A recent paper in PNAS describes the development of MiniPromoters: human DNA promoters of less than 4 kb, designed to drive gene expression in specific areas of the brain. The initiative is called the Pleiades Promoter Project, and so far they have confirmed brain-region specific activity in knockin mice for 27 of their MiniPromoters. The final goal is to produce 160 fully characterized MiniPromoters to drive gene expression in defined brain regions.
The project is a spin-off of the Mouse Atlas Project (hence the name “Pleiades”: in Greek mythology, the Pleiades were the daughters of Atlas). To create the MiniPromoters, the researchers have computationally identified regulatory regions associated with brain-region or cell-type enriched gene expressions. Information about region-specific expression came from the Mouse Atlas Project as well as from the Allen Brain Atlas, which maps the human brain.
Several MiniPromoters driving LacZ in different areas of the mouse brain. (Part of Figure 5 from PNAS paper)
The MiniPromoters are designed to work in both mouse and human brains. While the Pleiades website emphasizes the ultimate goal of selective target delivery in gene therapy, the MiniPromoters can also be used to drive reporter expression in cell types of interest, for example to follow development of particular areas of the brain. (more…)
Thomson Reuters has predicted who they think will walk away with the Nobel Prizes in medicine, chemistry, physics, and economics. Their predictions for the prize for Physiology or Medicine include six names in four areas:
– Douglas Coleman and Jeffrey Friedman, for the discovery of leptin
– Ernest McCulloch and James Till, for the discovery of stem cells
– Ralph Steinman, for the discovery of dendritic cells
– Shinya Yamanaka, for the development of induced pluripotent stem cells
What do you think? Are any of these scientists going to be on the podium in Stockholm in a few months, or someone else?
I asked on Twitter, where Dean Griffiths guesses the prize will go to Shinya Yamanaka and John Gurdon, but is rooting for Till and McCulloch. Marios Stavridis thinks it’s too soon yet for Yamanaka, but that Till and McCulloch are long overdue a win.
Here’s my own guess: I think I agree with Marios that it’s too early for a win for Shinya Yamanaka. He’ll get it eventually, but probably not yet this year. And like Dean I’m also rooting for Till and McCulloch (I did my PhD in Toronto, so they’re “the home team” for me) but I also think Coleman and Friedman have a good chance. I watched the video for their Lasker Award (see previous post on the Node) and the whole story just screams “Nobel Prize” to me.
We’ll know soon enough, because the winners will be announced on October 4.
Today, the Lasker Foundation announced the winners of their 65th annual Lasker Awards, celebrating biomedical research. The winners all contributed to scientific research with strong implications for medical advancements:
Lasker-DeBakey Clinical Medical Research Award
Awarded to Napoleone Ferrara for the discovery of the role of VEGF in angiogenesis and the development of an anti-VEGF therapy for wet macular degeneration
The status of the awards becomes clear when you realize that in the past 65 years, as many as seventy-nine Lasker winners have also received a Nobel Prize. Winners of the Lasker receive $250,000 per award, and a statue, which you can see in the video below.
In Napoleone Ferrara’s award announcement video, he and others describe the role of VEGF in angiogenesis and wet macular degeneration:
Coleman, Friedman, Ferrara and Weatherall will receive their awards on Friday, October 1, in New York City.
And a little quiz: Aside from all winning a Lasker award this year, what connects these three research topics? (The simplest answer is only five letters long, but you can be more complicated. No prize, just for fun.)
From 4PM UK time on Wednesday September 22nd, the Node’s server is going down for some maintenance. Work will continue for several hours, and will cover most of the working day in North and South America. Apologies for the inconvenience. I’ll schedule some things to appear on the Node’s Twitter account to read while the site is down.
I’m going to collect dates from my travel journal and batch post the most interesting bits. See this post for my introduction and an explanation for all of this. Enjoy!
May 12, 2007 Beijing, China
The flight was outrageously long, but uneventful once I boarded. I didn’t find out until I got to Logan airport that my flight was to La Guardia but connecting out of JFK, so I had to catch a cab across Brooklyn. Then it was a bit of a game of musical chairs to get my seat. I boarded late so that I didn’t have to take part in the herd of passengers. Since my first trip to China as a tourist, I’ve observed a collective rush to board flights in no particular boarding order, so I routinely wait until everyone else has settled and board nearly last. On this flight, I was supposed to be in Seat 42A, but there was a guy in that seat. He was supposed to be in 41A, but there was someone in his seat who was supposed to be in 40A. I decided “screw it” and ended up in 40A. That apparently very much confused my graduate student companion when he came looking for me midflight and I was not the person in 42A. I was dead to the world for most of the flight anyway, so I didn’t notice much of a thing. My brain is sort of mush right now from the jetlag, and we’ve started right to work in our colleague’s lab getting things ready. I got to see the Olympic stadiums this morning. They’re super cool. And the institute of zoology is really nice. It’s a new building with new lab space. I love new lab space. We’re going to finish getting things ready today and tomorrow and maybe have a bit of time to see the Great Wall and the Imperial Palace before we head off for Inner Mongolia. No Jerboas yet, but there is a great big Tibetan rabbit sitting in the corner of the desk watching me type. It’s Dr. Yang’s pet, and it’s a little snotty and keeps sneezing. Kind of funny to see a rabbit sneeze.
May 13, 2007 Beijing, China
All I’ve managed to do so far is eat and sleep, and I have been wonderful at that. Ms. Xia (a research associate in our collaborating lab) brought me to lab yesterday morning to get started on the preparations for the fieldwork. That didn’t take very long, so she took me to an outdoor recreation store (like REI) and then to a tourist souvenir market. I quickly decided that I needed lunch and sleep, so after trying to choke down a bacon, egg, and pickle (!) sandwich, she took me back to the hotel for a “nap”. Said “nap” turned into a 5 hour sleep. I woke up in time to catch dinner, read a bit of my book, and go back to sleep for a full night. I think I’ve shown that jetlag what’s for though. I will have to say that Shaoyuan, my graduate student, knows good food. With the exception of that questionable sandwich (for which he wasn’t present, and I should have known better since the menu was in English), all of our meals have been fantastic. I had a really beautiful pork and tofu dish last night, and brunch today was a bowl of spicy chow mein noodles with mushrooms and chicken. I may still lose a little weight on this trip, but it won’t be for lack of trying to keep myself full at all times. I’ve also learned from every country I’ve visited that it’s better to go to places with no English menus and point at other people’s plates if you have to. If you’re willing to risk eating calf intestine, you’re likely to get a fantastic meal.
May 14, 2007 Beijing, China
Yesterday I made enough paraformaldehyde to fix a horse. That excites me in a weird way. We’re pretty much ready to go now. Traps, lots of food (for us and rodents), DEPC water, PFA, tubes and tubes and tubes… After the prep work, I caught the train downtown and walked for about 2 hours to get to the Forbidden City to meet Shaoyuan. If it’s true that the best way to learn a city is to get lost in it, then I must know Beijing pretty well by now. I had no idea how EVERYTHING on the map is very very very tiny compared to real life. And to you Texans out there – you aint got nuthin on China. Nothing is bigger in Texas compared to this place.
I was doing fine on time until I got to Tiananmen Square. The Chinese flag in the square is lowered every day at sunset and is cause for a huge spectacle. They shut down all foot traffic past the flag as a crowd of several thousand forms. I had to take the underground passages to get around everyone. But not until after I snapped a fantastic shot of a guy posing in front of the police formation. That’s one thing I love about Asia. People here will pose for a picture in front of just about anything. As a result, I’ve started a bit of a collection of my own pictures of people having their pictures taken in front of random things :) So after a bit of a walk around, Shaoyuan took me to some famous restaurant where we had the most AMAZING duck I’ve ever eaten in my life. It was so juicy, and the skin was the most perfect brown crispy deliciousness.That’s it for now. I’m going to help get things ready to leave tomorrow and then we’re going back down to see the inside of the Forbidden City and visit Chairman Mao’s preserved remains. More later…
Hello Node Community:
I would like to inform you about the Development Travelling Fellowships. Are you a Graduate student or Post-doc wishing to make a collaborative visit to another lab?
You can apply to Development to fund your travelling expenses. Development offers up to £2,500, you do of course have to be working in the field of developmental biology and intend to visit another lab.
I am a graduate student from Indian Institute for Science Education and Research (IISER), Pune, India. I wish to share some of my work and life experiences in Japan from a recent visit. Our lab works on development and evolution of insect wings. I am interested in understanding the development of lepidopteran wings using Bombyx mori ( silkmoth) as a model system. Initially at my place it was an ordeal working experiments mostly for the lack of technical expertise on silkmoth experiments and lack of availability of resources.
We decided to carry out some experiments in the University of Tokyo, Kashiwa campus to study the development and evolution of insect wings, specifically lepidopteran wing development, using the silkmoth as a model organism. Expertise on studies in silkworm development is abundant in Japan as there are many research groups working on this various aspects of silkworm development. To be housed in one of the best universities in asia was a privilege and the facilities and research truly matched the stature of one of the best institutes in the world.
dissections all day!
I was in Prof. Haruhiko Fujiwara’s lab which works on Silkworms, Butterflies and different aspects of their genetics and development. The facilities in the lab were really state of the art, organization of the lab was immaculate and expertise vast which helped my work progress smoothly. One hurdle was definitely that of the language which I should admit was a more than what I anticipated, most people in the campus speak in Japanese, study and even discuss science in Japanese, but it seemed trivial with the kind nature of the people, every time they put an effort beyond their way to help you in every situation in lab or on outside. A little Japanese learned beforehand came in handy at times and also got a smile across people there who always appreciated generously for every one of my efforts to speak their language.
I started experiments here as soon as I came in but for a week or so they really did not work as I had to get adjusted to the setup and find the reagents and understand the instruments (some of which had complete Japanese menus!). With the help of the friendly lab members things moved rapidly and was able to understand the techniques they used and apply to solve issues which had troubled me in research so far. In a lab of around 20 people everyone chipped in whenever I had problems to trouble shoot with the best they could and made work progress fast and life easier. The discussions with my sensei (used to address professor in Japanese) were very helpful to understand the development of silkworm and to apply techniques like immuno histochemistry and RNA in situs. As these experiments were done in the lab on a regular basis and also the worms were studied extensively here, hence work moved smoothly and results were easy to come once I was settled in. I could work out all the standardization of Chromatin Immunoprecipitaion (ChIP) with the abundant silkworm resource which was excellently maintained. There wasn’t a single hindrance for an experiment no matter when I wanted to perform them because of the excellent maintenance of the larvae and the whole-hearted support of the lab.
During this trip I also had a golden opportunity to interact with other developmental biologists at the JSDB 2010 meeting at Kyoto. The discussions in the conference included various interesting aspects of developmental biology ranging from growth control, organogenesis to mathematical modeling. The meeting had over 300 poster presentations, where I also got an opportunity to present my work so far and discuss with the best researches in japan and also world-over. It was interesting to discuss with various interesting research projects from japan and other places, also helping understand our own research problems better and flashing some new and interesting insights.
with Prof Wieschaus at JSDB 2010, kyoto
The talks by Prof Eric Wieschaus and Prof Roel Nusse were enlightening and it was really a great opportunity to interact with these scientists, who were very encouraging and made the science more interesting , by inducing many new questions in the mind and also helping our research interests through superlative discussions. apart from the conference Kyoto as a citywas serene and beautiful, having been to Tokyo this part of the world seemed a page from the ancient and rich traditional Japan and a wholly different landscape from what I had seen or imagined.
People in Japan were very kind, polite, peace loving and sweet who helped in every step of my stay. There a lot of international students around especially in my residence where they were very cooperative and were as kind as Japanese themselves. They organized various events from the art of wearing Japanese yukata (traditional Japanese dress) to that of attending the local city festival on weekends. They helped with every problem and also make stay fun filled and enjoyable in every way. Cycling was the best transport in Japan for there were free lanes; it was always fun riding to university through a very beautiful park. For being a vegetarian the other constant problem was food, which I had to cook to survive in a land where nothing was vegetarian. The versatile kitchen facility eased out cooking for my survival and sometimes the vibrant community joined in usually watching football worldcup cheering for Japan or South Korea. It was the charm of the place and people around that made problems gradually melt away etching wonderful memories, easing life and making work enjoyable in a very pleasant ambience.
This visit helped move rapid strides in answering my research question and allowed me to learn newer methods to apply and progress in my research work. I am sure a lot of research problems will be solved and this work will raise new and interesting questions for me to pursue further ahead in research. I hope my experience will encourage more people to work across borders to learn the best from all the great learning centers and Japan in particular, which has people who work really hard and help each other to reach greater heights in their endeavors.
I would like to thank the Development and APDBN fellowships for their encouragement and generous support for my travel and stay in Japan. I would like to thank the Prof Fujiwara and University of Tokyo for the kind invite, support and warm welcome into their facility. My sincere thanks to the lab members of his lab and also other labs which helped and supported to the fullest, whose untiring help and encouragement helped me enjoy both work and stay in Japan. I would like to thank my supervisor Prof. Shashidhara and IISER pune for initiating this interaction and supporting all the way in my graduate study. I would like to thank node for allowing me to share my unforgettable memories of Japan.
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.)
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
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.
A recent paper in PNAS describes the development of MiniPromoters: human DNA promoters of less than 4 kb, designed to drive gene expression in specific areas of the brain. The initiative is called the Pleiades Promoter Project, and so far they have confirmed brain-region specific activity in knockin mice for 27 of their MiniPromoters. The final goal is to produce 160 fully characterized MiniPromoters to drive gene expression in defined brain regions.
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