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Bio Web Conferences – Critical discussions with developmental biologists for deep learning.

Posted by on February 10th, 2012

Dear Developmental biology community,

I would like to bring to your attention a potentially valuable resource for your teaching and research endeavors.  I am a neurodevelopmental biologist at Smith College.  I started teaching a course in Developmental Biology back in 2005, and since then have been utilizing web conferencing technology to bring the research behind concepts alive in the classroom.  My students have been interacting with leading scientists in the field of developmental biology holding organized Q&A video conferences focused on current and seminal research articles.  I am posting this to the Node as since I started using this pedagogical approach I have been recording these discussions, and with full consent provided, I have established an online repository of these recordings via my lab website.  I have each conference (40 now and growing) organized by topic for ease of searching, and each individual session is further broken down by specific question to facilitate quick access to your greatest interest.

Because these sessions are based on key research papers they are extremely applicable for any teacher or student to use in their own courses as supplemental resources to what is probably the very same topics being covered.  For instance, I often assign my students select conferences to watch to supplement their readings or coverage of the material.  Moreover, in class I will poise certain questions about a topic to my student and after some discussion, click on say, Dr. Cliff Tabin’s response to the similar question.  It provides a new and real perspective to the information that students truly appreciate and fosters long-term retention of the material.

There are also many other positive outcomes to both conducting and watching these conferences.  Namely students gain a very different and revealing perspective of not only where a particular field of Dev Bio is moving, but more personal understandings of who the scientists are and how they got to where they are today.  Listening to these remarkable scientists articulate their thinking process to address the research question is extremely illuminating to the developing scientist in your classroom.

So I invite and encourage you to check out these discussions as I am disseminating them for your benefit and use.  I hope you find them helpful.  Feel free to let me know what you think and, if you like them, how you might use them in your teaching.

“Bio Web Conferences” http://sophia.smith.edu/~mbarresi/lab/biowebconferences.html

Best regards,

Michael J.F. Barresi

P.S. additional post on stem cell documentaries coming….

 
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A wave from Quintay

Posted by on January 31st, 2012

The International course on Developmental Biology was a great experience, both instructive and mind-opening. All the students were shuttled to the remote and very small fishing village of Quintay, where the CIMARQ, the investigation centre where the course took place, is located. Originally a whaling station, this centre is dedicated to the instruction of professionals in the area of marine resources and has various branches of research mainly based in repopulation strategies of different species ranging from Sea Urchins to the delicious Conger eel or Sole fish. Their main objective is to provide small scale fish-farming to the general community. In fact, on the day of our arrival, after a Lecture on the history of and the main, original questions in Development by Dr. Roberto Mayor, we were given a short practical on Sea Urchin gamete harvesting and fertilization. This was followed by a very instructive tour of CIMARQ and its various projects, from seaweed culture (which is the main source of food for Sea Urchins) to the Conger and Cole fish tanks (see below). This course was unique in that it covered a wide range of developmental models instead of focusing on one or two: Throughout the twelve days of the course we had two days of each: Zebrafish, Xenopus, Planarian, Drosophila and Chick (plus a symposium and a first day tour). While including such a variety of different models may seem too optimistic (especially for just two days of each!), the truth is that the course was a huge success as proved by the fact that most of the experiments were successful. Our day schedule started with lectures and lab work in the morning. Then lunch, after which we spent most of the time in the lab and, after dinner, everyone attended presentations, by students, about their research. This part (the presentations) was a very good innovation this year and, given its success, it will probably continue in future courses. The discussions were very productive, and, from a student’s point of view, it was great having peak scientists listening, criticizing and suggesting experiments for my research. It was also good to share our areas of research between students since it was very different from the casual exchange of area of research in informal gossip. So, on to the course.

Zebrafish module

Zebrafish was coordinated by Dr. Kate Whitlock. The first Lecture was on Zebrafish basics (rearing and genetics) and embryo morphology. We then proceeded to the lab in which work consisted of cataloging the effects of different concentrations of alcohol in zebrafish development by observation under dissecting microscope of live embryo general morphology and craniofacial development. Afterwards, we carried out an immunohistochemistry protocol for the detection of neuron and neural crest markers so as to further characterize the effects of ethanol in early development. To sum up the results, I would say that the message ¨Vertebrate development and alcohol don’t mix¨ was extremely clear: The deleterious effects on general and craniofacial development were patent even without the need for immunohistochemistry. The second lecture by Kate focused on neural crest development and how neural crest cells migrate and interact with the neural tube and placodes to give origin to the olfactory system At the lab, we studied gene expression of three main neuron and neural-crest marker genes (shh, sox10 and six4b) using in-situ hybridization. Finally, we observed fluorescent-tagged transgenic lines and we compared the results with those of immunohistochemistry and hybridization.

Xenopus module

Xenopus was the next chapter in this course and, again, experiments were very successful (albeit with a lot of effort). We began with a lecture from Dr. John Gurdon on the history of Xenopus as a Development model and classic experiments followed by a focus on the regulation of induction by molecule gradients. In the lab, we tried some of those same experiments ourselves: After a brief introduction by Roberto Mayor on egg collection and fertilization, we injected GFP mRNA into two, four and eight cell embryos. The next step was to create Nieuwkoop recombinants by separating vegetable and animal poles from different embryos and then setting them one against the other so that the vegetable pole would induce growth and mesoderm tissue in the animal pole. The following task was to graft neural crest tissue from GFP labeled neurulas into normal ones. Although it took some practice, after a few hours we successfully observed neural crest cells migrating under the ectoderm. On the second day, Roberto took the stand for a lecture on the post-fertilization phenomena of the Xenopus embryo and on the development and function of the neural crest. The final (and most challenging) experiment was to perform a Spemann organizer graft. After about five or ten minutes of dissection, John Gurdon displayed, with a proud smile, a clean and very neat graft. Although John definitely made it look easy, I had like four or five embryos which attest to the contrary. This was the price of success however as, although most of us agreed that it was harder than it looked, we managed to come up with several grafts which, at least, looked quite tidy. Due to a power shortage (and consequent rise in temperature of the incubator) we were unable to photograph many of those embryos, but the truth is that we were all very satisfied with our achievements.

Planarian module

Planarian was an interesting module in that it is a relatively new model and that we didn’t focus on embryogenesis but on regeneration instead (although we did have a very interesting lecture on planarian embryogenesis, which involves very rare and interesting processes). Planarians have unparalleled regeneration capacities and can regenerate a whole organism from a very small portion of the parent planarian. Dr. Alejandro Sánchez Alvarado was the scientist who established planarians as research models and it was great having him! Alejandro’s lecture on the establishment of planarians as regeneration research models and the similarities and differences between regeneration and embryogenesis was astounding. In the lab, we started out by cutting up worms in as many ways as we could think of. Over the following days, we got to see strange or downright weird forms of planarians as they regenerated the parts we had cut off. A second experimental part of this module consisted of dissociating cells, staining with Hoechst and observing  the cellular morphology of neoblasts (stem cells) among other cell types. In the third part we observed the differences in target proteins and tissue-specific markers between worms under normal conditions and worms either treated with RNAi or cut in half. I particularly enjoyed taking photos of these last worms showing the progressive regeneration of these systems and comparing the velocity and sequence of events that lead to the new worms. This was one of my favorite modules since I didn’t practically know anything about planarians past what I studied in an early zoology course (which seemed boring at the time) and, now, I can’t read enough about them!

Drosophila module

This module was taught by Drs Trudi Schüpbach, Eric Wieschaus and John Ewer. The first lecture, by Eric Wieschaus, was an interactive talk about fly genetics and fly crossing. We discussed the screen with which he identified genes that regulated embryogenesis. This was incredible and very instructive, because most of the time, we read about results without taking into account the real work that had to be done to obtain them. In the lab, we carried out several observational experiments: We were given embryos from unknown crosses and had to hypothesize what the parents´ phenotypes were by peeling embryos or bleaching them, followed by immersion in halocarbon oil or fixing in hoyers mountant. Another part of the practical consisted of analyzing mRNA expression (or localization) and observing embryo morphology and movement using transgenic lines. With the help of Trudi Schüpbach, we  also dissected ovaries and looked at oogenesis in transgenic lines with either GFP-tagged histones or a membrane-bound GFP. The second day, lead mainly by John Ewer, we focused on later stages of development. John gave a lecture about larval growth, physiology and metamorphosis concentrating on the reorganizing of the neural system during the pupal stage. In the lab we learned how to locate and remove imaginal discs from 3rd instar larvae and we watched the retraction and regrowth of sensory neuron axonal arbors and dendrites during the pupal stage Worthy of mention was Eric’s incredible enthusiasm with experiments and his loud cheering when the results were revealed (captured in photo). For me, all of the faculty of the course were extremely good professors: Their lectures were very clear and they were all very open to questions or doubts and were very watchful and helpful in the lab. Eric, however, was something else. I can’t actually explain how or why, but, as an example, he took it upon himself to single handedly sharpen most of our pincers to ease embryo peeling and larval dissection!

Chick module

The chick embryo was the last model and one of the most challenging, not only because of the complexity of dissection and grafting, but also because of how tired we were. After learning how to set up New cultures, we performed two experiments: Node grafts and cutting embryos in half. The first experiment, which is analogous to the one done in Xenopus, was intended to demonstrate how Hensen’s Node induces other tissues. In the second experiment we separated posterior and anterior halves of the embryo and observed their development, since the cells of each half reorganized and redefined the embryo axis. As professor Claudia Linker pointed out, in both of these experiments we had an impressive success rate (>90%), something most of us were very proud of! Additionally, we learned two other very useful techniques which were applied on embryos that were not removed from the egg: Embryo injection with either DNA or a fluorescent label and electroporation of the DNA-injected embryos. Although the success rate was lower, we did get to see some embryos with pretty neat dye labels and even a few good electroporations. Claudio Stern gave two more lectures on the molecular regulation and timing of neural specification and induction and a very interesting and comprehensive one integrating molecular and cellular processes that control, occur during and give rise to gastrulation.

Summing up…

As a student, I was extremely grateful to have had the opportunity to participate in this course. All the faculty were extremely helpful, friendly and sympathetic. In my experience, the closest I can get to scientists of the stature as the faculty of this course is by asking questions at lectures (if I’m extremely lucky). Sharing at least two days with them was very productive and actually giving them) a short presentation was incredible! I was given very good advice on how to guide my research and I also had some very interesting questions (the sort of that great minds usually ask)! Apart from the advantages/tricks/advice I learned for the model I currently work with, this course was very mind-opening: I learned about models that I practically had never heard of before and I feel comfortable about working, for example, with Zebrafish , Xenopus or Chick, three models I never though I would do experiments with! I’m currently thinking about how I can relate my research to one of these models and, hopefully, get my hands dirty working a few months in a lab which uses such models. I would strongly recommend this course for anyone with a strong curiosity and willing to take a look ¨outside the box¨. Please contact me at gersabio@gmail.com if you have any particular doubts about the course or this article and this is the course website: http://biodesarrollo.unab.cl/I wanted to shout out a special thanks for the three organizers: Alfredo Molina, Ariel Reyes and Roberto Mayor, without whom this course would not have occurred, for their dedication and very good will.


Germán Sabio
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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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In Development this week (Vol. 138, Issue 3)

Posted by on January 4th, 2011

Here are the research highlights from the new issue of Development:

Wnt/PCP signalling, microtubules and gastrulation


During vertebrate gastrulation, convergence and extension (C&E) movements shape the germ layers to form the anterioposteriorly elongated body axis of vertebrate embryos. Non-canonical Wnt/planar cell polarity (Wnt/PCP) signalling regulates C&E by polarising the morphology and behaviour of cells, which suggests that the Wnt/PCP pathway might influence the microtubule cytoskeleton. Here, Lila Solnica-Krezel and co-workers investigate this possibility by assessing the position of the centrosome/microtubule organising centre (MTOC) relative to the cell nucleus and the body axes during zebrafish gastrulation (see p. 543). They report that MTOCs occupy a polarised position within the plane of the ectoderm and mesoderm, becoming biased to the posterior and dorsal/medial side of the cell between mid and late gastrulation. This polarisation, they report, depends on intact Wnt/PCP signalling. Conversely, microtubule disruption experiments show that microtubules are required to initiate the anterior localisation of Prickle, a core PCP signalling component. These and other results suggest that reciprocal interactions between Wnt/PCP signalling and the microtubule cytoskeleton are required during C&E gastrulation movements.



Skin deep: Adam10 regulates Notch signalling


Notch signalling plays a crucial role in the development and maintenance of the epidermis: the stratified epithelium that forms the skin’s outer layer and protects organisms from dehydration, mechanical trauma and microbial invasion. Now, on p. 495, Carien Niessen, Paul Saftig and colleagues reveal that the disintegrin/metalloproteinase Adam10, a `sheddase’ involved in Notch processing, is essential for epidermal integrity and Notch-mediated epidermal signalling in mice. The researchers show that epidermal-specific deletion of Adam10 in mouse embryos leads to perinatal death, impairment of the skin’s barrier function and an absence of sebaceous glands. Moreover, deletion of Adam10 in adult mice causes hair loss, epidermal hyperproliferation and cyst formation. These phenotypes closely resemble those produced by epidermal inactivation of Notch signalling. Indeed, the researchers report that epidermal loss of Adam10 severely impairs Notch processing and signalling in the epidermis. Together, these data identify Adam10 as the major Notch processing enzyme in the epidermis in vivo and as a central regulator of skin development and maintenance.



SAD (kinase) tales of neural-specific glycans


Several aspects of neural development and function rely on the regulated expression of specific glycans, but what are the mechanisms that govern neural-specific glycosylation during embryogenesis? On p. 553, Michael Tiemeyer and colleagues report that Sugar-free frosting (Sff) – the Drosophila homologue of SAD kinase, which regulates synaptic vesicle tethering and neuronal polarity in nematodes and vertebrates – drives neural-specific glycan expression in the Drosophila embryo prior to synaptogenesis. They performed a genetic screen for mutations that affect the expression of neural-specific N-linked glycans known as HRP-epitopes; neural expression of HRP-epitopes requires ectodermal expression of Tollo, a Drosophila Toll-like receptor. Analysis of the sff mutant recovered from this screen reveals that Sff modulates glycan complexity by altering Golgi dynamics in neurons that respond to Tollo transcellular signals. The researchers propose that multiple protein kinases facilitate flux through divergent Golgi processing pathways, thereby sculpting tissue-specific glycan expression patterns during development.



nanos1: novel structure-based translational regulation


During development, translational control of mRNAs regulates gene expression. Translational control is usually achieved through binding of trans-acting factors to mRNA untranslated regions but, on p. 589, Mary Lou King and co-workers reveal a novel, structure-based mechanism for translational repression of Xenopus germline nanos1. Nanos translational repressors maintain primordial germ cell identity during development. nanos1 RNA is transcribed during early oogenesis and stored in germinal granules. Surprisingly, the researchers report that, unlike other mRNAs, nanos1 RNA translates poorly after injection into Xenopus oocytes. Thus, sequestration within germinal granules cannot explain translational control of nanos1 mRNA. Instead, they report, a secondary structural element immediately downstream of the mRNA start site is necessary and sufficient to repress the initiation of nanos1 translation through steric hindrance of ribosome scanning; insertion of 15 nucleotides between the start codon and this element relieves repression. Although structure-based translational regulation is common in prokaryotes it has not been observed before in eukaryotes and represents a new, developmentally important mode of nanos1 regulation.



Fast Nodal/Lefty movements set LR asymmetry


Nodal and its feedback inhibitor Lefty instruct left-right (LR) asymmetry in vertebrates, but what controls the spatial distribution of these ligands in the embryo? On p. 475, Lindsay Marjoram and Christopher Wright address this question by expressing functional epitope-tagged Nodal and Lefty from grafts implanted into tailbud Xenopus embryos. Both ligands move long distances along the extracellular matrix (ECM), they report, with Lefty moving faster than Nodal. Moreover, sulphated proteoglycans in the ECM seem to facilitate Nodal movement. Thus, the researchers propose, Nodal autoregulation aided by rapid ligand transport underlies the anteriorward shift of Nodal expression along the left lateral plate mesoderm (LPM), with higher levels of chondroitin-sulphate proteoglycan in more mature anterior regions providing directional transport cues. Finally, they report, Lefty moves from the left to the right LPM, a result that strengthens LR patterning models that involve active blocking of right-sided Nodal expression. Future molecular studies into how Nodal and Lefty interact with sulphated proteoglycan-rich ECM should provide additional insights into the establishment of LR asymmetry.



Moved to radial intercalation by PDGF-A


Radial intercalation – a common morphogenetic process in which cells from germ layers deep in developing embryos interdigitate into more superficial layers – is essential for the tissue rearrangements that occur during gastrulation. Here (p. 565), Erich Damm and Rudolf Winklbauer use scanning electron microscopy and time-lapse recordings to analyse radial intercalation in the prechordal mesoderm (PCM) during Xenopus gastrulation. They show that this process involves cell reorientation in response to a long-range platelet-derived growth factor A (PDGF-A) signal and directional intercellular migration towards the ectoderm, the source of this signal. The PCM, they report, fails to spread during gastrulation when endogenous PDGF-A signalling is inhibited. However, expression of a short-splicing isoform of PDGF-A, but not of a long-splicing form that binds to the extracellular matrix, rescues PCM radial intercalation. These results provide the first insights into the molecular basis of radial intercalation movements in the vertebrate gastrula and identify distinct roles for PDGF-A isoforms during gastrulation.



Also…


As part of the Evolutionary crossroads in developmental biology series, Pauline Schaap introduces Dictyostelium discoideum, a social amoeboid that exists as both uni- and multicellular life forms, studies of which have provided key insights into the evolution of multicellularity.
See the Primer article on p. 387.



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An interview with Patrick Tam

Posted by on November 25th, 2010

(This interview by Kathryn Senior originally appeared in Development on November 23, 2010)

Patrick Tam’s research is focused on the cellular and molecular mechanisms of body patterning during mouse development. He agreed to be interviewed by Development to talk about his interest in mouse development, new concepts in gastrulation, X-linked diseases and his dream of an African safari.

Did you always intend to have a career in developmental biology?

I was lured into science at high school as I listened to my biology teacher reminiscing about his romance with plant biochemistry during his university days. It was really no surprise that I chose biology over medicine as my degree and then headed onto postgraduate research without a second thought. It might sound incredible but there was not a proper course on developmental biology (or embryology, as it was known) in the entire Bachelor of Science curriculum of my university in those days. To fill this gap in my education, I made a definite decision to study rodent embryo development – first in Hong Kong, and later in London with Michael Snow. This was a time when research in mouse development was taking off in a big way in the UK and so the rest, as they say, is history.

What has influenced your decisions about institutions and locations?


Before I finished my PhD, I had already accepted a faculty position in the newly founded Medical School at the Chinese University in Hong Kong. Luckily, I did manage to squeeze in one year of postdoctoral training at the University of Texas at Austin. This proved to be critical for broadening my research experience and I learned a great deal more before taking on the job back home.

Joining a young institute happened to be a good decision: there were ample start-up resources and also the flexibility that I needed to be able to run the laboratory the way I wanted it. The academic appointment offered relatively stable support for my research during this formative phase of my career. The downside was coping with the demand of teaching commitments, and being the only laboratory working on mouse development made it quite hard to maintain research momentum. My next move to a research institute in Australia was a very positive one as it allowed me to develop further in a research-intensive and intellectually stimulating environment. Having access to first-rate facilities and interacting and networking with a larger community of developmental biologists enabled me to focus and move forwards much faster.

You have been a great pioneer in applying micromanipulation and embryo culture research for investigating early mouse development: how did you get into this originally?

My PhD project was to characterise the developmental fate of an active multiplying population of cells in the epiblast of the gastrulating mouse embryo. I had little idea how challenging this would turn out to be! Initially, we focused our efforts on developing a reliable whole-embryo culture method by tweaking the protocol established by Dennis New for culturing rat embryos. We then tried to apply the conventional `slash and burn’ and `cut and paste’ techniques to study cell fate and tissue differentiation. I owe Rosa Beddington an enormous debt of gratitude for introducing me to the art of embryo manipulation during my sabbatical at Oxford University in the mid 80s: my collaboration with her has had a lasting impact on my career. Ultimately, my postgraduate project evolved into a consuming exercise of fate-mapping all three germ layers and their immediate derivatives. The work took three decades but realizing that I had completed my original objective to the best of my ability was a very satisfying moment in my scientific career. Read the rest of this entry »
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