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BMCDBer Rebecca Beer Gets 2nd in Aquaneering 2013 Art of Science Photomicrography Calendar Contest

November 27, 2012 1 comment

Description of contest: 2013 Art of Science Photomicrography Calendar Contest

Aquaneering Inc.
Images depicting studies with zebrafish, xenopus, or other aquatic species were judged on both technical execution and artistic rendition by an outside panel of both science and art professionals. The three winning photos will be featured on Aquaneering’s 2013 calendar, which will be distributed in the January issues of ALN and Zebrafish Magazines. Aquaneering builds high quality aquatic environments for laboratory animals, including zebrafish and xenopus.

The earliest germ cells in the zebrafish ovary contain a population of germline stem cells. In this double transgenic adult zebrafish ovary imaged via fluorescent confocal microscopy, the ziwi promoter drives expression of mCherry in all germ cells (red) including early stage germ cells, while the vasa promoter drives expression of eGFP only in later stage oocytes (green), and DNA has been stained with DAPI (blue).

“Big Data” Seminar TODAY!

November 27, 2012 Leave a comment

Escaping the sea of “Big Data” in Biomedical Research: Building a knowledge continuum for Life Scientists with Linked Data and Semantic Web Solutions

Helena F. Deus, PhD

Unit Leader, Bioinformatics and Systems Biology

Digital Enterprise Research Institute

National University of Ireland, Galway

 

4-5 PM, Tuesday, December 4, 2012

Room 4202 GBSF

Data is central to any medical decision. Since the introduction of “omics” technologies, petabytes of biological data has been generated on a daily basis in labs around the world. The complexity involved in generating, mining and integrating this data forced its specialization into various subdomains – genomics, metabolomics, lipidomics, etc.  However, significant challenges remain in linking this wealth of data to clinical applications in a scalable and robust way.

Categories: Seminar Announcements

BMCDB Movie Screening of Soylent Green

November 21, 2012 Leave a comment

6pm Tuesday, LSA 1022

27 November 2012

We shall be screening a movie with popcorn and beer and wine provided.

Please do not spoil the ending of this movie.

🙂

BMCDB presents:

Soylent Green

Starring: Charlton Heston

This movie takes place in a dystopian future where scientist have ruined the planet.
The opening scene is Manhattan, population 50,000,000.  Social commentary

Yes, you may add commentary, why else would we have drinks?

Amazing microbial diversity uncovered in the “Jungle” of our belly buttons

November 15, 2012 Leave a comment

In a bizarre, but very interesting (and potentially hilarious) bit of science, Robert Dunn’s group at UNCS started investigating the “microbiome” of the human belly button. Using 16S rDNA libraries they analyzed 60 belly buttons they isolated 2,368 bacterial species, of which 1,458 could be new to science. Most people appeared to have about 67 species inhabiting their belly buttons. While the initial sample size was quite small it was still a stunning result to find so much microbial diversity inhabiting our oft forgotten belly buttons.

From “Microbial fauna in your belly button is like a ‘tropical forest” by

The whole thing started about two years ago, when an undergrad sampled a colleague’s belly button bacteria to send it to him as a Christmas card. Biologists, the quirky people that they are, quickly picked up on this idea.

The basic idea is that the belly button is one of the least scrubbed places of the human body, making it one of the most pristine bacterial environments humans harbor – which could kind of explain why some people are totally grossed out by navels.

….

Not even a single strain appeared on all subjects, but 8 were found in over 70 percent of subjects; and when one of the species found often was present, others followed in great numbers.

“That makes the belly button a lot like rain forests,” Dunn said. In any given forest, he explained, the spectrum of flora might vary, but an ecologist can count on a certain few dominant tree types. “The idea that some aspects of our bodies are like a rain forest—to me it’s quite beautiful,” he added. “And it makes sense to me as an ecologist. I understand what steps to take next; I can see how that works.”

The study was published in PLOS ONE: A Jungle in There: Bacteria in Belly Buttons are Highly Diverse, but Predictable

The belly button is one of the habitats closest to us, and yet it remains relatively unexplored. We analyzed bacteria and arachaea from the belly buttons of humans from two different populations sampled within a nation-wide citizen science project. We examined bacterial and archaeal phylotypes present and their diversity using multiplex pyrosequencing of 16S rDNA libraries. We then tested the oligarchy hypothesis borrowed from tropical macroecology, namely that the frequency of phylotypes in one sample of humans predicts its frequency in another independent sample. We also tested the predictions that frequent phylotypes (the oligarchs) tend to be common when present, and tend to be more phylogenetically clustered than rare phylotypes. Once rarefied to four hundred reads per sample, bacterial communities from belly buttons proved to be at least as diverse as communities known from other skin studies (on average 67 bacterial phylotypes per belly button). However, the belly button communities were strongly dominated by a few taxa: only 6 phylotypes occurred on >80% humans. While these frequent bacterial phylotypes (the archaea were all rare) are a tiny part of the total diversity of bacteria in human navels (<0.3% of phylotypes), they constitute a major portion of individual reads (~1/3), and are predictable among independent samples of humans, in terms of both the occurrence and evolutionary relatedness (more closely related than randomly drawn equal sets of phylotypes). Thus, the hypothesis that “oligarchs” dominate diverse assemblages appears to be supported by human-associated bacteria. Although it remains difficult to predict which species of bacteria might be found on a particular human, predicting which species are most frequent (or rare) seems more straightforward, at least for those species living in belly buttons.

 

BMCDB TGIF Nov 16th @ 5:30 in LSA 1022

November 15, 2012 Leave a comment
Gobble gobble BMCDBers!
 
Come out and take a load off this Friday at 5:30 PM in 1022 LSA for this month’s TGIF! We’ll be having the standard staple graduate student diet of assorted pizzas and beer, in addition to freshly baked baguettes with spinach dip, an organic spring salad mix and tasty sun chips, and for the wine connoisseurs  we’ll be serving an Argentinian Malbec and a Californian White Zinfandel and a Californian Chardonnay. If get lost and can’t find where the party is at, just wander around the first floor of LSA and we’ll be bumpin’ 2 CHAINZZZ!
 
Also good luck to the BMCDB Bowlaz’ tomorrow, Gordon “Ball Master/Guttermouth” Walker, John “King Pin” Riggs, Johnathan “Unbowleavable” Diehl, Matthew “Pin Hunter” Blain-Hartung, and Ralphington “Big Em McCracken” McNeilage. Watch them bowl out of control at 6 to 8 PM tomorrow, Thursday November 15 at the MU bowling alley, and if you go, don’t forget to wear your BMCDB swag!
 
Bring the Dean’s Cup home fellas!
 

(`-`) (._. ) (· – ·) ( ._.) ( ‘ -‘)

   The TGIF Committee

(`-`) (._. ) (· – ·) ( ._.) ( ‘ -‘)

 

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“Modulating conformation and dynamics to interrogate cellular ubiquitin-deubiquitinase signaling”4:00 p.m. 1005 GBSF Auditorium

November 14, 2012 Leave a comment

The Genome Center & Structural Biology Focus Group Presents:
Dr. Jacob Corn
Genentech
Early Discovery
“Modulating conformation and dynamics to interrogate
cellular ubiquitin-deubiquitinase signaling”
Ubiquitin is a highly conserved eukaryotic protein that interacts with a diverse set of
partners to act as a cellular signaling hub. Intriguingly, ubiquitin has recently been
shown to be conformationally flexible, is postulated to underlie its multifaceted
recognition. Using computational and library-based means, we interrogate core
mutations of human ubiquitin that modulate its conformational dynamics and find that
human deubiquitinases involved in tumorigenesis are sensitive to ubiquitin’s
conformational state. Using this insight, we engineer new states of ubiquitin that act as
high-affinity deubiquitinase (DUB) probes to inhibit DUB activity in human cells. We
also find that certain DUBs are exquisitely sensitive to the rate with which ubiquitin
switches between states, and show that strict maintenance of the kinetics of ubiquitin’s
motion is necessary for the survival of eukaryotic cells. These results reveal the key
role protein motion plays in a major disease-associated signaling network, and for the
first time demonstrate the importance of “invisible” conformational dynamics in vivo.

Wednesday, November 14th, 2012
4:00 p.m.
1005 GBSF Auditorium
Cookies & Coffee will be provided before the seminar
Faculty Host: Justin Siegel (jbsiegel@ucdavis.edu)
(If you wish an appointment with the invited speaker, please contact the host.)

Bowl so hard, that ish cray

November 7, 2012 Leave a comment

Greetings BMCDBers!

The GSA has asked me to bread the word about the Annual Graduate & Professional Student Dean’s Cup Bowling Competition on Thursday, November 15 from 5:45pm-8pm. There will be trophies for first, second, and third winning graduate groups; gift cards to the winning team members; and free souvenirs, food, and drinks to those present at the event.

I’m sure we could wrangle ourselves another glorious trophy to parade around Briggs/LSA. There may be a lot of other Biology-related groups competing, but none of them have game like our alphabet soup biology grad group.

There’s a minimum of 2 players and a maximum of 5 players. Contact me, Ben Yuen (btyuen@ucdavis.edu), if you’re interested.  The deadline is Monday, November 12.

Also, cheerleaders for your team are welcome and will also have free access to souvenirs, food, and drinks!

Thanks!
Bento Box Yuen

You can download the application here! Then send it to Ben!

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