Under the microscope

Posted by on February 15th, 2012

Cambridge University Research has recently launched a series of videos called “Under The Microscope”, that showcase some of the microscopic research carried out at the university. Two of the eight videos they’ve published so far have featured developmental biology:



PhD student Matt Benton talking about beetle development.



Research fellow Erica Watson describes mouse development.

The “Under the Microscope” videos are meant for a wider audience, and it’s interesting to read some of the comments the videos get on YouTube, from people who are sometimes only thinking about development for the first time. But I thought even the seasoned developmental biologist might enjoy having a look at them.

Find all the videos on their video and audio page.
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Bio Web Conferences – Critical discussions with developmental biologists for deep learning.

Posted by on February 10th, 2012

Dear Developmental biology community,

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

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

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

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

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

Best regards,

Michael J.F. Barresi

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

 
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SDB Collaborative Resources (CoRe) Launched

Posted by on January 27th, 2012

The Society for Developmental Biology (SDB) has launched SDB Collaborative Resources (CoRe), an online collection of images, movies, and diagrams for learning and teaching developmental biology.  SDB CoRe is a free and open website developed to help increase understanding of developmental biology at all levels.




SDB CoRe is easily-searchable and can be browsed by topic, organism, or featured objects.  All objects have short descriptions aimed at helping users learn something about development with glossary words highlighted in green.  Object pages contain references as well as  links to related CoRe objects, links to reviews in the soon-to-be-launched WIREs Developmental Biology, and when relevant, to original research papers in SDB’s official journal Developmental Biology.  All users can create a My CoRe account in order to comment on an object or save it in their favorites.


SDB needs your help in building this community resource!  We are looking for visuals that help explain basic concepts in developmental biology across numerous plant and animal species.  Here are the guidelines for submitting to CoRe.  If you are an SDB member you can login to CoRe with your email address to submit.  Non-members that would like to submit to CoRe please contact me at info@sdbcore.org.  If you have any questions or suggestions for the site please email me as well.  Enjoy SDB CoRe!
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PHD Comics on the big screen

Posted by on November 17th, 2011

The web comic Piled Higher and Deeper (PHD) has been commiserating with graduate students since 1997. And now you can watch the comics come to live on the big screen, as universities and institutes across the world (including Antarctica!) are screening the PHD movie.

Fans of the comic will recognize most of the jokes, but now the individual 3-panel strips have been turned into a full-length movie with a plot that summarizes the main story of the long-running comic. The film was shot in its entirety at the Caltech campus last spring, and all actors are students and staff from Caltech. As they’re by and large professional scientists rather than professional actors, the acting isn’t always very sharp, but they did a great job at bringing the comics to life. The trailer below gives a good indication of the film.

PHD Movie Trailer from PHD Comics on Vimeo.



Most screenings are only open to students from the hosting institution, but I was lucky to hear about an open screening at University College London. Even though the screening was open to absolutely everyone, the lecture theatre was not entirely full. Perhaps it really does appeal specifically to grad students? Nevertheless, the people who did attend seemed to enjoy the film, and laughed at every joke. Even the ones that you could see coming from a mile away if you were familiar with the comics.



But this was not just any screening: it was one of the few that PHD Comics creator Jorge Cham was attending. After the film, science-loving comedian Robin Ince hosted a Q&A with Jorge and with Alex Lockwood - the actress (and graduate student!) who plays the character of Cecilia in the film. Alex initially kept her role in the film a secret from her advisor. “I didn’t tell him I was doing it for a while, but his wife is really nosy on Facebook…” Once he found out, he was a lot more excited about the film than she was – as long as she still got her work done, of course.

Despite being based largely on the existing comic strips, the end of the film breaks a longstanding tradition. In the fourteen years that Piled Higher and Deeper has been running, the main character was never named. In the film, he finally introduces himself. When this came up during the Q&A, Jorge explained why the student didn’t have a name to begin with: “First I was just kind of lazy, but then it became a funny thing. It took my own professor about four years until he learned my name.” But now, wanting to give the film a more interesting resolution, the student gets a name. “I figured it was about time. And I can always deny that it’s not comic-canon, that it’s just movie-canon…”

After the Q&A, we caught up with Jorge and asked him how the film translates to international audiences. It’s set in the US, where PhD degrees can regularly take 5-7 years, and many jokes are based on the fact that graduate school takes forever. My own favourite joke involves Cecilia’s encounter with a high school classmate:



But in the UK, where several universities have now screened the film, PhD degrees are much shorter than in North America. Do the jokes hold up?

“Well I heard that the guitarist from Queen took 35 years to finish his PhD, so I think he pulls up the average,” jokes Jorge, “But I think what translates the most is that feeling of uncertainty, feeling stuck and not being quite sure what you’re going to do next. That’s international.”

Regular readers of the Node may recall that we’ve interviewed Jorge before, and that he mentioned a “biologist character” that would appear in the comic very soon. What is happening with that, we wanted to know. “That’s still coming, but probably not for another year, at least.” Aww. But of course, this is the man who has turned procrastination into a career: Jorge left research several years ago to pursue the comic full time, and to give talks about procrastination to graduate students. To tie in with the various posts we’ve had on the Node about alternative careers, we asked him what he learned in his PhD degree that he still uses today.

“Many things. I think part of what I do as an artist is trying to discover where the truth is - or at least ask the question “where is the truth?” - and being able to think analytically in a big picture sense but also being able to drill down, and work on the minutiae of the details. I think the PhD gives you that kind of macro/micro vision at the same time. But mostly it just gives me the ability to avoid questions…”

If you’d like to see the movie yourself, here is a list of places that are showing it. And if you’re a bit more patient (now there’s something you learn in grad school!) you can wait for the DVD release, tentatively planned for Pi Day (March 14) next year.
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PhD Movie

Posted by on September 26th, 2011

Whether you’re familiar with the web comic or not, most of you will probably recognize your own current or past career as a graduate student in the new PHD Comics movie.

PHD Movie Trailer from PHD Comics on Vimeo.



It’s playing at university campuses across the world. If your city is not on the list, don’t fret: the website contains information on how to organise a screening at your own institute. Now if someone in Cambridge would like to host a screening, I’ll be there!

(See last year’s interview with Jorge Cham on the Node.)
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The Cell – Finalist in the Labby awards – Please vote to help us win.

Posted by on June 16th, 2011

The Cell: An Image Library is honored to be named a finalist in the website Labby Awards. Please help us win this award and vote for us at the site below. Please be patient if the site does not load right away and apologies for cross posting. Please tell your friends to vote for us as well.

http://the-scientist.com/2011/06/15/2011-labby-website-finalists/
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Embryonic development informs adult heart repair

Posted by on June 9th, 2011

After a heart attack, heart muscle is irreparably damaged, but a paper in Nature now reports that adult mouse hearts have a source of progenitor cells that can form new muscle cells after heart injury.

A few years ago, studies showed that embryonic epicardial progenitor cells contribute to the cardiomyocyte lineage in developing mouse hearts. These cells were marked by the expression of a key embryonic epicardial gene, Wt1, but Wt1 is not expressed in adult tissues.

The group of Paul Riley at UCL now reactivated Wt1 expression in adult mouse hearts by priming them with thymosin β4 (Tβ4) and inducing injury. This pointed to an adult pool of progenitor cells, marked by Wt1, which could form new cardiomyocytes after myocardial infarction. What’s more, this process was upregulated in response to Tβ4. A few years ago, Riley’s group already showed that Tβ4 also induces formation of blood vessels from epicardial progenitors.

In a video interview with The Scientist, Riley summarized his paper, and emphasized how they built upon previous studies in embryonic heart development to find this new source of adult myocardial progenitors.

Repairing hearts from thescientistllc on Vimeo.



“The key point for us has always been moving back to embryonic development and identifying cells that are key to formation of the organ, that would then translate to repair in the adult.” – Paul Riley (from the interview above)

How exactly Tβ4 induces increased Wt1 expression and cardiomyocyte formation isn’t yet known, but could this be a new therapeutic for heart attack patients? Unfortunately, Tβ4 is not the most practical drug. It would need to be administered before a heart attack, so could only be used as a preventive measure for people who already know they’re at risk, and it’s not available as a pill – only as injection. But a big step toward any form of therapy would be to find out how Tβ4 works at a molecular level to differentiate the progenitor cells to cardiomyocytes upon injury, and, as Riley mentions in the video above, that will be the next step in their research.

update: F1000/The Scientist have some more videos from this lab on their blog.

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iBioMagazine – Breakthroughs in Genetics

Posted by on April 18th, 2011

iBioMagazine is a quarterly web magazine featuring videos by some top scientists in the life sciences. The videos are aimed at students, and cover scientific topics as well as information about careers or science in society.

The latest issues has as theme “Breakthroughs in Genetics”, and the accompanying videos are all quite interesting:

* Mario Capecchi - The Birth of Gene Targetting

* H. Robert Horvitz - Discovering Programmed Cell Death

* Eric Wieschaus - Finding Genes That Control Development

All iBioMagazine talks are also available on YouTube. Eric Wieschaus’ talk is embedded below:



The iBioMagazine talks make for great introductions to scientific topics, but for more in depth videos, check out their sister site iBioSeminars, where you can watch entire lectures online, for example these talks about developmental biology and evolution.



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A new view on eye development

Posted by on April 7th, 2011

ResearchBlogging.orgYou’ve seen the news: ES cells generate a 3D retinal structure. But what does this tell us about eye development?

In the developing embryo, the first step toward a functional eye is the formation of the optic vesicle from the neural tube. This optic vesicle then invaginates to form an optic cup, which in turn develops into the outer pigmented layer of the retina and the inner neurosensory layer.

Normally, this all takes place in the context of the developing organism, next to neighbouring tissues. But, in a paper published in Nature this week, the Sasai lab at the RIKEN institute in Japan describes how they generated an optic cup in culture, from mouse embryonic stem cells.

The lab had previously generated retinal precursors from mouse ES cells in culture, but those did not form three-dimensional structures. In this new study, they changed the cultured medium by adding Matrigel (containing basement-membrane components). This initiated the formation of small, polarized, spheres after six days in culture. These spheres then invaginated to form the optic cup structure, as shown in this video from the study:



The immediate relevance of this paper is the increased understanding it offers in the mechanisms behind eye development. The study suggests that formation of the retina occurs to a large extent via an intrinsic order that does not entirely depend on external forces. That does not mean that neighbouring tissues have no influence at all, but this influence appears smaller than previously believed.

While this does not mean that we can make custom eyes on demand just yet, the study does have some other clinical implications: If we can generate functional retina from induced pluripotent stem cells taken from patients’ tissues, these could be used in drug testing or disease modeling, and help increase our understanding of diseases that cause blindness.

Read more:
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A walk in the park is a walk amongst development

Posted by on March 10th, 2011

[updated 25/3/2011] Video was temporarily removed from Vimeo. Will repost it when it’s back up.
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