the Future of Research symposium

Posted by , on 27 August 2014

FORposter

You may have noticed a recent trend in the perception of the graduate and postdoctoral experience, be it in the state of our mental health; or perceived career goal of “academia-or-bust”; or maybe you’re just keeping your pulse on leading US academics warning of the imminent dangers of a flawed biomedical research system or the need for a fair deal for PhDs and postdocs?

You’re certainly not alone – a group of postdocs in the Boston area are organizing the Future of Research symposium to be held October 2-3. The goal is for young scientists-in-training to come together, discuss aspirations for a better future for the scientific enterprise.

What will the symposium involve?

We will have concerned scientists and policy-makers in attendance, including a message from Senator Elizabeth Warren, a keynote address from Henry Bourne, and panel discussions. Participants will also have the opportunity to give voice to their concerns through a variety of workshops focusing on important themes relevant to how we work, and how we will work.

What are the themes of the workshops?

We have an ambitious set of topics to cover:

1) Metrics of success:

– How we measure publication, funding and tenure
– Do we reward certain approaches to science, and penalize others?
– Do we ignore teaching in evaluating researchers?

2) The structure of funding:

– How stable is the funding situation (focusing on the US) and how tenable?
– Should there be a change to how funding is awarded in relation to training PhDs and postdocs?

3) The structure of training:

– How should graduate and postdoc training be done?
– Is there too much focus on a career in academia and not enough on “alternative” careers?
– Are PhDs in the US too long?

4) The structure and sustainability of the workforce:

– Do we have too many PhDs and postdocs?
– Should lab sizes be limited?
– Should we train more staff scientists and research associates and establish permanent, non-PI scientific positions?

These are just some of the issues we could consider: please feel free to comment below or tweet to suggest more (also see below for ways to get involved). We also want to keep the issues of efficiency and competitiveness in our minds when discussing all these issues. For example, is it possible that a significant amount of funding is wasted by deliberate or unknowing competition? Can the scientific enterprise be improved by greater sharing of data earlier in the traditional publication process?

How can I get involved?

Come to the symposium! But if not, there are other ways to make your voice heard and we want to hear from all sorts of researchers in all sorts of places:

Pre-register and/or sign up for updates at futureofresearch.org

Follow @FORsymp

Like our Facebook page and join our group

Join our LinkedIn group

And feel free to comment below; and spread the word amongst your colleagues, both within developmental biology and in other academic fields. We hope that this event will give us a basis to make a statement to the research community about the issues facing trainee scientists and academics, possibly with the production of a white paper. Therefore we hope to receive comments and feedback on what you think.

In the build-up to the meeting, there will be a series of posts on different topics where again, we would be grateful for feedback and comments on your thoughts.

The Future of Research symposium will be held at Boston University October 2-3 2014.

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Categories: Careers, Discussion, Events

Left-right asymmetry, embryonic development, and more

Posted by , on 26 August 2014

Hello there, first time posting on The Node! Every so often Wiley compiles a small selection of recent research on a particular topic, and the most recent is on the topic of developmental biology. This includes some special issues from journals with reviews on:

The first two special issues are free to read and download. There is also a free chapter from our leading book on evolution and development.

If you’re interested, the link to these is here.

Hope it’s useful!
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Postdoctoral fellowship in neural stem cell and developmental neurobiology

Posted by , on 24 August 2014

Closing Date: 15 March 2021

The Division of Developmental Biology and Neuroscience along with Pediatric Neurosurgery at Cincinnati Children’s Hospital (#3 children’s hospital in USA) have openings in Dr Tim Vogel’s lab for postdoctoral Research Fellows to study neural stem cells, glial progenitors, and developmental neuroscience, focusing on cilia and cell signaling in murine models. We have a large group of developmental neuroscientists that work with our laboratory at one of the top children’s hospitals in the USA.

The major goals of our research are to understand neural stem cell differentiation and ciliary signaling mechanisms that lead to a common neural developmental condition seen in humans (For details see Nature Medicine 18, 1797–1804 (2012)). Our lab employs a number of ciliopathy mouse genetic models with in vivo and in vitro systems to study the genesis of hydrocephalus. These include novel in vivo cilia subcellular imaging techniques, molecular /cellular neurobiology, protein biochemistry, genetic, and pharmacological methods.

Our lab has a strong interest in translational neuroscience research and is focused on developing novel medical therapies in our cilia models.

For more information about current projects see: http://www.cincinnatichildrens.org/research/divisions/n/neurosurgery/labs/vogel/default/

Or see : http://neurojobs.sfn.org/jobs/6425490/postdoctoral-fellowship-in-neural-stem-cell-and-developmental-neurobiology

We will be attending the annual SFN meeting to discuss the position with applicants. Schedule a time to meet with members of our lab.

For More Information: Contact: Tim Vogel   Tim.vogel at cchmc.org
Please send a brief statement of scientific/research interests, your curriculum vitae, and a list of 3 references.

Highly motivated postdoctoral candidates with experience  in neuroscience, genetics, developmental biology, molecular/cellular biology, regenerative biology, or biochemistry are encouraged to apply. A strong background in biochemical, cellular, neuroscience, genetic, or developmental biology in mouse models is preferred.

NOTES:
2 openings.
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Outreach Program: “Ciencia Al Tiro” (Science Immediately)

Posted by , on 21 August 2014

Ciencia Al Tiro (Science Immediately) is an Outreach program developed to encourage interest in science and technology. Our inspiration was to help the situation of education in Chile where there is an extremely large difference in the quality of education among schools. According to an OECD assessment of student performance, Chile has the largest gap in Latin America in performance between the private and public schools and this gap has the strongest correlation in the region with socio-economic level. This inequality in education is driven and maintained by the extreme inequality in income distribution in Chile (The Economist, December 13, 2007). Thus, because the poor quality of education in Chile is an urgent problem, we named the program “Ciencia Al Tiro” (Science Immediately; www.cienciaaltiro.cl).

We initiated our program, which is based in the Interdisciplinary Center for Neuroscience, University of Valparaiso, in 2008 using a semester to develop the hands-on workshops with the idea that the students learn about science through performing experiments and constructing projects. Valparaiso is a very poor city and our University, which is located on Cerro Playa Ancha, is within 10 minutes of some of the most underprivileged schools in the country. Starting in 2009 we implemented the workshops in our neighboring poor public schools focusing on junior high school students. Our workshops are designed and taught primarily by graduate students, although the program is open to all scientists. Initially we went to the schools to implement the workshops where as “Tias” and “Tios” (aunt and uncle, the children refer to teachers and adults a tios) we give a very short introduction (10 minutes maximum) and then start the activity.

We design science workshops to convey not only basic concepts, but also to incorporate concepts of climate change and energy efficient technology, to develop awareness and prepare the students for a future where energy will be very expensive. Thus understanding fundamental concepts in science will help resolve problems throughout life by providing a better understanding of the world around us. Our workshops cover a wide variety of topics; we build things like simple motors, solar ovens, thermometers, hand warmers, reactors for biogas, and we teach concepts for example math through the use of a compass (calculate distances and angles), nitrogen cycles through an aquaponics activity, neuroscience through building a neurons and creating a neural circuit, a theatre to explain how a solar electric panel works, genetics via Drosophila, and of course because my lab works on zebrafish we do a zebrafish development day.

 

students & zebrafish

DNA demonstration

 

Because of the sad state of the public schools we implemented two major projects to convey how science can help with the quality of life. In one school we renovated a science room incorporating concepts of energy efficiency (insulation and double paned windows) because there is no heat in the schools. The school sits at the edge of the hill facing the open sea and temperatures can reach 6 C in the winter. Using programmable temperature sensors, our students measured the temperatures over several months in the room that we renovated and in the adjoining room showing that the insulated room had a much more stable temperature i.e. much warmer in the winter. We were awarded the Chile Verde (“Green Chile”) national recognition (Chile Verde 2010, Caso 48, page 71; http://www.porunchileverde.cl/chile-verde-2012). More recently (2011) we installed solar showers in a different public school because many children have no hot water at home. The showers were for the children and school employees so the whole community of the school learned about the technology (http://www.cienciaaltiro.cl/index.php/energia-eficiente/duchas-solares). We had an inauguratiohttps://thenode.biologists.com/wp-content/uploads/2014/08/DNA-demonstration.jpgn and it was a treat to see the students explaining to public politicians the differences between solar electric and solar thermal energy.

After doing our workshops over the years one of the most important things that captures kids’ (and adults’) attention is a dissecting microscope. They are usually fascinated first by the dirt in their fingernails before focusing on the zebrafish embryos. In addition we use the compound microscope to show the kids brain slices with labeled neurons as part of our neuroscience workshop. As scientists we often forget how really cool microscopes are. Also animals, they love the aquaponics workshop because they have fish (zebrafish) and plants in their classroom. Finally the kids like to see if the project they built functions, for example we make three types of solar ovens and then compare which style of oven gets the hottest. We then use the ovens to cook hard-boiled eggs and cookies that they can then eat. This knowledge extends beyond the students, their parents (usually the mother) often want to learn about solar ovens and if our students have siblings in the same school they often show up at the end of class to see the fish, look at neurons in the microscope, or watch fruit flies in their vials.

Because of the challenges of leaving equipment in public schools (theft is a big problem in Chile) and because we lacked space at the university for our equipment (purchased  with Millennium Science Inititaive Outreach funding): dissecting microscopes, compound microscope with a camera system, an E-Rack system used to work with zebrafish, and an Aquaponics System, we pursued a new model where, through private funding, we renovated an old house in Valparaiso near the university and the first floor is a science center dedicated to Ciencia Al Tiro. With the new science center we have initiated long-term projects with seventh and eighth graders including a project to fabricate fish food from restaurant waste. We use fish in the aquaponics system to test whether the fish (a fish found in the local reservoir called Chanchitos) like the food and use zebrafish to look at potential effects on egg laying. A second group is working with our hedgehog “Dominque” to see learn about circadian rhythms using a sensor that detects the revolutions of her wheel when she runs to measure her activity pattern (she runs 4-5 kilometers a night!). A third group is measuring watt usage and luminescence to test whether it is really true when the light bulb packages say “uses 9 watts, illuminates like 40 watts”. A small group of eighth graders returning from last year is investigating the effects of pH on plant growth and the nitrogen cycle using the aquaponics system in our greenhouse. The students will be applying to the regional science fair in October for a chance to present their projects, let’s hope all goes well!

 

Kate and Aquaponics kids

 

We did an extra experiment this year. I organized the Latin American Zebrafish Network Course and Symposium in Valparaiso in April. We decided to incorporate a morning of outreach and had some of our students from Ciencia Al Tiro interview our invited scientists including Dr. Monte Westerfield (USA), Dr. Derek Stemple (UK), Dr. Lila Solnica-Krezel (USA), Dr. Nora Calcaterra (ARG), and Dr. Flavio Zolessi (UR). Our students had previously participated in a workshop we ran on how to be a scientific journalist. Because of potential language problems all students were paired with a Tio or Tia who spoke English. It was a delightful event, the students not only asked about science but also the country of origin, some scientists are born in one country, yet live in another. We often forget how many opportunities we have as scientists, to travel, to meet new people, and to exchange ideas. All of this happiness and interest was conveyed in the morning of interviews. Our kids were left with the impression that science is not only “bakán” (cool) but also a tremendous doorway to understanding far away places.

 

students and research scientists

 

One of the main challenges of our project is that we work with children that come from very rough situations, at times some care takers (called “apoderados”; not everyone has a “Mom” and/or a “Dad”) think we are doing “tonterias” (foolishness). But we easily forget these moments when we see the kids’ excitement, when their “apoderados” show up at their end of the year presentation and are so excited that their kids have done such a cool project. On a personal level there are days where I am overwhelmed by the need, the need for exciting and interesting programs for young people, so many parents want their children in our program, yet we are small; a drop in an ocean of need, but I always remind myself and our group that we are an important drop.

Outreach is an activity that is urgently needed because it teaches young scientists to communicate ideas clearly to non-scientists. Outreach is also important because it drags us out of our labs and we as scientists become more visible to the public, not just to the students but also their families and their communities. Sadly outreach is highly undervalued in the research science community; it does not produce papers, or if so papers of low impact, it brings in little money, and there is an understated idea that those who are not good enough to do research do outreach. It takes creativity and intelligence to meet the challenge of conveying the excitement and importance of science. Our philosophy is that science is everywhere and knowledge is a gift that cannot be stolen.

If you want to develop a program, I would make sure there is some way of valuing the time spent in outreach activities, especially if you are a young untenured professor. Learn how to write projects for funding and learn the culture of the school where you might work, sometimes they are not keen on having outsiders come in, it can be hard on the ego to have doctorate students teaching alongside a science teacher. I would try and remember your own childhood, what did you like in school, what drove you crazy in school. I clearly remember that when I was bored or the teacher was not very good I would skip class. I think there are basic principals, everyone is curious, everyone wants to look through the microscope, play with a computer, but the older you get the more it is bashed out of you.

CAT Book CoverFinally, for those who might be interested, we will be publishing a book in the coming months (before the end of the year) called La Alegria de la Ciencia (The Happiness of Science) which has 12 of our most popular workshops. As a native English speaker I became aware that many of the on-line resources for science projects are in English. Most people, at least in Chile, do not speak English, or do not speak it well enough to understand the information on line. Thus the book is in Spanish; there is no English translation. It is a very pretty book with the workshops related to Chile and specifically Valparaiso. For example, Cata, our main character, ponders why the trolleys (electric) do not belch black smoke like the city buses. We have partial funding for the book so we hope to make it available at reduced cost, please write me (kathleen.whitlock@uv.cl) if you are interested. In addition the plan is to make an electronic version available through our website.

 

 

Outreach logo new squareThis post is part of a series on science outreach. You can read the introduction to the series here and read other posts in this series here.

 

 

 

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Yoshiki Sasai: stem cell Sensei

Posted by , on 21 August 2014

This obituary first appeared in Development.

 

Stefano Piccolo looks back at the life and research of his friend and colleague Yoshiki Sasai.

 

Yoshiki Sasai2On 5 August 2014, Yoshiki Sasai died at the age of 52, near to the RIKEN Center for Developmental Biology in Kobe, Japan. This is the institute that he had helped to establish and painstakingly driven to become a world-leading research institution. The scientific community mourns the loss of one of its giants. But for those of us fortunate enough to have enjoyed Yoshiki’s friendship, or to have been transformed by his teachings and intellectual intensity, the grief of his death is devastating. He was a pioneer in the fields of developmental and stem cell biology, and here I will try to summarize and celebrate his exceptional legacy.

Yoshiki Sasai was born in Hyogo, Japan, and grew up playing baseball and cultivating the noble discipline of Kendo (the Japanese martial art that uses bamboo swords). Like other members of his family, he entered medical school, receiving his MD from the University of Kyoto in 1986. However, after completing an internship in internal medicine, he was frustrated by the limited biological understanding involved in routine clinical practice. He wanted to get at the root of the fundamental principles by which cells and tissues, particularly the brain, operate in health and disease. He therefore left the hospital halls to join the neurobiology laboratory of Shigetada Nakanishi as a PhD student. There, he became intrigued by how neural cells control their differentiation status. He was a gifted molecular biologist and, during his PhD, he identified mammalian HES family members and revealed their anti-neurogenic properties (Sasai et al., 1992).

For his postdoc, his instinct for cutting edge research brought him to southern California, to work on early Xenopus embryology in the laboratory of Eddy De Robertis (HHMI, UCLA). I vividly remember the day I first met Yoshiki. I was a newcomer to the De Robertis laboratory, just arrived in Los Angeles from Italy, and he was the senior postdoc of the lab. The respect he garnered from Eddy and the rest of the team was palpable. A few weeks after arriving at UCLA, Yoshiki had already cloned a new secreted factor, Chordin. This discovery held the key for what was then one of the biggest mysteries in developmental biology: the workings of the Spemann organizer. This fragment of the early embryo serves as signaling source to induce the nervous tissue and pattern the body plan, but its inner workings were yet unknown (De Robertis, 2009). Yoshiki had found that Chordin was expressed precisely in the organizer; moreover, injection of chordin mRNA was sufficient to generate a twin body, thus recapitulating the effects of transplantation of the organizer tissue. His first paper had already appeared in Cell (Sasai et al., 1994), and when I arrived in Los Angeles, Yoshiki was about to publish his second landmark discovery in Nature: the observation that neuralization of naïve cells induced by Chordin could be reversed by BMP4 (Sasai et al., 1995). Eddy made it clear that now it was my turn to venture into the biochemical mechanism for the Chordin-BMP antagonism. Of course, I had no idea where to start, so I was directed to Yoshiki for practical advice. At our first meeting, he effortlessly noted down a long list of ‘to-do’ experiments, with such rigor, logic and in-depth analysis of potential pitfalls and necessary controls to leave me at the same time captivated and intimidated. I still have those lab notes with me! By following that to-do list, it took only a few months to show that Chordin is not providing the embryo with any signal, but rather depriving it from the BMP signal, physically trapping BMPs in the extracellular space (Piccolo et al., 1996). Yoshiki was thus a central figure in establishing the notion in the late 1990s that the neural fate is a default state (Sasai and De Robertis, 1997).

Yoshiki treasured the essence of these discoveries: for embryonic cells, we often must remove external instructions, rather than adding them. Remarkably, with minimal external cues, cells apparently ‘know’ what they have to do, and can initiate entire developmental programs. By 1996, Yoshiki had returned to Japan to take up a position as associate and then full professor at Kyoto University. In 2003, he moved to Kobe, to the newly established RIKEN center. Through the years, he continued to work with the frog model system, providing seminal findings on the transcription factors involved in neural patterning and on the mechanisms responsible for sizing the embryo (Inomata et al., 2008). In parallel, he was using embryonic stem cells (ESCs), which he essentially considered the mammalian counterpart of the naïve frog embryo ectoderm cells that he had neuralized with Chordin. In his lab, lessons obtained in the frog model system were applied to ESCs, and vice versa (Sasai et al., 2008).

Yoshiki had a unique ability to see things clearly while others were left wandering in the dark. Creative intuition was then coupled with an ability to conceive straightforward experimental approaches, many requiring a patient, almost ritual, optimization in perfect Japanese style. He established a mouse ESC culture system containing minimal exogenous growth factors, a system that allowed cells to spontaneously slip into a telencephalic progenitor fate (Watanabe et al., 2005). Another major innovation was the discovery of an efficient method to culture human ESCs (Watanabe et al., 2007; Ohgushi et al., 2010). Until the mid-2000s, advances using human ESCs had been hampered by the fact that, unlike mouse ESCs, human ESCs are vulnerable to dissociation, and thus are lost through passaging. Yoshiki was not discouraged by this trivial, yet apparently insuperable, limitation: he systematically searched for chemical compounds able to sustain human ES passaging. One of these, a ROCK inhibitor, instantly did the trick and allowed human ESCs to survive through multiple passages; this compound is now routinely used in the field of ES and induced pluripotent stem cell (iPS) research.

It was the follow-up to his initial ESC work that made Yoshiki a scientific superstar. Inducing some specific types of neural cell types was too easy for Yoshiki; his challenge was to generate entire parts of the mammalian brain in the Petri dish. At that time, no techniques existed for generating organs from stem cells in culture. Earlier attempts to coax cells into organs by putting them on artificial scaffolds had been met with mixed success or had floundered. Keeping faith with his ‘less-is-more’ approach, Yoshiki not only removed growth factors from his ESC cultures; he also removed cells from the tissue culture plastic on which they are normally maintained, and grew them in suspension as floating spheres in Matrigel. He sensed that freeing stem cells from any external impediments would allow them to follow their own inner biological script (Sasai, 2013).

The results were awe-inspiring. Yoshiki and his colleagues showed that when their neuroepithelial ‘balls’ reached a given size, they started to form complex three-dimensional brain structures. In a series of seminal papers, they reported the generation in a dish of cortical tissue, of optic cups covered with a multilayered retina and of functioning pituitary glands (Eiraku et al., 2011, 2008; Suga et al., 2011). Yoshiki saw the emergence of these tissues under his microscope as a sort of living origami: he had only to adjust the initial conditions and then the tissue would continue its ordered folding and progressive assembly spontaneously, without external instructions. Size, topology and differentiation were all orchestrated by mysterious ‘self-organizing’ principles. When he repeated his famous optic-cup experiments with human ESCs, the induced eyes were, in fact, very human in terms of size and photoreceptor types (Nakano et al., 2012). Species-specific differences appeared to be intrinsically encrypted in cells, and blossomed under his in vitro organogenesis conditions. When I met him at a meeting and asked whether he would now rush to apply these astonishing findings to human retinal disorders, he answered “No way, the specialists should take credit for that. I will only be their consultant”. Indeed, he had already conceived what was for him the next frontier: getting a handle on the nature of tissue’s self-organizing scripts, which he sensed were a consequence of both a chemical and a biomechanical chain of events (Eiraku et al., 2012).

Those who met Yoshiki on the conference circuit will certainly remember that he was an outstanding lecturer. His talks were perfectly punctuated with wit and a sense of playfulness. Others may have met him in the evenings of the many symposia organized at his institute as the exuberant RIKEN bartender (he expected tips, too!). The more private Yoshiki was a positive, charismatic and generous man. And it was impossible to resist being fascinated by a man who could talk passionately about so many diverse things, whether the topic was Japanese culture, the delicacies of an Italian risotto or evolutionary plasticity.

Hopefully, Yoshiki’s ‘eyes-in-vitro’ will help treating blindness in the future. But whatever the translational legacy of his work, he was certainly a visionary scientist, who opened our eyes to the wonders of developmental and stem cell biology and its potential for mankind.

Goodbye Sensei, we miss you.

 

References:

De Robertis, E. M. (2009). Spemann’s organizer and the self-regulation of embryonic fields. Mech. Dev. 126, 925-941.

Eiraku, M., Watanabe, K., Matsuo-Takasaki, M., Kawada, M., Yonemura, S., Matsumura, M., Wataya, T., Nishiyama, A., Muguruma, K. and Sasai, Y. (2008). Self-organized formation of polarized cortical tissues from ESCs and its active manipulation by extrinsic signals. Cell Stem Cell 3, 519-532.

Eiraku, M., Takata, N., Ishibashi, H., Kawada, M., Sakakura, E., Okuda, S., Sekiguchi, K., Adachi, T. and Sasai, Y. (2011). Self-organizing optic-cup morphogenesis in three-dimensional culture. Nature 472, 51-56.

Eiraku, M., Adachi, T. and Sasai, Y. (2012). Relaxation-expansion model for self driven retinal morphogenesis: a hypothesis from the perspective of biosystems dynamics at the multi-cellular level. BioEssays 34, 17-25.

Inomata, H., Haraguchi, T. and Sasai, Y. (2008). Robust stability of the embryonic axial pattern requires a secreted scaffold for chordin degradation. Cell 134, 854-865.

Nakano, T., Ando, S., Takata, N., Kawada, M., Muguruma, K., Sekiguchi, K., Saito, K., Yonemura, S., Eiraku, M. and Sasai, Y. (2012). Self-formation of optic cups and storable stratified neural retina from human ESCs. Cell Stem Cell 10, 771-785.

Ohgushi, M.,Matsumura, M., Eiraku, M.,Murakami, K., Aramaki,T., Nishiyama, A., Muguruma, K., Nakano, T., Suga, H. and Ueno, M. et al. (2010). Molecular pathway and cell state responsible for dissociation-induced apoptosis in human pluripotent stem cells. Cell Stem Cell 7, 225-239.

Piccolo, S., Sasai, Y., Lu, B. and De Robertis, E. M. (1996). Dorsoventral patterning in Xenopus: inhibition of ventral signals by direct binding of chordin to BMP-4. Cell 86, 589-598.

Sasai, Y. (2013). Next-generation regenerative medicine: organogenesis from stem cells in 3D culture. Cell Stem Cell 12, 520-530.

Sasai, Y. and De Robertis, E. M. (1997). Ectodermal patterning in vertebrate embryos. Dev. Biol. 182, 5-20.

Sasai, Y., Kageyama, R., Tagawa, Y., Shigemoto, R. and Nakanishi, S. (1992). Two mammalian helix-loop-helix factors structurally related to Drosophila hairy and Enhancer of split. Genes Dev. 6, 2620-2634.

Sasai, Y., Lu, B., Steinbeisser, H., Geissert, D., Gont, L. K. and De Robertis, E. M. (1994). Xenopus chordin: a novel dorsalizing factor activated by organizer-specific homeobox genes. Cell 79, 779-790.

Sasai, Y., Lu, B., Steinbeisser, H. and De Robertis, E. M. (1995). Regulation of neural induction by the Chd and Bmp-4 antagonistic patterning signals in Xenopus. Nature 376, 333-336.

Sasai, Y., Ogushi, M., Nagase, T. and Ando, S. (2008). Bridging the gap from frog research to human therapy: a tale of neural differentiation in Xenopus animal caps and human pluripotent cells. Dev. Growth Differ. 50 Suppl. 1, S47-S55.

Suga, H., Kadoshima, T., Minaguchi, M., Ohgushi, M., Soen, M., Nakano, T., Takata, N., Wataya, T., Muguruma, K. and Miyoshi, H. et al. (2011). Self formation of functional adenohypophysis in three dimensional culture. Nature 480, 57-62.

Watanabe, K., Kamiya, D., Nishiyama, A., Katayama, T., Nozaki, S., Kawasaki, H., Watanabe, Y., Mizuseki, K. and Sasai, Y. (2005). Directed differentiation of telencephalic precursors from embryonic stem cells. Nat. Neurosci. 8, 288-296.

Watanabe, K., Ueno, M., Kamiya, D., Nishiyama, A., Matsumura, M., Wataya, T., Takahashi, J. B., Nishikawa, S., Nishikawa, S.-i. and Muguruma, K. et al. (2007). A ROCK inhibitor permits survival of dissociated human embryonic stem cells. Nat. Biotechnol. 25, 681-686

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The Node at the GSA Xenopus Meeting

Posted by , on 21 August 2014

The Node is on its way to California, to attend the GSA Xenopus meeting, starting in Monterey this Sunday (24th August). If you are attending the meeting, do say hello to our community manager if you see her- Cat would love to hear your thoughts on the Node! We are also looking for someone to report from the meeting, so if you would like to blog about it get in touch. We look forward to meeting you there!

 
Node Xenopus

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Postdoctoral Position in Left-Right Asymmetric Organ Morphogenesis

Posted by , on 21 August 2014

Closing Date: 15 March 2021

NIH-funded postdoctoral position is available in the Nascone-Yoder laboratory at North Carolina State University (NCSU) to study left-right asymmetric organ morphogenesis. The successful applicant will utilize both Xenopus and the emerging amphibian model, Lepidobatrachus (Budgett’s frog), to elucidate the cellular and molecular basis of gut and/or heart looping.

We are seeking a self-motivated individual with a Ph.D. in cell and developmental bio, and at least one peer-reviewed publication.  A strong background in molecular biology must be demonstrated, with experience in bioinformatics, frog models, organogenesis, IHC techniques, and/or confocal microscopy also highly desirable.

North Carolina State University is situated in the heart of the Research “Triangle” (as delineated by the three relative locations of NCSU, Duke University & University of North Carolina at Chapel Hill).  The Nascone-Yoder lab is located in the Department of Molecular Biomedical Sciences at the NCSU College of Veterinary Medicine, currently ranked 3rd among the top veterinary colleges in the nation.

Review of applications will begin immediately and will continue until the position is filled. Please send a CV, including a list of three references, and a statement of research interest by email to:    Nanette Nascone-Yoder, nmnascon@ncsu.edu

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Accelerated Frogs: Developmental Biology meets Particle Physics

Posted by , on 20 August 2014

I previously wrote a post about the development of a 4-D X-Ray Tomography technique for imaging early Xenopus embryos. Frog embryos are opaque due to their yolky composition and this has proved a challenge for traditional optical microscopy of events in the early stages of Xenopus embryo development. However Julian Moosmann, Ralf Hofmann and Jubin Kashef at Karlsruhe Institute of Technology (KIT) recently developed a technique using an X-ray setup from a synchrotron beamline to generate images of the frog embryo which they used were able to track events in gastrulation and neural crest migration.

They recently had some beam time at the Advanced Photon Source in Argonne National Laboratory, IL, USA and they kindly invited me along to participate in some frog X-rays.
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The Advanced Photon Source at Argonne National Laboratory.

 

The basic principle of the process is that electrons are accelerated in a linear accelerator (to >99.999% the speed of light) and this beam of accelerated particles is further accelerated by electrical fields to >99.999999% the speed of light in a booster synchrotron, which also uses magnets to focus the beam. X-rays are generated by perturbing the path of the electrons to make them oscillate in the large storage ring. There are 35 tangential lines (we were in Sector 32, with assistance from APS staff members Alexey Ershov and Xianghui Xiao in setting up and operating the beam) which receive X-rays for experimental use, using optical setups tailored for the particular uses required by researchers.

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Top panels: The Experiment Hall. Bottom panels, left: The hatch containing the experimental room for Sector 32 and right: the line carrying the beam from the storage ring to the hatch.

 

The team from KIT place frog embryos (fixed or living) in front of the beam in the setup shown below: an Eppendorf tube containing a well of agarose to hold the embryo in a fixed position is mounted on a rotating stage. For each tomogram, a 360˚ image is generated and for living samples, images are taken at multiple timepoints to generate a 4-Dimensional tomogram across space and time.

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Setup of the sample holder (left, Eppendorf tube on pink stand) in front of the beamline (right).

 

Obviously having 30 keV of X-ray radiation fired at them doesn’t make for happy frog embryos and after some time they are unable to be imaged further. This is an obvious caveat to the technique but one that can be manipulated through exposure times, much as one would limit the exposure of samples for fluorescence imaging in an optical setup.

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Left in charge of the beam by myself for a few hours!

 

Look out for this technique as it is developed further; it is clear that the images generated will give us a new view of embryology.

Please feel free to comment/ask questions – a further extended blog will likely appear at Beware of the Frog!
Further information and events:

No terrifying mutant frog monsters/comic-book villains were generated in this work.

For more info about the Advanced Photon Source please visit their website.

Ralf and Jubin are both giving talks at the upcoming Xenopus conference – Ralf will give a talk at 9am on August 27th entitled, “X-ray phase contrast microtomography: 4D livecell imaging of structural development” and Jubin will give a talk at 9.40 am entitled, “Cadherin-11 localizes to focal adhesions and promotes cell-substrate adhesion”.

Many thanks to Mike Levin at Tufts University for funding my trip out to APS.
References:

Moosmann, J. et al. X-ray phase-contrast in vivo microtomography probes new aspects of Xenopus gastrulation. Nature 497, 374–377 (2013).

Moosmann, J. et al. Time-lapse X-ray phase-contrast microtomography for in vivo imaging and analysis of morphogenesis. Nature Protocols 9, 294-304 (2014).

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Postdoc position – Cell and Developmental Biology, John Innes Centre, UK

Posted by , on 20 August 2014

Closing Date: 15 March 2021

A 3-year postdoctoral position is available in the Sablowski lab at the Cell and Developmental Biology Dept., John Innes Centre, Norwich, UK. The successful candidate will work on a project that combines genome-wide association mapping and quantitative image analysis to reveal novel genes that control stem architecture in Arabidopsis.
 

Plant architecture depends in large part on the on the size and shape of the stem, which vary widely in nature and in crops. The genetic and developmental basis for this variation, however, is mostly unknown. Knowledge about stem ontogenesis and novel genetic variation that modifies stem development is not only of fundamental interest in plant development and evolution, but also has great strategic potential for crop improvement.
 

An effective approach to reveal the genetic basis of natural variation is genome-wide association studies (GWAS), and in recent years Arabidopsis has emerged as a powerful model for GWAS. Also in the last years, novel imaging and quantitative, 3D image analysis methods have created unprecedented opportunities to study the cellular basis of plant growth. In this project, we combine both approaches to reveal the genetic basis for natural variation in stem development and the mechanism of action of the underlying genes.
 

A PhD in cell biology, development or molecular biology is required. The ideal candidate will have a proven record of scientific productivity and will combine rigorous and creative thought with attention to detail and ability to integrate their own project and results with knowledge from the relevant literature. Good knowledge of statistics, experience with Arabidopsis genetics, confocal microscopy, image analysis and knowledge of programming languages (R, Python) will be advantageous.
 

To apply, please go to: http://www.jic.ac.uk/training-careers/vacancies/2014/08/postdoctoral-research-scientist-sablowski-lab/
 

For further details about the lab, visit http://www.jic.ac.uk/STAFF/robert-sablowski/sablowski.htm

 

 

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