13th Annual Northeast Student Chemistry Research Conference (NSCRC)

The timing and location of this conference would seem to make it ideal for undergraduates to present their research — follow the links below if interested.

April Jewell of the NSYCC wrote:

As Chair of the Northeast Section Younger Chemist Committee (NSYCC), I would like to invite the Undergraduate and Graduate Students and Post-Doctoral Candidates from your department to participate in the 13th Annual Northeast Student Chemistry Research Conference (NSCRC). I would appreciate it if you would forward this information on my behalf. The NSCRC will be held at Northeastern University’s Curry Student Center on Saturday, April 30th, 2011.

The Northeast Student Chemistry Research Conference (NSCRC) is organized for students by students. It is devoted to the research of undergraduate, graduate, and post-doctoral chemistry students, providing a relaxed atmosphere for students to share their work. The day-long event features student poster and oral research presentations, a keynote speaker, awards, and catered lunch. The conference encourages students to network and get feedback from their peers. The 1st NSCRC was held April 24, 1999 at the Massachusetts Institute of Technology (MIT).

The deadline for abstract submission is Friday, April 8th, at 5pm. Please visit our website at nsycc.org for submission instructions.

Turning germline cells into neurons

Piali Sengupta discusses the most recent research in how nerve cells are programmed to develop in “Cellular reprogramming: chromatin puts on the brake“, published in the Feb 22 issue of Current Biology.

Fishing for neurons

Let’s say you’re a fisherman/woman trawling for tuna out on the azure-blue waters of the Pacific. Tuna’s your desired catch, but as you drag your net through the water you notice that all manner of aquatic life gets ensnared, to say nothing of styrofoam flotsam, plastic bottles, used automotive parts, and syringes. The FDA has guidelines about these sorts of things and the folks back at Trader Joe’s won’t tolerate even trace amounts of dolphin in their tuna. Bottom line is – you need your tuna to be pure. However, fishing individual tuna out of the sea one by one is extremely labor intensive, and though it may achieve high purity, you’ll be hard pressed to meet your production quotas.  The point of all this?

Scientists in the Nelson Lab at Brandeis fish for neurons. And not just any neurons, mind you, but very specific types. The end goal is to harvest their mRNA in order to “read out” their global gene expression using microarrays or sequencing based methods. They’re not alone in these pursuits; on the contrary, cell-type-specific gene expression profiling is a burgeoning field. However, like the analogy of fish in the sea, neurons exist in a complex and crowded environment, and isolating specific cell types requires some ingenuity. Different labs have used very different methods. In a recent study published in PLoS ONE, Okaty et al. compiled and re-analyzed all of the publicly available mouse brain, cell-type-specific microarray data (including their own) in order to ask the question: can they detect evidence of contamination, “stress effects” (more on that below), or any other kind of peculiar artifacts stemming from the purification (“fishing”) methods themselves? The short answer: Yes they can.

Some methods are fairly low throughput – fishing out one cell at a time.  The Manual cell sorting method (a home grown method) dissociates brain tissue, keeps the cells alive in artificial cerebrospinal fluid (almost literally seawater), and then the cell fisherman/woman hand picks labeled cells from the cell suspension with a glass pipette under a microscope (how they’re labeled isn’t terribly relevant to this discussion). This would be like collecting seawater, transferring the fish to less dense holding tanks with artificial seawater and then sorting the yellowfin tuna from the chub mackerel, etcetera. Another of the lower throughput methods is called Laser Capture Microdissection (LCM), where the extracted mouse brain is preserved through formalin fixation or flash freezing. Then thin tissue sections are made with a microtome, and individual cells are carved out of these tissue sections with a laser beam. This would be roughly approximate to freezing a volume of seawater, and then carving out the frozen fish of choice with a laser beam (sounds complicated). The primary difference between these two methods is that Manual sorts dissociated cells, whereas LCM extracts cells from intact, but preserved tissue.  Methods like fluorescence activated cell sorting (FACS) and immunopanning (PAN) also sort dissociated cells, and with the aid of flow cytometry, automated fluorometry, and/or the power of antibody selection (cell-type-specific bait), these methods greatly exceed the yields afforded by Manual cell sorting (imagine a dense network of narrow canals in which each fish is entrained in a high velocity stream, and an automated detection system diverts tuna into one channel, chub mackerel into another, and dolphin into another). Finally, a method called translating ribosome affinity purification (TRAP) bypasses the need to sort cells and “pulls down” tagged ribosomes, mRNAs in tow, from non-preserved tissue homogenate (a process which defies fishing analogy).

As you might expect, Manual cell sorting, along with FACS and PAN, achieve the highest purity (lowest amount of contamination), whereas LCM and TRAP show strong evidence of contamination from off-target cell types. Another concern is that the stress of dissociating cells or maintaining them in artificial media may perturb gene expression (think nervous, angry, wild fish in a cramped fish tank). However, only in the case of PAN data is there evidence of these effects (elevated levels of stress-response, cell death, and immediate early genes). Finally, the TRAP method extracts only mRNAs that are actively being translated, thus differences between TRAP data and data obtained by other methods may also reveal patterns of posttranscriptional regulation. For the full story, please refer to the paper.

addendum: see also Okaty et al. J.Neurosci. 31(19):6939-6943, 2011

What are best friends for? Insights from 10 million friendships

Why do people have best friends? Why do we think of some individuals as “better” friends than other individuals? Why rank friends at all? And what is so special about the apex of the ranking, our “best” friend?

Peter DeScioli, a Kay Fellow at Brandeis University, and colleagues recently shed light on these questions by collecting a dataset of over 10 million people’s friendship decisions from the MySpace social network. The results support the “alliance hypothesis” which is based on the idea that people depend on their friends in conflicts. The findings were recently published in the journal Perspectives on Psychological Science.

MySpace has a feature that allows users to rank their “Top Friends,” providing a unique data source for testing how well different variables explain people’s rankings of friends. The alliance hypothesis predicts that people will feel closest to friends who rank them higher than others. Here’s why: If you need your friend to take your side in an argument, then they will have to side against someone else—which is unlikely if they are better friends with your adversary. The fewer people ranked above you, the more you can rely on your friend to take your side. According to the theory, people unconsciously track this strategic information and it shapes how we feel about our friends.

It turns out that the importance of friend rank was highly significant. Comparing first- and second-ranked friends, 69% chose for first-rank the individual who ranked them better. This was a considerably larger effect than the next best predictor, geographic proximity. The effects of sex, age, and popularity were small by comparison. Moreover, friend rank increased in strength when the analysis was extended to first- versus third- through eighth-ranked friends. In short, we now have 10 million more reasons to wonder if human friendship might be more strategic than it seems.

Other comment:



Thomas, Epstein to Collaborate with Discovery Museums on Dreyfus Foundation Grant

The Discovery Museums (Acton, MA), in collaboration with Professors Christine Thomas and Irv Epstein (Brandeis chemistry department) and Brandeis’s American Chemical Society Student Affiliates Chapter have received funding from the Camille and Henry Dreyfus Foundation to develop and implement a project called Reaction Station: Adventures for Young Chemists.

Pilot tests of a prototype Reaction Box with students

The project aims to enhance and promote hands-on chemistry experiences for youth in schools and museums. Implementation of the project involves first designing “Reaction Stations,” comprised of large plastic boxes with holes cut out for gloved hand access, and then carrying out educational and experiential programming for children using these Reaction Stations. As children are often enticed by messy, smelly, or otherwise highly-reactive experiments, these portable Reaction Stations (similar in concept to gloveboxes used by members of Professor Thomas’s Lab) will provide a safe way for children to engage in experiments that are often avoided in school or museum settings due to their messy nature.

Denise LeBlanc, Director of Learning Experiences at The Discovery Museums (and also a former research scientist in the Rosenstiel Basic Medical Sciences Research Center on campus), anticipates much success from the Reaction Stations. LeBlanc and Thomas will devise various experiments for children to carry out. Possibilities include: identifying a mystery substance as part of a “crime scene,” testing the pH of common household items, exploring reactivity of everyday chemicals that, at first glance, seem inert, and other experiments that introduce children to topics of polymers, chromatography, phase changes, etc.

Undergraduate students in the American Chemical Society Student Affiliate Chapter will work with the children as model scientists and helpers. Throughout the duration of the year, undergrads from the chemistry department will partake in demonstrations and lessons at the museum in Acton, MA, as well as offsite through various after-school programs. Beyond conducting demonstrations in a museum or school setting only, the Reaction Station will be a teaching tool that educators can bring to their own classrooms or other venues to perpetuate their students’ engagement in chemistry and hands-on research. Says Thomas, “Making research understandable and accessible to children at a young age is pivotal in the development of new generations of chemists.”

The Reaction Station: Adventures for Young Chemists proposal was one of 19 grants awarded this year. Other recipients include universities and museum/science outreach organizations who intend to advance the chemical sciences through innovative projects.

An alternative to scuba diving

Many promising medicinal agents (anti-cancer, anti-bacterial, anti-viral and anti-fungal) have been discovered among the diverse molecules produced by marine organisms. However, scuba-diving to harvest sponges and algae is not usually a practical way of obtaining usable quantities of these compounds, especially if they are present only in trace quantities in the source organisms.

A recently published paper in Organic Letters from the laboratory of Assistant Professor of Chemistry Isaac Krauss is the first to present a synthetic laboratory approach to the preparation of the bromophycolides, originally isolated from Callophycus Serratus, a red algae which was collected off the coast of Fiji. Although these compounds were shown to posses anti-tumour, anti-HIV and anti-malarial properties, algae collected in a second expedition to Fiji apparently contained none of the natural product (hence the desirability of a laboratory synthesis). The bromophycolides are a structurally unique family of natural products containing brominated asymmetric carbon centers and large 19-membered rings. This paper illustrates the preparation of the bromophycolide A and D ring system in high enantiomeric purity via a short (9-step) synthetic sequence.

Susan Band Horwitz (PhD ’63) receives AACR Lifetime Achievement Award

Susan Band Horwitz, Ph.D., will receive the Eighth AACR Award for Lifetime Achievement in Cancer Research. Horwitz is being recognized for pioneering research in the mechanism of the anticancer drug Taxol and for contributions to the understanding of how this microtubule-stabilizing drug arrests cell division, which eventually leads to cell death, especially of cancer cells.

Horwitz received a bachelor’s from Bryn Mawr, then came to Brandeis to do her graduate studies. According to a profile in PNAS by Tinsley H. Davis,

“At that time, there were few graduate schools that were very receptive to women,” [Horowitz] recalls. “Women were not very prominent on the faculty or in the student body.” One university stood out from the others, however. Brandeis University (Waltham, MA) had just started its graduate program in biochemistry. “Brandeis was a new and exciting place, and the people there wanted it to succeed,” says Horwitz, “yet it also had a relaxed atmosphere that was really perfect for me.”

Once at Brandeis, Horwitz worked with Nathan Kaplan, chairman of the newly formed Biochemistry Department. Her Ph.D. dissertation (1963) involved bacterial metabolism of sugar alcohols.

While juggling raising children and doing part-time postdoctoral research (some things haven’t changed so much over the years!), Horwitz became interested in pharmacology and anticancer agents. She joined the faculty at Albert Einstein College of Medicine in 1970, where she has remained since, currently serving as the Rose C. Falkenstein Professor of Cancer Research and co-chair of the department of molecular pharmacology.

Horwitz’s academic career has been vastly productive, in terms of research, publications and awards, but perhaps more significantly in terms of her research’s impact on millions of cancer patients worldwide. Her current research focuses on new natural products with similar mechanism to Taxol, looking for ways to enhance therapeutic value and to avoid drug resistance.

The AACR Award for Lifetime Achievement in Cancer Research was established in 2004 to honor an individual who has made significant fundamental contributions to cancer research, either through a single scientific discovery or a body of work. These contributions, whether they have been in research, leadership or mentorship, must have had a lasting impact on the cancer field and must have demonstrated a lifetime commitment to progress against cancer. Horwitz will receive the award at the Opening Ceremony of the AACR 102nd Annual Meeting.

Thomas named 2011 Sloan Research Fellow

Assistant Professor of Chemistry Christine Thomas has been named a 2011 Sloan Research Fellow. These two-year fellowships are awarded to early-career scientists in recognition of distinguished performance and a unique potential to make substantial contributions to their field. Research in the Thomas laboratory focuses on the design and synthesis of new transition metal complexes to examine the fundamental interactions between different components of bifunctional catalysts with the ultimate goal of uncovering new transition-metal catalyzed bond activation processes related to renewable energy. Since starting in the Chemistry department at Brandeis in 2008, Thomas and coworkers have developed a series of bimetallic catalysts that utilize metal-metal interactions to attenuate redox potentials and promote the activation of small molecules such as hydrogen, alkyl halides, and carbon dioxide.

The Thomas lab has an energetic and talented team of researchers

Arne Ekstrom ’96, PhD ’04 and Mikhail Ershov MA ’00 were also named as 2011 Sloan Research Fellows. Ekstrom received a B.A. in Biology and Psychology from Brandeis, and after getting an M.S. at U. Arizona, returned and completed a Ph.D. in Neuroscience here in 2004, working with Michael Kahana. After a postdoc at UCLA, Arne took a position as an Assistant Professor in the Center for Neuroscience at U. California, Davis. His lab studies spatial memory using EEG and fMRI techniques. Ershov came to Brandeis from Moscow State Univ. and received an MA in Math in 2000 bofore going on to Ph.D. work at Yale and a faculty position at U. Virginia. Ershov is being recognized for research contributions to various aspects of group theory.

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