Here’s an uplifting story about how a farmer and a developmental biologist met online and started a collaboration.

Earlier this month, I attended the annual Science Online conference in London. This year’s speakers included Sir Martin Rees of the Royal Society, former Member of UK Parliament Evan Harris, and a good selection of people who are involved in using the Internet to either communicate or facilitate scientific research.

One of the speakers in several panels was science writer and blogger Ed Yong, of the blog Not Exactly Rocket Science. On the first day of the meeting he spoke on a panel about science journalism, and on the second day he was on involved in a discussion about interacting with your readers online. He gave some good advice there, about communicating with your readers and knowing who they are. In Ed’s case, his audience is very general, including scientists as well as non-scientists, so his readers could very well be anyone.

On Saturday, Ed posted an anecdote that shows exactly how broad his readership is, and what he does to engage them. Since one of his tips at the Science Online meeting was to simply link to other blogs when they write it just so much better, I’ll send you back to his place for the full story, and will just summarize it here:

Several months ago, a paper came out about gynandromorph chickens. To refresh your memory: these chickens are female on one side of their body and male on the other side, and by studying them the group of Mike Clinton in Edinburgh revealed that in chickens sex identity is determined early in development and is autonomous for all cells (rather than being regulated by hormone levels). Ed wrote about the paper on his blog, and recently Paul Sanders, a farmer in Missouri, found that very post when he was looking for information on a curious-looking chicken (pictured left) that was born on his farm. Ed then put him in touch with Mike Clinton, and the resulting e-mail conversation between Sanders and Clinton shows how they’re going to collaborate to further investigate the development of gynandromorphic chickens. Since Sanders has access to the bird as well as the parents of the bird, Clinton can carry out more detailed genetic analysis. According to one of Clinton’s e-mails, Sanders’ observations about the size of the egg alone are already an indication that one of the theories about gynandromorphic development — that these animals originate from eggs with a double yolk — is not likely to hold ground!

It’s good to see the reader interaction that Ed mentioned at Science Online in action, and leading to collaborations in developmental biology! Do you know of any other examples of interesting collaborations in the field? We’d love to hear!

(Image credit: Paul Sanders.)

(4 votes)

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The RIKEN CDB seeks laboratory heads to lead independent laboratories under the following two Programs. Applicants can choose to apply for a specific position, or allow the search committee to assign them to an appropriate position during the course of the evaluation.

1. Position

・Team Leaders (Creative Research Promoting Program)
The CDB is looking for creative young researchers (preferably those who have obtained a PhD within the last 10 years) who aspire to break new ground within areas of animal development and regeneration, and related research areas.
・Unit Leaders (Center Director’s Strategic Program)
The Unit Leader position is for scientists in the early stages of their career to conduct research in a small-scale laboratory. Highly motivated scientists eager to achieve breakthroughs in next-generation developmental biology in the areas listed are encouraged to apply.

2. Selection Process

Research proposals should be focused on the specific field of research for each program. The initial screening process will be based on the applicant’s application and 5-year research proposal. This will be followed by a final selection process, which includes an interview and seminar. Strong emphasis will be placed on the quality, feasibility and originality of the research proposal; priority will be given to proposals that take full advantage of the CDB’s facilities and resources, and advance challenging new concepts. Female and foreign scientists are strongly encouraged to apply.

The selection process will begin November 1, and will continue until suitable candidates have been selected.

Please visit our website for more detail: http://www.cdb.riken.jp/en/index.html

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Hello Node folks.  My name is Kim Cooper, and I’m a postdoctoral fellow with Cliff Tabin at Harvard Medical School.  I recently spoke at the SDB meeting in Albuquerque, and Eva Amsen approached me about contributing to the Node.  The primary reason is because I’m working on a fun animal that takes me off to China for field collections and has sent me down a rough road of learning to breed an exotic in captivity.  The animal is a jerboa.  It’s a bipedal desert rodent related to rats and mice.  They’re native to northern Africa through the Middle East, Central Asia, and northern China.

I’m interested in this adorably bizarre animal because it is an excellent model for evolutionary novelty in the limbs.  They have elongated hindlimbs with enormous feet that have only three toes and metatarsals that are fused into a single bone.  This gives them a long bounding stride upright on their hindlimbs, and they really only use their forepaws for feeding, digging, and grooming.  They are very efficient movers – they can hop three meters in a single leap and a meter straight in the air when startled.

The gist of what I’m doing with these animals involves collecting embryos from pregnant females soon after the come out of hibernation and breed more or less synchronously in northern China. The embryos are fixed and preserved in methanol and then shipped back to Boston for further developmental studies. I’m taking a two-pronged approach by candidate gene analysis and RNASeq to identify genes that are expressed differently in the three-toed hindlimb of the jerboa compared to the five-toed forelimbs and fore and hindlimbs of a near relative – the mouse.

I’m excited to share field collection stories from China and experiences with starting the colony.  The field stories are easy since I’ve been keeping a travel blog for about 5 years now and can cross post from previous years until the next field season starts again in the spring.  So stay tuned.  As a teaser I can tell you I’ve been chased by camel ticks in the desert, slept in a yurt near the border with Pakistan, and come home with typhoid.  But I’ve had some great times and met a lot of wonderful people along the way.  And collected a lot of jerboas.

(5 votes)

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(This interview by Kathryn Senior originally appeared in Development on September 7, 2010)

Ken Zaret is Joseph Leidy Professor in the Department of Cell and Developmental Biology, the Associate Director of the Institute for Regenerative Medicine, and the Co-Director of the Epigenetics Program at the University of Pennsylvania School of Medicine. He agreed to be interviewed by Development and talks about his life as a scientist.

What originally set you on the road towards a career in science?

As a teenager, I loved puzzles of all kinds, and doing science is about solving puzzles. I have also always enjoyed being out of doors. Hiking is one of my favorites, and I originally wanted to be a naturalist; traveling the world and studying different forms of life was really appealing. In high school, I received a fellowship from the National Science Foundation to do research at a medical school in Philadelphia, which exposed me to laboratory science. Then, in college, I had several inspiring biology professors. When I took biochemistry, it all came together and I knew I wanted to do research.

How has your career progressed and what has influenced your decisions about institutions and locations?

When I was 30, I started my own lab at Brown University, which attracts great students, has a highly collegial faculty and, being located near Boston, is part of a larger scientific community. I benefited from the stimulating environment – and I learned developmental biology. After about 13 years, I was recruited to the Basic Science Division at the Fox Chase Cancer Center in Philadelphia. This was a good move for me, as I enjoyed the focus of being at a research institute instead of a university but, after 10 years, Fox Chase began to pursue mainly translational research and I felt it was right for me to move back to academia. I have been at the University of Pennsylvania since then and I greatly enjoy the diverse and active research life that it offers; working there is highly stimulating.
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The server that the Node runs on is going to receive some general maintenance between 6:30 PM UK time tonight and early tomorrow morning. This may affect our visitors in North America (and the early risers at the other end of the Pacific) so please be patient if anything seems to not be working during this period.
The down time could be as brief as 30 minutes, and everything should work again on Friday. Thanks for your understanding!

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New format for job postings
You may have noticed some job ads for postdocs appearing on the Node. Until today, these ads appeared with the rest of the posts, but we now changed how job ads are displayed on the Node, to make them stand out from the rest of the content. This makes it easier for people who are looking for jobs to find the ads, and less intrusive for those who aren’t looking for work.

Job ads no longer appear in the main body of the site, with the rest of the posts, but are accessible in three other ways;
-The three most recently posted ads are listed by title in the sidebar (between “recent comments” and “events”) on all pages of the Node. They can also be accessed from the archive in the sidebar
-The Jobs category lists all job ads
-Jobs have their own RSS feed, which can be reached from the page containing all the different feeds on the Node. If you want to receive both regular Node content and job ads, you need to subscribe to both feeds.

Adding an announcement for a job opening in your lab works exactly the same as writing a post. Make sure that you have the title field filled in, and that you select the category “Jobs”. Job postings don’t show up in the main body of the site, but in the sidebar only. There is also a separate RSS feed for job postings.
(The previous paragraph has also been added to the e-mail that new authors receive.)

Finally, the Help page has been updated to reflect these changes.

E-mail updates about the Node
Currently, e-mail updates about new Node posts arrive as a “daily digest”, and will probably still include job ads. It’s also possible to set these updates to occur after every post (which is approximately once per day at the moment anyway) and have users select which categories they would like to receive in e-mail. In that case, if you only want e-mail notifications of interviews, or everything except job ads, you can change those settings.
The choice between digest or per-post cannot be made at the individual user level, unfortunately, so we have to make one decision for everyone. Let us know please, in the comments, what you would like: the option to select which categories to receive in e-mail, OR the daily digest. (In both cases, you have the option to turn notifications off entirely through the WordPress dashboard.)

(2 votes)

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

Nr5a receptors reset EpiSC pluripotency

Rodent embryonic stem (ES) cells that are derived from blastocysts self-renew without mitogenic growth factors and robustly colonize chimaeras, whereas egg cylinder-derived stem cells (EpiSCs) require fibroblast growth factor and contribute poorly to chimaeras. Nevertheless, expression of a single reprogramming gene, such as Klf4 or Nanog, can return EpiSCs to a molecular and developmental pluripotent ‘ground state’. Now, on p. 3185, Ge Guo and Austin Smith use a genome-wide genetic screen to identify other molecules that can reprogramme EpiSCs. By using piggyBac transposition to randomly activate endogenous gene expression in mouse EpiSCs and by selecting for undifferentiated colonies in the absence of growth factors, the researchers unexpectedly identify the Nr5a nuclear receptors as potent inducers of ground state pluripotency. Intriguingly, they also show that, unlike previously identified reprogramming factors, Nr5a receptors do not play a role in ES cell renewal. Together, these results highlight the usefulness of EpiSC conversion (in defined culture) as an experimental system for studying molecular reprogramming.

EGFR-Notch signalling makes (proneural) waves

During neurogenesis in the Drosophila optic lobe, a wave of differentiation that converts neuroepithelial cells into neuroblasts sweeps across the neuroepithelial sheet in a medial to lateral direction. This differentiation wave is preceded by the ‘proneural wave’: the transient expression of the proneural gene lethal of scute [l(1)sc]. Now, Tetsuya Tabata and colleagues report that EGFR and Notch signalling play pivotal and coordinated roles in proneural wave progression in the Drosophila optic lobe (see p. 3193). They show that EGFR signalling is activated in neuroepithelial cells and induces l(1)sc expression. Transient, spatially restricted expression of Rhomboid regulates EGFR, they report, and Rhomboid expression is regulated by the EGFR signal, a feedback loop that moves the proneural wave laterally. The researchers also report that Notch signalling, which prolongs the proneural state, is regulated both by itself and by EGFR signalling. Based on these results, the researchers propose that coordinated sequential EGFR and Notch signalling regulates proneural wave progression, which, in turn, induces neuroblast formation in a precisely ordered manner.

Hand2 on heart: promoting cardiac fusion

The embryonic heart tube forms from bilateral groups of cardiomyocytes that move towards the embryonic midline where they merge. The transcription factor Hand2 is essential for this ‘cardiac fusion’ but its downstream effectors are unknown. By studying zebrafish heart development, Deborah Yelon and colleagues now identify Fibronectin as a component of the Hand2 pathway that mediates cardiac morphogenesis (see p. 3215). By performing transplantation experiments between wild-type and hand2 mutant embryos, the researchers show that hand2 regulates cardiac fusion by altering the environment through which the cardiomyocytes migrate. Next, they show that fibronectin 1 (fn1) expression is increased in hand2 mutant embryos. Finally, they report that reduction of fn1 function rescues cardiac fusion in hand2 mutant embryos but not the apicobasal polarity defect that is also seen in these embryos. Thus, the Hand2 pathway regulates cardiac morphogenesis by establishing an appropriate environment for cardiac fusion by limiting Fibronectin function but it establishes the apicobasal polarity that is needed for heart tube extension through another, unidentified, effector.

Wise up to Wnt’s role in tooth development

The number, size and shape of mammalian teeth vary widely – just compare a person’s smile with a dog’s ‘smile’. But what controls the patterning of dentition? Mutations in Wise (Sostdc1), which encodes an inhibitor of Lrp5- and Lrp6-dependent Wnt signalling, cause patterning defects in tooth development in mice. Now, by investigating the pathways modulated by Wise, Robb Krumlauf and co-workers show that crosstalk between Wnt and other signalling pathways controls mouse tooth development (see p. 3221). The researchers use genetic experiments to reveal that Wise suppresses the survival of vestigial tooth buds in the normally toothless region between the incisors and molars by inhibiting Lrp5- and Lrp6-dependent Wnt signalling. They also identify the Fgf and Shh signalling pathways as major downstream targets of Wise-regulated Wnt signalling, and show that Shh acts as a negative-feedback regulator of Wnt signalling. Thus, the researchers suggest, variations in the expression of signalling modulators such as Wise could underlie the evolutionary diversity in mammalian dentition.

Del1-ving into forebrain development

During early embryogenesis, morphogen gradients specify the neural plate along the anterior-posterior axis. Canonical Wnt signalling causes the posteriorization of neural tissues. Consequently, Wnt signal attenuation in the embryo’s anterior region is required for the determination of the head region; but how is this achieved? On p. 3293, Hidehiko Inomata, Yoshiki Sasai and co-workers reveal that modulation of canonical Wnt signalling by the extracellular matrix protein Del1 (Developmental endothelial locus-1) is essential for forebrain development in Xenopus embryos. Del1 overexpression expands the forebrain domain, the researchers report, whereas Del1 functional inhibition represses forebrain development. They show that Del1 function in neural plate patterning is mediated mainly by inhibition of canonical Wnt signalling downstream of β-catenin. Notably, however, Del1 inhibition of canonical Wnt signalling involves the Ror2 (receptor tyrosine kinase-like orphan receptor 2) pathway, which is implicated in non-canonical Wnt signalling. These data suggest that Del1 promotes forebrain development by creating a local environment that attenuates the cellular response to Wnt signals via a unique pathway.

Extracellular signal PARtners asymmetric division

Asymmetric cell divisions generate cell diversity during development, and the orientation of the axis of these divisions determines the future position of differentiated cells. But is the asymmetrical localization of the polarity (PAR) proteins that control asymmetric cell division regulated by extracellular or intracellular signals? On p. 3337, Yukinobu Arata and colleagues answer this controversial question. In C. elegans embryos, the P0 zygote and the P1, P2 and P3 germline cells undergo a series of asymmetric divisions. By examining the development of these germline cells in vitro, the researchers show that, although PAR-2 is distributed asymmetrically in P2 and P3 cells in the absence of extracellular signals, the orientation of PAR-2 localization in these cells depends on their contact with endodermal precursor cells. Other experiments indicate that the endodermal precursor cells control the orientation of PAR-2 localization by extracellular signalling via the MES1/SRC1 pathway. The researchers propose, therefore, that Src is an evolutionarily conserved molecular link that coordinates extrinsic cues with PAR protein localization during asymmetric cell divisions.

Plus…

KNOX genes: versatile regulators of plant development and diversity

Plant KNOX homeodomain transcription factors maintain pluripotent stem cells in the shoot apical meristem, and recent studies have uncovered novel roles for the KNOX proteins in sculpting plant form and its diversity, which Angela Hay and Miltos Tsiantis review. See the Review on p 3153

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Recently a paper in Science caught my attention since its title combines the words mitotic recombination with patients and Ichthyosis. Having worked with Drosophila during my PhD and now being in a vertebrate lab, I’m well aware of the existence of tools to induce mitotic recombination to generate somatic clones of mutant cells in certain tissues. So I had a closer look at the paper to understand more about the spontaneous occurrence of mitotic recombination in humans.

“Ichthyosis with confetti” (that’s what it’s called!), or IWC for short, is a very rare sporadic skin disease. Patients display red skin because their skin barrier is defective and they often die of bacterial infections. The reason the disease carries the word confetti in its name is that in the first year of life, the otherwise reddish body starts to be covered in pale spots, resembling confetti, which increase in number and size with age.

Now it has been found that these pale spots are clones of “revertant” cells arising through mitotic recombination. Most cells in the body of IWC patients are heterozygous for a spontaneous dominant mutation in the keratin 10 (KRT10) gene that causes the red skin disease phenotype. The exact mutation in KRT10 differs between patients, but all of the mutations result in frameshifts in the same alternative reading frame of KRT10. The product of this is an arginine-rich peptide that mis-localizes to the nucleolus and thereby disrupts the keratin filament network of skin cells. The pale clones of revertant cells are formed when mitotic recombination causes loss of heterozygosity in KRT10, so that these clones no longer carry the mutation and therefore behave like normal cells. Reversion to wild type occurs at very high frequency, suggesting a general increase in the rate of mitotic recombination in these individuals. It is not yet known what causes this elevation.

So, what did I learn from this? Mitotic recombination in multicellular organisms is not just a peculiarity that can be useful for experiments in model systems, it also occurs naturally in humans. For reasons still unknown, its rate can be increased when beneficial for the cells affected. Cancer cells appear to exploit this phenomenon, increasing the rate of mitotic recombination to speed loss of heterozygosity of tumor suppressor mutations to promote their survival and growth.

Who knows, one day induction of mitotic recombination to remove undesired mutations might even be used as a therapy in humans, as long as the homozygous mutant sister cells eliminate themselves as seems to be the case in IWC. As always, the frightening part in this scenario is the possibility of losing control and causing unwanted and potentially harmful mutations. We’ll see.

Choate KA, Lu Y, Zhou J, Choi M, Elias PM, Farhi A, Nelson-Williams C, Crumrine D, Williams ML, Nopper AJ, Bree A, Milstone LM, & Lifton RP (2010). Mitotic Recombination in Patients with Ichthyosis Causes Reversion of Dominant Mutations in KRT10. Science (New York, N.Y.) PMID: 20798280

(5 votes)

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“Why are there no pop hits about Arabidopsis?” sings Karmadillo. Even though their Arabidopsis song is not a pop hit (yet?) either, Karmadillo can at least lay claim to the honour of having performed it alongside other science-themed songs on the “Reproductive Stage” at the virtual 2010 Geek Pop festival.

The song celebrates Arabidopsis as model organism, with such lines as: “That the public don’t know you, that’s unfair, but they can get your genome, thanks to TAIR.” The music video also has plenty of lab footage showing Arabidopsis in action:

Rishi Nag, the main man behind Karmadillo, lives and works in Cambridge, so I managed to catch up with him this summer and ask him about the song and how he came about writing it.

Rishi, my first question is maybe a bit obvious, but why are there no pop hits about Arabidopsis?

I think it just never hit the romantic side that roses have. The song that I wrote was meant to be about this plucky little plant that a lot of biology work is being done on.

Why did you write the song?

I work in the Department of Plant Sciences [at Cambridge University] and we had a Christmas revue at the end of the year, where people from various departments were getting together do all kinds of songs. I had the idea to write the song for that, but didn’t get it done in time. Then there was this festival called Geek Pop at the start of the year, and I had some time off over Christmas so I managed to sit down and record it. Having a deadline to submit it for Geek Pop was quite a motivating factor to finish it. [Before that] I think I just had the chorus stuck in my head for a while.

How have people responded to it?

Oh, it’s been really popular, so that’s been really nice. I wrote another song called “Brownian Motion” which is more of a physics song, which I think has been my most popular of the Geek Pop songs, I’m afraid.

How did you get interested in science?

I work in the group run by David Baulcombe, [and] I’m actually a bioinformatician/web designer. Essentially my background was nothing to do with biology, and then a couple of years ago I started doing the website for a pan-European EU-funded project called SIROCCO, dealing with [RNA] silencing in various institutions. Through that I’ve started learning more about bioinformatics, and taking on a bigger role in that. It’s been really interesting and exciting for me. I have a background as a DSP (digital signal processing) software engineer. That’s quite dead scientifically in that what you’re doing commercially is as good as it will get for the most part. Then to come into bioinformatics and learn about genetics and genes just really whetted my appetite again for science and its processes.

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by Valerie Butler

Most of us, I’m sure, can remember that AHA moment in school when we realized that science is pretty cool. Imagine how it might be for a student enrolled in a school lacking the resources to teach science well, or who was never given the opportunity to excel in anything, let alone science. What if the opportunity for an AHA moment never arrived?

This is, unfortunately, the truth for many primary and secondary school students, and it is especially so for low-income and predominantly minority communities. Students from disadvantaged backgrounds often carry stereotypes that scientists are old, white men who are out of touch with society, and many youth believe that science careers are out of their reach. The challenge then, is how to excite children about science such that they want to make a career of it?

In the United States, and now in Melbourne, Australia, science educators are doing just that with a K-12 outreach program called BioEYES. A former BioEYES student, Dasha, in a thank you note summed up the challenge facing science educators:

“I just wanted to thank you for coming to our class. I think you thought we were the worst class you ever had. All our teachers say that. Thank you for letting us use your microscope.”

BioEYES reaches out to children like Dasha who have internalized the message that they are among “the worst” and appoints them to an esteemed role, that of research scientist. By stepping into this role, students feel important and get excited about science, and for the first time they are encouraged to see this career is open to them. BioEYES plants seeds of enthusiasm for science and learning that helps inspire kids to stay in school and, for some, to pursue careers in science, engineering, math and technology fields.

One reason for the success of the BioEYES program lies in its fun, hands-on activities using live zebrafish. Over the course of the week that the BioEYES Outreach Educators are in the classroom, students learn to use the scientific method, cross the fish, observe embryo and larval development daily under a microscope, and record their findings. They learn about and are encouraged to consider scientific careers. Depending on the grade level taught, concepts in ecology, vertebrate development, stem cells and genetics may be explored. On the last day of the program, students in all grade levels observe the beating heart of a zebrafish larva. For most, this is their first glimpse of an actual heart pumping in real time, and inspires a strong visceral reaction unlikely to be duplicated by a video or picture. Many students express delight and amazement, and truly see the fish as like themselves.

Modeled on the successful BioEYES program established in Philadelphia in 2002 by Dr. Steven Farber and Dr. Jamie Shuda, BioEYES has educated more than 35,000 students nationwide. At present, one school district in the United States has their own fulltime, dedicated BioEYES Educator, and a second school district expects to develop a BioEYES Teacher Leader position for the 2010-2011 school year. In August 2010 BioEYES went international when we implemented our program in Melbourne, Australia.

Part of the appeal of BioEYES is the support it offers to teachers, many of whom (especially at the primary school level) have minimal training in science education. Prior to the BioEYES unit, teachers attend a training workshop that introduces them to the program and curriculum. For their first two years of participation, teachers co-teach the unit alongside a BioEYES Outreach Educator. In the third and subsequent years, teachers may be designated “Master Teachers” and they can teach the unit independently with materials provided by BioEYES. Master Teachers deliver the program at significantly reduced cost to BioEYES and they free Outreach Educators to work in classes that have not yet participated.

BioEYES is a nonprofit tax-exempt organization and currently operates out of the Carnegie Institution for Science in Baltimore, MD; the University of Pennsylvania in Philadelphia, PA; Notre Dame University in South Bend, IN; and Monash University in Melbourne, Australia. We have been able to deliver our programs to tens of thousands of children at no cost to their schools because of the generosity of individuals, foundations and corporations. Not surprisingly we have a close partnership with the Society for Developmental Biology not only because we are using  a developing model organism, we both share the goal of fostering a more scientifically literate society. We of course welcome your support!

Check out this video of BioEYES in action:

BioEYES in Baltimore County

For more information please visit our website, www.bioeyes.org.

(6 votes)

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