Stem cells on the Slovenian slopes

Posted by on February 6th, 2012

A couple of weeks ago, around 70 stem cell scientists gathered in the beautiful ski resort of Kranjska Gora, Slovenia, for the sixth meeting organised by the European Stem Cell consortium EuroSyStem. Although the snow wasn’t up to much (as the photo proves – just take a look at the opposite side of the valley!), the lack of fresh powder left more time for the science. And there was a lot of great science to be discussed…

Hans Clevers (Hubrecht Institute) kicked things off in the first of two outstanding plenary talks, with the latest developments on intestinal stem cell homeostasis, including beautiful demonstrations of how two innovative technologies – in vitro organoid culture, and the “Brainbow” cell labelling technique – have provided insights into the life of the Lgr5+ crypt stem cell. The name of Charles Leblond came up often in his talk: neither I nor many in the audience had ever heard of him, but his insights into stem cell self renewal, as well as his development of autoradiography, definitely earn him a place in the stem cell Hall of Fame (see here for a summary of his achievements).

The following day took us on a whistle-stop tour of model organisms, with planaria, flies, zebrafish, salamanders and Arabidopsis all taking their turn in the spotlight. After that, mammals took centre stage, with talks covering the whole spectrum of the stem cell field, from lineage determination and ES cell reprogramming, to aging and cancer. Prize for “Unsettling Animal Photo of the Week” (with apologies to the Guardian newspaper for blatant plagiarism of their feature) goes to Tom Rando (Stanford), whose lab has provided striking insights into systemic effects of aging from heterochronic parabiosis experiments – essentially grafting two mice together. Take home message: if you need a blood transfusion, you really want a young person’s blood! Other highlights included a lively debate on the Immortal Strand hypothesis following talks from Shahragim Tajbakhsh (Institut Pasteur) and Peter Lansdorp (Terry Fox Laboratory), and a detour into the molecular mechanisms regulating autophagy from Paul Coffer (University Medical Centre Utrecht).

Finally, the scientific program ended with an impressive demonstration of what money and technical resources can achieve, when coupled with hard work and – most importantly – a sharp nose for sniffing out an interesting story. The second plenary speaker, Huck Hui Ng (Genome Institute of Singapore), presented a tour-de-force analysis of the transcriptional and post-transcriptional networks underlying reprogramming, self-renewal and differentiation.

But the real talking point of the meeting came on the Wednesday evening, when we were fortunate enough to be joined by Arnd Hoeveler from the European Commission, who came to talk about future funding from the EC for stem cell research. While the direction the EC’s framework program is taking – towards funding mainly translational research – may not have gone down universally well with the audience of mostly basic researchers, we were given a fantastic forum to discuss science funding and politics with someone who clearly cares deeply about advancing science in Europe, and who faces a tough challenge to convince the political elite of the importance of the kind of research that this meeting was all about.

I’ve only had the chance to mention a few of the great talks, but all in all this was a fantastic conference, seamlessly organised by the EuroSyStem team. So thanks to them, the speakers and the rest of the participants for putting on an eye-opening and stimulating meeting. Now, if only they could have arranged for better piste conditions, it would have been just perfect!
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PhD student position at the British Heart Foundation Regenerative Medicine Laboratory

Posted by on January 26th, 2012





 

EU Initial Training Network searches for 1 PhD Student

CardioNeT – Our Initial Training Network in Cardiovascular Research offers 1 PhD student position at the British Heart Foundation Regenerative Medicine Laboratory, Department of Physiology, Anatomy and Genetics, University of Oxford, UK.

Funded by EU’s FP7, CardioNeT comprises twelve partners from both the academic and industrial sectors and aims to implement a highly multidisciplinary, intersectoral and competitive training programme in cardiovascular research through cutting-edge projects and extensive training in complementary areas.

We are looking for:

  • Enthusiastic researchers with a Masters Degree in biomedical sciences and interest in cardiovascular research

  • Previous lab experience will be valued

  • Good spoken and written command of English

  • The PhD may incorporate, although will not be restricted to, one of the following research projects:

  • Epicardial signalling during myocardial regeneration in zebrafish

  • Identifying the source of new vasculature during zebrafish coronary vessel repair

  • The role of inflammation and fibrosis in the regenerating zebrafish heart

  • Small molecule induction of human adult epicardium-derived progenitor cells in cardiac repair


We offer:

  • 3-year contract to undertake a PhD in cardiovascular biology

  • A highly multidisciplinary, intersectoral and competitive training programme in cardiovascular research

  • Integration in a European network of scientific excellence, with short stays in partner labs

  • Access to state-of-the-art infrastructures

  • Very competitive salary (€45,714 per annum)

  • Extensive complementary training


Eligibility:
Researchers must be in the first four years (full-time equivalent) of their research careers and have not yet been awarded a doctoral degree at the time of recruitment. In addition, researchers must not have resided or carried out their main activity (work, studies, etc) in the UK for more than 12 months in the 3 years immediately prior to 14 February 2012. There is no restriction on the nationality of the researcher to be hired.

Interviews will take place in Oxford between Wednesday 22nd and Friday 24th February 2012. The studentship will start on Monday 1st October 2012.

Those interested please send CV, a cover letter justifying the interest of the applicant in the project, and the names of two referees to sally.harte@dpag.ox.ac.uk

General enquiries should be addressed to paul.riley@dpag.ox.ac.uk

Application deadline: 12 noon on Tuesday 14th February 2012
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Doing Science in Barcelona

Posted by on November 22nd, 2011

Blog entry

When thinking Barcelona, what first comes to mind is probably the football and Olympic games, the beaches, relaxed Mediterranean lifestyle, siesta and long nights out. All of it is accompanied with the Gaudi’s whimsical architecture at the background as an extra bonus. People usually go to Barcelona for a vacation or … for a science meeting. I was in this colorful city already several times because of science and always loved the place. And then a perfect chance came to spend a little bit more time in Barcelona when I was awarded the Development Travelling Fellowship supporting my visit for collaborative purposes. I was hosted by the lab of Enrique Martin-Blanco at IBMB at the University of Barcelona and the main goal of my stay was to work out the conditions for measuring protein activity during early zebrafish development. I embraced this opportunity to learn more about the place and its local customs by living there. What follows, are some of the experiences I have made in those two months in Barcelona.

Science reflection

Despite the economical situation and the ever-tightening budget, people do amazing science in Barcelona. I was exposed to a rich spectrum of different projects during the lab group meetings and also during department seminars. The microscopy facilities were impressive and I was happy to have more that one choice for a particular setup to use in my experiments. I could test different excitation and emission combinations as well as various optical variants to find the best conditions for imaging. Although the facilities were very busy and shared by many labs, I could get access to all the necessary equipment to conduct experiments and collect enough data that kept me busy with the analysis when the microscopes were occupied by other data hunters. Here, I would like to express my deep gratitude to the members of Enruque’s lab and to the heads of the facilities for making my time there very smooth in terms of organization and planning. The first two weeks were made very easy for me, because the girls who were working with zebrafish, made all the necessary arrangements such as booking injection stations and the microscope slots, preparing certain reagents and also making spare time to show me around. This was an enormous help during the short visit when every second counts.

As other travelers here had already commented, a good thing about going to a different place is that it allows refreshing ones thinking and the general attitude to the lab routines. For example, it became clear very quickly how spoiled we are back home in Germany. While it is good to focus on the work without thinking much about the costs involved, one can get easily carried away and waste unduly amount of reagents and materials. While I never felt limited in any reagent or equipment I had to use during my visit, it became apparent how important is to be economical in the way one works. For example, it is perfectly possible reusing the plastic Petri dishes in which the embryos are kept, which is often for half a day only. There is no good reason for discarding the dishes. It is not about the cost of the dishes, which is rather low, bur more about the plastic waste that is generated that way. Certainly, it made me think more carefully of the amount of waste produced in a lab and I keep applying my new working habits.

Cultural differences

When in Spain, do like Spanish do, or at least try to. I was very curious about the local customs and the differences between the Spain and Germany.

People in Barcelona are very friendly and one can easily get around with speaking English, but knowing a few words in a local language would definitely be helpful. Barcelona is the capital of Catalonia, therefore there are two official languages spoken in Barcelona: the Catalan and Castilian Spanish, which could be very confusing at the beginning, especially when trying to read the signs. It always makes a nice impression if you could say “bom dia” instead of “bueans dias” and some other simple phrases in Catalan.

Strangers at the street and in a public transport stare at one another much more directly than they do in Germany. That was a striking difference from the way the strangers interact in Northern Europe, where people mind their own businesses. The personal distance is much shorter and in the metro it would be very normal to lean over to see better the book a fellow passenger is reading.

For someone who is used to have a lunch break at 11:30, which is typical in Germany, it might be a bit unusual to shift this time for an hour or more. People in Spain normally go for lunch around 1 pm or later. It is very typical to conclude the lunch with a coffee and maybe a cigarette.

It was relatively easy to find a place to stay. I got a room in a shared apartment with four other people in a very nice neighborhood with large streets and beautifully designed houses. Every day going to the metro, I would fight my way to get in because of the tourists crowding in front of casa Battlo, one of the famous Gaudy houses turned into museum, right next to the station. My flatmates were on various kinds of the study exchange programs or other types of visits and all from different backgrounds, which was a very enriching experience. I feel very lucky with my choice because I had the nicest flatmates, easygoing and very friendly.

Although it is acceptable, I would not advice drinking the tab water. It is full of chlorine, which gives a peculiar taste to it. The bottled water is relatively cheap and the 5 to 8 liter cans are available everywhere. Barcelona is rather expensive city but good deals are possible. There are plenty of grocery stores and little private kiosks that run till late but the price range could be huge and I spent some time comparing prices before deciding where to shop.

The sunlight is very intense in Barcelona and I was constantly using sunglasses. My room had no curtain and the effect was amazing: I did not need an alarm clock anymore getting up with the sun every day. If only the sun could get up a bit later on the weekends!

Barcelona is generally a very safe city but one must be wary of the theft, which is apparently a very popular business in the tourist areas. It is well known and has been discussed thoroughly in many blogs giving travel advices. The thieves will try to steal the stuff from you while you are admiring the architecture and other street wonders. Being vigilant and keeping an eye on your belonging is enough to stay away form the trouble.

How to find a piano


While this would not be an issue for the most visiting scientists, I felt desperate facing with the idea of spending two months without a piano. That’s why during the first week I kept annoying my colleagues asking them to call different piano stores and enquire about a possibility of renting one. Soon it became clear that renting a piano for two months is not an option. I found a place nearby where I could play for a small fee, but I could never make it there during the opening hours. At the end I was quite lucky to find a cheap digital piano on ebay, which I could later re-sell to one of the colleagues who got inspired and decided she wanted to perfect her musical skills.
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Stand With Science

Posted by on November 21st, 2011

A group of graduate students at MIT have written a letter on behalf of American graduate students, urging the United States Congress not to cut science funding. The Congress Joint Select ‘super’ Committee on Deficit Reduction will make their decision later this week, and today is the last day to sign the letter.

If you’re in the US, have a look at the Stand With Science website for more info.

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Dates for your calendar

Posted by on November 7th, 2011

Dates for your calendar
This is a selection of upcoming dates of interest, but it’s by no means an exhaustive list. We’ll try to do these once in a while, but don’t hesitate to write your own posts to let people know about similar deadlines, or leave a comment below. Also make sure to check the eligibility of all scholarships and grants before applying.

Conference registration opening.
November 8 - Start of abstract submission for the ISSCR meeting (June 13-16, 2012)
December 1 - Start of registration for the ISSCR meeting

Conference registration deadlines.
Keystone announced a few upcoming deadlines for conference abstract submissions, including dates for the following meetings:
November 9 – abstract & scholarship deadline for “The Life of a Stem Cell: From Birth to Death” (March 11-16, 2012)
November 16 – early registration deadline for “Angiogenesis: Advances in Basic Science and Therapeutic Applications” (January 16-21, 2012)
November 17 - early registration deadline for “Epigenomics” joint with “Chromatin Dynamics” (January 17-22, 2012)
November 22 - early registration deadline for “Cardiovascular Development and Regeneration” (January 22-27, 2012)
November 30 - abstract & scholarship deadline for “Non-Coding RNAs” joint with “Eukaryotic Transcription” (March 31 - April 5, 2012)

Grants and fellowships:
November 18 – Application deadline for the NSF Graduate Research Fellowship Program (GRFP)
December 16 - Application deadline for the Wellcome Trust’s New Investigator Award
December 16 - Application deadline for the Wellcome Trust’s Senior Investigator Award

Travel funding:
December 1 – The very last day to apply to The Company of Biologists Direct Travel grants, which fund travel for conference attendance. These grants are being discontinued.
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Site update and dates for your calendar

Posted by on September 15th, 2011

Scheduled Node Maintenance:

This weekend (September 16-18) we’re upgrading the system that the Node runs on (WordPress), so you may not be able to access the site at times. Everything should be working again on Monday, but as always, if you spot anything unusual, let us know.

Update 18/9: the site upgrade is now complete, and everything works - as far as we can tell (again, do let us know if something seems weird.)

Dates for your calendar
In the recent survey about the Node, a few people asked to be kept up to date of various scholarships and registration deadlines. Here is a selection of upcoming dates of interest, but this is by no means an exhaustive list. We’ll try to do these once in a while, but don’t hesitate to write your own posts to let people know about similar deadlines, or leave a comment below. Also make sure to check the eligibility of all scholarships and grants before applying.

Conference registration deadlines.
Keystone announced a few upcoming deadlines for conference abstract submissions, including dates for the following meetings:
September 19 – abstract & scholarship deadline for “Angiogenesis: Advances in Basic Science and Therapeutic Applications” (January 16-21, 2012)
September 20 – abstract & scholarship deadline for “Epigenomics” joint with “Chromatin Dynamics” (January 17-22, 2012)
September 21 – abstract & scholarship deadline for “Cardiovascular Development and Regeneration” (January 22-27, 2012)
October 6 - abstract & scholarship deadline for “Gene silencing by small RNAs” (February 7-12, 2012)

Grants and fellowships:
October 11 - The NSF announced an application deadline of October 11 for Postdoctoral Research Fellowships in Biology (PRFB). For 2012 this fellowship is limited to certain areas: (1) Broadening Participation in Biology; (2) Intersections of Biology and Mathematical and Physical Sciences; and (3) National Plant Genome Initiative Postdoctoral Research Fellowships.
November 1 – Sir Henry Wellcome PostDoctoral Fellowships. See their website for other grant deadlines.
November 18 – NSF Graduate Research Fellowship Program (GRFP)

Travel funding:
September 30 – Deadline for The Company of Biologists Direct Travel grants, which fund travel for conference attendance.
October 31 - EDEN has research exchange funds available for US-based eco-evo-devo researchers (graduate students, postdocs, faculty).
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Development of electroreceptors: a “sixth sense”

Posted by on May 23rd, 2011

Hi there! My name is Melinda, and I’m a postdoctoral researcher at Cambridge University in the UK in the lab of Dr. Clare Baker (http://www.pdn.cam.ac.uk/staff/baker/). I’ve just wrapped up my research trip to work on paddlefish embryos in the southeastern state of Georgia in the United States, generously funding by the Development Travelling Fellowship award!

We are used to experiencing the world with five senses: sight, smell, taste, touch, and hearing. Many of these sensory systems are generated by placodes, which are regions of thickened ectoderm found in the embryonic head that generate a variety of peripheral sense organs, such as the otic and olfactory placodes, which form the inner ear and nasal epithelium, important for hearing and smelling, respectively. Hearing and balance are mediated by the mechanical displacement of tiny ¨hairs¨ on specialized sensory ¨hair cells¨ in our inner ears (also simply called mechanoreceptors).  In fish and aquatic amphibians, a series of lateral line placodes generates the lateral line system, which also contains modified mechanoreceptor hair cells, much like those found in the inner ear. These are used to detect changes in the local water environment important for prey or predator detection and schooling behaviors. In addition to the mechanoreceptors, another type of modified hair cell can be found in all major aquatic vertebrate groups: these are the electroreceptors, distributed in fields of “ampullary organs” on either side of the lateral lines of mechanosensory hair cells.

As the name suggests, electroreceptors allow animals that possess them to detect weak electric fields in water. Similar to mechanoreceptors, this is also used to find prey and for orientation. However land vertebrates (including reptiles, birds and mammals), as well as frogs and most modern bony fish (such as teleosts), have lost this ancient ¨sixth sense¨. They are still found in many aquatic vertebrates including jawless fish (lampreys), cartilaginous fish (sharks, rays), primitive bony fish (e.g. sturgeon, paddlefish), and even some amphibians (salamanders). Interestingly, in a few groups of modern bony fish, such as catfish and “electric fish”, electroreceptors have been independently “re-invented”. Although an evolutionarily ancient sense, electroreceptors were only discovered in the 1950s, and very little is known about their development or formation, i.e., how they develop in the embryo, what genes control their development, and what makes the difference between the sensory hair cells that detect changes in electric fields and those that detect water movement.

That’s where the North American paddlefish (Polyodon spathula) can help! This is truly an incredible animal. It has the most electroreceptors of any living vertebrate: between 50,000 and 70,000 “ampullary organs” per adult, many of them located on their rostrum or “paddle”, which is an extension of their cranium that accounts for nearly a third of their total body length (typically 1-2 meters).  Although a vulnerable or “threatened” species, conservation and farming efforts have made this primitive fish commercially viable as a source of caviar (No, I’ve never tried it…maybe it’s just me, but I’m not crazy about the idea of eating what I study), thus allowing us to obtain embryos for studying hair cell, and more specifically, electroreceptor development.

Now, contrary to what people initially think about my “field” trips, I don’t even see the adult fish! I go to the lab of collaborator Marcus Davis at Kennesaw State University, which is located on the outskirts of Atlanta, Georgia. The actual process of fertilizing the embryos is done in Missouri at Osage Catfishieries (osagecatfisheries.com) by the Kahrs family, a terrific family owned business that we’ve worked with over the years. Fertilization is external, so mature adults are injected with hormones that, along with weather conditions, dictate whether they are ready to be squeezed  (or in the case of males “milked” for sperm). So like buying from Amazon, I get an approximate delivery date and anxiously wait until I get an email saying the box of embryos is on the way. Once there, our game faces come on and, it’s at least 14 days of working all kinds of hours to ensure we maximize the one or two clutches we get per year. That means all experimental manipulations (e.g. injections, electroporations, drug treatments) need to be done in a short amount of time, in addition to the husbandry and collection of fixed specimens for future work. To say it´s intense at times is an understatement.

For me, one of the biggest challenges working at this university is that they are still in “transition” from their previous role as a small two-year college to a large four-year undergraduate college trying to advance scientific research. To give you an idea of what this means, there are no graduate students or postdocs, and I am the first postdoctoral researcher to ever visit this department. While I do get to interact with other faculty and undergraduate students, for the most part, I work alone. While I appreciate the chance to get caught up on all the podcasts I let pile up, it’s a very different environment to what I’m familiar with. Also as a former “commuter” school, it is located just off the major interstate, convenient for drivers, but not close to town. So any excursions require driving, thus making it more difficult to explore the area when you are limited for time.

However, two of my favorite things about going to Georgia (besides working on paddlefish, of course) are southern food and spring thunderstorms. Coming from England, I know drizzling rain. But in Georgia, with little warning, thunder and lightening just roll in. It can be quite a show and then 15 minutes later it’s completely gone and if it’s still daylight, the sun comes back out. Usually, it’s no big deal and quite normal around here. This year was different though. Across much of the southern United States, many states experienced the worst storms and tornados in nearly four decades! Luckily, the area I was visiting was spared much of the destruction: we only had a couple of power outages, but it did make for a few sleepless nights. All in all, not a bad season.

To see a juvenile paddlefish eating, check out this video I took:

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Science – The Bigger Picture

Posted by on May 1st, 2011

This is a retelling of the student and post-doc workshop from the second day of the BSDB/BSCB joint spring meeting that took place in Canterbury at the University of Kent. The session emphasised the need for accurate science and scientific involvement in public communication. It ended up a bit longer than I’d intended, but this is something I’m really enthusiastic about and felt it needed to be shared in detail. I hope you find it helpful.




Panellists:

Dr Peter Wilmshurst – A consultant cardiologist, known for his refusal to falsify or withhold data in pharmaceutical studies. He was being sued for libel and slander by NMT medical until the company entered liquidation in April.

Rose Wu – A representative for the charity Sense about Science which works tirelessly despite limited funding to improve the public image of science, aids accurate reporting of scientific issues in the media and campaigns for further government support for research.

Dr Jenny Rohn – A UCL post-doc by day. Also known for her punditry, she runs the popular science communication website lablit.com has been interviewed numerous times for tv and radio. She has published numerous stories and editorials and two fictional novels Experimental Heart and The Honest Look, communicating science through the engaging and emotional personal lives of scientists. She was also central to the campaign to save UK science funding.

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Travel fellowships deadline approaching

Posted by on April 21st, 2011

The next deadline for Development’s travelling fellowships is coming up on April 30, and Development would like to encourage you to apply if you are a graduate student or postdoc planning to work for a few months in a distant lab. Have a look at the fellowship site for the full requirements, and read these stories from previous recipients on the Node:

Tetyana (from the Ukraine) went to India:
Research Snippets from the Land of the Tiger
The Maggot Meeting 2010

Cristian (from Chile) went to Germany:
Developing Science in a Far Country: The Paradoxes of Life

Shreeharsha (from India) went to Japan:
Research in the Land of the Rising Sun

Dávid (from Hungary) went to Japan:
Nippon

Terry (from the US) went to Israel:
International Experience

Giovanni (from Italy) is currently in the Netherlands:
A nice Lab Experience in Amsterdam


If you’re planning a lab exchange as part of your research, don’t forget to apply for travel funding before April 30. Good luck!



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Wellcome to the Node

Posted by on April 19th, 2011



Hello ‘the Node’, it’s very nice to be here. :) This is the first of my cross-posts between the Wellcome Trust and The Node talking about myself and the research I’m doing in my PhD. You can find my first posts for the Wellcome Trust here and here. I try to write in a way that is accessible to all, so I hope you enjoy them.

Hopefully, science permitting, you’ll be seeing a lot more of me around here and I’m looking forward to meeting many of you at the upcoming BSDB-BSCB spring meeting.

Me, myself and my PhD

Hi, I’m Jonathan Lawson and I’m here to share my experiences as a developmental biology PhD student in Cambridge. I’m 23 and have already spent four years in Cambridge as an undergraduate, which gave me a BA/MSci in Biochemistry. Although I spend a lot of time in the lab, outside of work I spend a lot of time dancing and my other major passion is baking. I am currently web editor for the student run Cambridge science magazine BlueSci. I am writing these blogs as part of a collaboration between The Node and my benefactors, the Wellcome Trust.

My course is one of the Trust’s Four-year PhD Programmes, it is unusual in that, in the first year, we have a choice of labs we can join, spread across different departments at the University. Each student chooses three labs to join, each for a short nine-week project. This is too short a time to make any significant contributions, but it does allow you to get a good idea of what work is going on in the lab, and whether you will fit in well with the social dynamic. At the end of the first year we choose to join one of these labs for our full 3-year PhD project. This allows students to better understand a lab, and the work, before joining for the long-term, the idea being that students generally feel happier and are more likely to complete their PhD.

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