Postdoctoral Positions are available for highly qualified and motivated candidates to study the physical principles of morphogenesis in the Davidson Laboratory at the University of Pittsburgh in the Department of Bioengineering. The laboratory focuses on studying the molecular-, cellular, and tissue-scale processes that regulate mechanical properties and force-production during morphogenesis. Projects involve a combination of biophysics, cell biology, bioengineering, and embryology.

Candidates will have recently completed a PhD and have strong background in either biophysics, cell and developmental biology, or cell- and tissue- mechanics. Candidates with expertise with biochemistry, quantitative microscopy, microrheology, microfabrication or computer simulation are preferred. The research environment at the University of Pittsburgh includes a dynamic community of bioengineers, developmental biologists, cell- and tissue-level biomechanics, and theoretical biologists. Nearby resources include the John A. Swanson Micro and Nanotechnology Laboratory and the Pittsburgh Supercomputing Center. Contemporary Pittsburgh is a diverse vibrant city undergoing a renaissance led by world class Universities and the University of Pittsburgh Medical Center. The University of Pittsburgh is an Equal Opportunity Employer. Women and minorities are especially encouraged to apply.

Interested applicants should forward their statement of research interests, CV, and a list references to:

Lance Davidson
Department of Bioengineering
Biomedical Science Tower 3, Room 5059
3501 Fifth Avenue
University of Pittsburgh
Pittsburgh PA 15260
(email) lad43@pitt.edu
(web) http://www.engr.pitt.edu/ldavidson/

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Worth 1000 words?

http://blogs.nature.com/news/thegreatbeyond/2010/08/a_zebrafishs_first_minutes_of.html

[update 31/8: I added the first of the videos (below) – Eva]

(The original paper is in Science)

(2 votes)

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It seems that following on the tracks of Cell Press, which is reducing the maximum number of supplemental figures to one per manuscript figure, now J. Neuroscience is doing away with it altogether. Hooray?

I agree that it is not a very good thing at times that the amount of Suppl Figs has risen (or sunk) from useful to occasionally ridiculous (20+ figures!). Yes, it is useful to be able to add a few control experiments, or the validation of a mouse knockout, and a good place to put especially large datasets, but now it’s become an excuse to either bury data that isn’t super solid (in hopes that reviewers won’t pay too much attention), or from the other side, an open invitation for reviewers to ask for more (It’s like a reverse Oliver Twist: “Can I have more please?”; “MORE!?”).

And for the most part, it’s a rather annoying exercise to have to go download the suppl materials. Why can’t journals not put the supplementary pdf together with the main paper pdf? I do it all the time, it’s a simple feature in Acrobat, so is that so much to ask for from a publisher? Cell Press does it, Nature Cell Biology does it, but that’s about it.

So, Supplementary/Supplemental figures/data? Good, bad, ugly? Discuss. Perhaps we can help influence some journals that are paying attention.

(3 votes)

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Some Canadian postdocs are awaiting the next academic year with bated breath: will they earn less than they did during their PhD, or twice as much as their colleagues?

Canada’s 2010 research budget, announced this past spring, was full of surprises for the thousands of postdoctoral researchers in the country. To promote top-level talent, the government put aside $45 million for the next five years to award a select group of postdocs with $70,000 per year. These Banting post-doctoral fellowships are almost twice as much as the average Canadian postdoc salary of approximately $35,000-$40,000. Applications for the prestigious awards have opened on August 10, and are being accepted until November 3, 2010. But the lucky few who get the top awards will also receive another, slightly less pleasant, surprise: postdoctoral fellowships in Canada are no longer tax exempt. Even postdocs who previously paid no taxes on the funding they received, will be charged next year. Until now, postdoctoral stipends often fell under the same – tax-free – umbrella as student scholarships. Surprisingly, this now means that a fully-funded PhD student can end up with more money than they will receive as a postdoc paying taxes on a basic postdoc fellowship!

With such mixed funding news, reactions from young Canadian researchers have been all across the board. What do you think: is the $45 million well spent on the new competitive awards (boosting the international prestige of these researchers, and perhaps being a way out of the previously discussed issue of “too many postdocs”), or would you rather have seen a continuation of the tax exemption for postdoc stipends? The Banting fellowships are open to international applicants, too: would knowing that there was a very small chance of a competitive postdoc salary lure foreign researchers to Canada, or would it succeed in keeping Canadian graduates from seeking top funding elsewhere in the world?

(image by lsiegert on Flickr)

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Many of you are probably familiar with the web comic Piled Higher and Deeper (PhD), which chronicles the lives of graduate students and perceptively points out some of the peculiarities of academia. Recently, we met up with the comic’s creator, Jorge Cham, and talked about graduate school, recognizable academic situations that cross all disciplines, and procrastination.

(Thanks to Node readers Kat, Pablo, and Sandra for providing some of the questions.)

When did you start drawing Piled Higher and Deeper?

I started during my first term in grad school, so I was definitely not supposed to be drawing comics. I was a teaching assistant, I was a research assistant, I was taking classes – but I saw this ad in [The Stanford Daily] newspaper calling for comics, and I just thought I would submit something nobody had ever really written about or made fun of: people trying to get their PhDs.

How did you manage to find time to combine that with grad school itself?

I didn’t sleep a lot during that semester! But I started publishing a new comic five days a week, and that quickly became only three times a week.

Many of your readers, including myself, grew up with your comic throughout grad school. Meanwhile, some of us have graduated, but a lot of your characters still haven’t. Are they ever going to graduate?

Yeah, the series will not go on indefinitely. I definitely have endings or events for all of the characters, whether they graduate or not.

Will there be a spin-off postdoc comic then?

Heh! Well, they might become postdocs. One of the characters is now a postdoc, but it will probably still be called “Piled Higher and Deeper”

We noticed that the comic works well for a lot of different fields. The readers of the Node are all developmental biologists, and you don’t have a biologist character in the PhD comics, but a lot of the things are still recognizable. Do you notice that a lot of the situations you write for, for example, the engineer characters are applicable to any field?

I do it on purpose. When I first started grad school I happened to know a lot of people who were in many different fields: Anthropologists, economists, engineers, geophysicists – and they were all friends! Just listening to them I could tell that they were all sharing the same experience. So for me, from the very beginning that was something that was interesting to me, so that’s the way I wrote the comics. I grounded the characters in a specific department, so that there’s a bit of realism there, and you get the sense that they are doing something. But I try to write the dialogue so that it generally speaks to academics and grad students in all disciplines.

That being said, there are specific things that biologists have to deal with that don’t occur in other fields, like the fact that you have to take care of living things on the weekend. Has anyone ever requested a biologist character?

Yeah, a lot. In fact, I’m very familiar with the idea of being beholden to experiments like that, because I worked in a neuroscience lab for two years. Somebody once described it as “your life being run by the menstrual period of rats”. I have a character who is going to focus on biology, but probably not for another year or year-and-a-half.

You also travel around to give talks about procrastination. A lot of visitors to the Node drop by during a break from work, and I’m sure they’d like to know if there’s any value to procrastination.

I don’t like to talk about whether procrastination is good or bad. I just like to talk about the fact that you do it, and that you probably do it for a reason. There’s a lot of flexibility in grad school, and it always feels like it never ends. There’s always something more that you could be doing – something more that you should be doing –so a lot of times people find themselves procrastinating. What I like to say is that procrastination is not necessarily bad, but that it’s sometimes an important part of the creative process, and can reveal what you really want to do, and what your real passions are. If you find that you’re not spending as much time as you should be on, for example, writing this particular chapter for this particular professor, it maybe means that you don’t really want to write it. Instead of feeling bad about it, you should just realize it, and focus on something else.

Finally, one of our readers in South America asked when you’re coming to the Southern Hemisphere

You just have to invite me – that’s pretty much how it works!

Part of a collection of panels Jorge drew at Sci Foo, where we met for the interview.

Part of the interview in audio format:
[audio:https://thenode.biologists.com/wp-content/uploads/2010/08/jorge-cham.mp3|titles=jorge cham]

(6 votes)

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(This interview by Kathryn Senior originally appeared in Development on August 10)

Shin-Ichi Nishikawa is Group Director of the RIKEN Center for Developmental Biology in Kobe, Japan, where his stem cell research focuses on understanding the mechanisms involved in cell differentiation. He joined Development as an editor in 2009. We interviewed Shin-Ichi to find out about his interest in developmental biology, about the event that made him change career from being a practicing physician to a researcher, and his current research interests.

Looking back, when do you first remember being interested in science?

This was quite early in my life, when I was still a pupil at elementary school. I remember very clearly the day that the Sputnik satellite was launched by the Soviet Union – on October 4, 1957. I heard the news and was amazed that something the size of a beach ball had been sent into orbit around the Earth. We didn’t know it then, but this was the dawn of the space age, the beginning of the space race and the start of my life-long passion for science.

What path did you follow in your early career?

I was desperate to work in a scientific field but I was not good at maths or physics, so becoming a researcher in physics or space technology wasn’t really an option. I decided to study medicine and got my MD at the Kyoto University School of Medicine in 1973. I then worked as a chest physician for about 7 years, completing an internship and residency at the Kyoto University Chest Research Institute. My plans at that stage were to carry on in medicine, and I would very likely have stayed on track if I had not caught hepatitis when treating one of my patients.
(more…)

(5 votes)

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The Bicoid gradient, epigenetic control of BMP signalling, haematopoietic stem cells and more…here are the highlights from the current issue of Development:

The Bicoid gradient gets into shape without nuclei

Morphogen gradients provide key positional information during embryogenesis but how they are established is not well understood. A gradient of the transcription factor Bicoid is known to provide Drosophila embryos with positional information along their anterior-posterior axes. Since Bicoid is enriched in nuclei, nuclei have recently been proposed to act as potential traps or sites of degradation that could slow down Bicoid diffusion from the anterior pole and hence contribute to the observed Bicoid gradient. On p. 2857, Oliver Grimm and Eric Wieschaus address this issue experimentally and find that the Bicoid gradient is shaped independently of nuclei. Using mutated Bicoid with impaired nuclear localisation, they show that the resulting gradient of this protein is indistinguishable from that formed by normal Bicoid protein. They also show that the initial centre-to-surface redistribution of Bicoid and the scaling of the gradient are not influenced by Bicoid nuclear accumulation. Based on these findings, the authors propose that nuclei do not play a role in shaping the Bicoid gradient.

Spinal cord development BuMPs into epigenetics

During spinal cord development, transcription factors and signalling proteins, such as the BMPs, are involved in neural tube (NT) patterning and in inducing neural differentiation. Although epigenetic modifications are known to regulate the expression of key neural development genes in stem cells, whether they have a role in spinal cord development remains unclear. On p. 2915, Marian Martínez-Balbás and colleagues study histone H3 lysine 27 trimethylation (H3K27me3) in vivo during chick embryo neurogenesis. They show that global levels of H3K27me3 increase along neurogenesis and regulate BMP signalling within the NT. Using microarray analysis, they find that the expression of Noggin, a BMP inhibitor, is repressed by H3K27me3. Importantly, they show that, in response to BMP activity, the histone demethylase JMJD3 interacts with the Smad1/4 complex to demethylate and thereby activate the Noggin promoter. This reveals a novel pathway by which BMP signalling can regulate its own activity within the spinal cord by modulating expression of its inhibitor Noggin.

microRNA regulation of Hox genes: RNA tails matter

The Hox family of transcriptional regulators plays a central role in specifying segment identity along the anteroposterior axis of animal bodies. The Drosophila Hox gene Ultrabithorax (Ubx) is dynamically expressed during development and controls the development of posterior thoracic and anterior abdominal segments. On p. 2951, Claudio Alonso and colleagues show that during development the Ubx gene produces multiple transcripts that vary in their visibility to microRNAs (miRNAs). They demonstrate that different parts of the embryo express Ubx transcripts that contain variable 3′ UTRs, each harbouring a distinct set of miRNA target sites. The differential distribution of these transcripts during development is independent of miRNA-mediated degradation but is instead due to an in-built system that processes mRNAs according to developmental context. They also show that other Hox genes, such as Antennapedia, abdominal-A and Abdominal-B, exhibit similar developmental RNA processing and propose that developmental processing of 3′ UTR sequences is a general molecular strategy that allows spatiotemporal control of mRNA-miRNA interactions during development.

Haematopoietic differentiation: lessons from development

Efficient production of haematopoietic stem (HPS) cells from embryonic stem (ES) cells or from induced pluripotent stem (iPS) cells requires a thorough understanding of haematopoietic differentiation pathways. On p. 2829, Gordon Keller and colleagues show that generation of HPS cells from ES and iPS cells follows the same steps as haematopoietic development in the embryo. They induced ES cells with known agonists of embryonic haematopoiesis (activin A, BMP4 and VEGF) and identified two temporally distinct populations of cells expressing the haematopoietic marker Flk1. The gene expression profiles, cell surface markers and lymphoid potential of the early Flk1-positive population resemble those of the first site of embryonic haematopoiesis, whereas the cells that expressed Flk1 at a later stage correspond to a later stage of haematopoiesis. The ability to identify and isolate different stages in the progression from ES or iPS cells to HPS cells will facilitate the study of the generation of blood cell lineages and might improve the efficiency of production of transplantable cells.

Branching out: strigolactones modulate auxin transport

Shoot branching in plants occurs after bud activation in axillary meristems, which are stem cell clusters along the shoot. This process is repressed by strigolactones by a poorly understood mechanism. One model suggests that strigolactones do not act on the bud directly, but inhibit shoot branching by preventing auxin transport out of the bud. Ottoline Leyser and co-workers now show, on p. 2905, direct evidence in support of this model. The researchers treated Arabidopsis stem segments with a synthetic strigolactone, GR24, and found that this reduced auxin transport. Furthermore, they ruled out a direct effect of strigolactones on bud growth by showing that treatment of a solitary bud with GR24 alone had no effect on bud outgrowth, but that GR24 increased the inhibitory effect of an additional auxin source. In addition, they demonstrated that GR24 enhanced competition between two buds on the same stem. Collectively, these data support the model that strigolactone inhibits shoot branching by regulating the efflux of auxin from axillary buds.

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I’ve just come back from a lab retreat in a country house in Sussex, UK. The weather was good and we had our scientific sessions, ranging from discussions on Sonic Hedgehog signaling in the neural tube to the latest super-resolution imaging techniques, outdoors in the courtyard. However, every once in a while, we would be interrupted by a group of white peacocks.

We thought they were albinos, but once I was back in London I did some research and found that white peacocks do not necessarily have a defect in pigment formation, as is the case for albinos. The feathers of peacocks (and several other birds) acquire most of their iridescent color by using optical phenomena such as interference, diffraction and scattering of light. This property is known as structural color and for peacocks it results from way the nanostructure of their feathers interacts with light. For different colors, these different nanostructures are on the scale of the perceived colors’ wavelengths. White peacocks seem to have an altered nanostructure in the barbules (secondary branches) of their feathers.

The birds intrigued me and I wanted to find out how the nanostructure of white peacock feathers is different from the more colorful varieties. However, I couldn’t find anything on this (Does anyone know? Please comment!). Instead I came across something else that took me in a different direction: The development of dinosaur feathers.

How do you study the development of a dinosaur? The obvious way is to compare a younger and an older fossil of the same species, and in China, Xu and colleagues have done just that. They discovered two juvenile specimens of the oviraptorosaur Similicaudipteryx. One is younger than the other and the structures of specific wing and tail feathers differ dramatically between the specimens: Those of the younger one have a ribbon-like structure proximally, whereas the older specimen displays longer feathers without ribbon-like features. This was unexpected because in modern birds, feather morphology does not change after hatching. The researchers concluded that Similicaudipteryx might have undergone molting of feathers at some stage after hatching. Of course, molting takes place in modern birds but it doesn’t result in such severe changes in morphology.

So far, so good. But what really struck me were their speculations about how this change in morphology might have been taking place molecularly. In modern feathers, bone morphogenetic protein (BMP), noggin and sonic hedgehog (SHH) regulate the formation of the different feather components. SHH induces apoptosis between the barbs (primary branches) of the feather. Without SHH, a continuous, ribbon-like structure would form, which is probably what happened in the proximal part the younger dinosaur’s feathers. Xu and colleagues speculate that in Similicaudipteryx, the induction of SHH and other barb-specifying genes were delayed compared to modern birds, where these genes are strongly expressed during the growth of even the earliest feathers. SHH, the regulator of neural tube patterning I deal with every day is thought to have a role in the development of strange dinosaur feathers!

If only we could make a transgenic dinosaur. Then again, maybe not.

(7 votes)

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Today is the first day of the SDB meeting in Albuquerque. The program looks amazing, and I’m looking forward to many of the talks. The meeting is held jointly with the Japanese Society for Developmental Biologists, so many of the attendees came all the way from Japan.

Development and the Node are here in Albuquerque as well. You can find us at the Company of Biologists booth as well as in the audience at the talks.

We hope to summarize the meeting on the Node afterward, but could use some help, because try as we might, we can’t be everywhere at once! So if you’re at the SDB meeting, and would like to help us out by summarizing part of the event for the readers of the Node, please get in touch. You can leave a comment here, send an email, or track me down in person. We ask, at this particular meeting, that you get in touch before writing, because we’ve agreed with the conference organizers to write a report the “old fashioned way” on the Node – meaning that speakers’ permission will be asked before posting the report. If you want to write something, please do let us know and we’ll contact the speakers for you.

Here are some reports from previous society meetings on the Node:
– BSDB/BSCB meeting part I, part II, part III
– SFBD/JSDB meeting
– ISSCR meeting
See also our general tips for blogging from meetings.

I’m looking forward to an interesting meeting, and hope to see some of you here!

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