Phi Beta Kappa Elects 51 Division of Science Students

Phi_Beta_Kappa_KeyThe Brandeis chapter of Phi Beta Kappa recently elected 97 new members. Of the 97, at least 51 undergraduate students are majors in the Division of Science (Biochemistry, Biological Physics, Biology, Chemistry, Computer Science, Mathematics, Neuroscience, Physics and Psychology).

Congratulations to the following new Phi Beta Kappa members from the Division of Science:

Biochemistry

Malia Barbra McAvoy
Yehonatan Otzar Meschede-Krasa
Juhee Park
Lior Rozhansky
Hanchen Zhao (double major with Chemistry)

Biological Physics

Abigail Rose Knecht

Biology

Ignatius Ang
Zachary Ian Fried
Jenna Leah Kahane
Ariel Jennifer Katz
Yang Li
Yixuan Liao
Alice Yuan Meng
Khang Vi Nguyen (double major with Chemistry)
Danielle Marie Quintin
Sarah Shin

Chemistry

Khang Vi Nguyen (double major with Biology)
Soobyung Park
Noam Isaac Saper
Hanchen Zhao (double major with Biochemistry)

Computer Science

Kenneth William Foner
Huy Quang Mai
Grady Berry Ward (double major in Mathematics)

Mathematics

Cameron Zhang Fen
Trevor Weiss Kafka
Linda Li
Huy Quang Mai
Stefan Stanojevic
Zhengyang Zhou
Daniel Jackson Kutner (double major in Physics)
Murielle Claire Tugendhaft
Grady Berry Ward (double major in Computer Science)

Neuroscience

Jessica Allison Haley (double major with Psychology)
Kiera Gillian Sarill (double major with Psychology)

 

Physics

Wei Zhong Goh
Stefan Stanojevic
Daniel Jackson Kutner

Psychology

Kyra Jordana Borenstein
Hannah Dvorah Caldwell
Nicole Danielle Cardona
Avi David Cohen
Annie Cui
Jason Michael Desimone
Emily Rose Friedman
Jonathan David Gilman
Clara Emily Gray
Cecilie Gromada
Sarah Jessica Hack-Chabot
Jessica Allison Haley (double major with Neuroscience)
Jessica Lynn Lieberman
Danielle Mizrachi
Emily April Mostow
Linda Sue Nakagawa
Talia Michelle Portal
Jenna Louise Rice
Kiera Gillian Sarill (double major with Neuroscience)
Aliza Naomi Shapiro

See full story on BrandeisNow.

Undergraduate Lab Tours Begin

Are you an undergraduate interested in gaining research experience by working in a lab at Brandeis? Not sure how to find a lab to work in?

The Biology Undergraduate Department Representative (UDRs) have created the Lab Tour Program. The first tour was held on Monday, April 13th. Lead by Biology junior, Sarita Biswas ’16, undergraduates toured the Dorothee Kern, Daniel Oprian and Chris Miller labs. Although a Biology major, Sarita has worked in Kern’s Biochemistry lab for nearly a year. During the tour, students were shown lab equipment and specialized research rooms (cold room, autoclave room) in the Volen Center. Throughout the tour, Sarita discussed the research that is being done in the labs.

Following the tour, Rashieda Pugh ’16 (UDR) and Sarita sat down with the students. Sarita discussed the kind of projects that she has worked on in the past year. Both Sarita and Rashieda shared their experiences in finding a suitable lab to work in, how they find a project to work on once in the lab, and the time commitment during the summer and academic year.

Some of the many questions asked:

  • Will there be a someone there to guide me? There is always a graduate student or postdoc mentoring you.
  • How do you find a lab to work in? Review the faculty webpages, find research that interests you and then email the professors. Do not write all the professors a generic email about opportunities in their lab. It’s unlikely to work. Take the time to find out what kind of research goes on in each lab. Target labs in which you have a genuine interest. Be prepared to show up in person and talk intelligently about research projects with the faculty member. Be prepared to emphasize what you have to offer – skills acquired in courses or other jobs, your dedication and willingness to apply yourself, your reliability and punctuality, your ability to communicate clearly and concisely, etc.
  • Is lab research considered an internship? Yes, it is very much like an internship.

Their advice is that there are a lot of labs here at Brandeis and a lot of ways to find rewarding research experience in a lab!

The Lab Tour continues on April 16th.

John Wardle Named Division of Science Head

John Wardle, Division of ScienceSusan Birren, Dean of Arts and Sciences, has announced that John Wardle, Professor of Physics, will be the new Head of the Division of Science.

The following is Susan’s email:

“I am pleased to announce that John Wardle will be the new Head of the Division of Science.  John is an astrophysicist and Professor of Physics and is a former chair of the Physics department.  In his new role he will oversee science-wide programs and initiatives, including the summer undergraduate research program and will work with Division of Science faculty and staff to identify new directions for the division.  I am delighted that he has agreed to take on this role and I hope that you will join with me in welcoming him.

We all owe a debt of gratitude to Eve Marder who, as the first Head of the Division, created and steered many of the priorities of the Division.  During her time as Head, Eve ably represented the Sciences at Brandeis and beyond, worked to make the Summer Undergraduate Science Program a flourishing success, changed the way we trained students and postdocs in the ethical conduct of research, and worked tirelessly to secure funding and recognition for the Sciences.  Thank you Eve!”

Tenure-track faculty position in Biochemistry

The Department of Biochemistry at Brandeis University invites applications for a tenure-track faculty position, to begin Fall 2014. We are searching for a creative scientist who will establish an independent research program and who in addition will maintain a strong interest in teaching Biochemistry at the undergraduate and graduate levels. The research program should address fundamental questions of biological, biochemical, or biophysical mechanism. Brandeis University offers the rare combination of a vigorous research institution in a liberal-arts college setting. The suburban campus is located 20 minutes from Boston and Cambridge and is part of the vibrant community of academic and biotechnology centers in the Boston area. The application should include a cover letter, curriculum vitae, statement of research accomplishments and future plans, copies of relevant publications, and three letters of reference. Applications will be accepted only through AcademicJobsOnline at https://academicjobsonline.org/ajo/jobs/3366. Additional inquiries may be directed to Dan Oprian, Professor of Biochemistry (oprian@brandeis.edu). First consideration will be given to applications received by December 1, 2013.

Brandeis University is an Equal Opportunity Employer, committed to building a culturally diverse intellectual community. We particularly welcome applications from women and minority candidates.

How bacteria resist fluoride

Fluoride anion is everywhere.  Released into water through the natural weathering of rocks, it’s present to the tune of 5 mM in toothpaste, 30 μM in Cape Cod bay, and 17 μM in Massell pond at Brandeis.

Fluoride levels in our environment (graph).001

Fluoride in the environment, measurements by Ashley Brammer (Miller lab)

Since F is ancient, ubiquitous and toxic to microbes, it’s not surprising that bacteria have evolved defenses to expel it from their cytoplasm.   In an article published in eLife on August 27, 2013, Randy Stockbridge, Janice Robertson, and Luci Partensky from Chris Miller’s lab describe one of these microbial defenses, a fluoride channel called Fluc.  The channel provides a pathway for F to exit the cell across the membrane at a rate of 107 ions per second, while rigorously excluding Cl in order to avoid catastrophic membrane depolarization. The world-record 10,000-fold selectivity isn’t the only remarkable aspect of Fluc, however. The Fluc channel is built on an antiparallel dimer scaffold, with one of the subunits facing the exterior of the cell, and the other facing the interior. Only one other modern-day membrane protein is known to dimerize like this, but the arrangement recalls the inverted structural repeats that are a common, important motif for membrane transporters. Inverted repeats are the product of an antiparallel dimer, like Fluc, that duplicated and fused eons ago.  The sequences drifted over time until the duplication was undetectable by sequence similarity, and the plethora of membrane transport proteins built on this plan was only discovered when the 3-D structures were solved. The Fluc family provides the opportunity to study microorganism resistance to an ancient xenobiotic, as well as membrane protein architecture from an evolutionary origin.

For more, you should read the paper:

Stockbridge RB, Robertson JL, Kolmakova-Partensky L, Miller C. A family of fluoride-specific ion channels with dual-topology architecture. eLife. 2013;2(0):e01084. PMCID: 3755343.

PS: If you’re wondering about the tea on the bar graph, tea plants accumulate F in their leaves.  Cheap teas, made from older tea leaves, actually carry a lot of F, and if you drink a couple quarts of lousy tea a day, you can give yourself skeletal fluorosis.

A facilitated diffusion confusion dissolution

To udirectbindfd1tilize the information contained within a cell’s genes, the enzyme RNA polymerase must find the beginning of each gene (the promoter).  Finding the beginning is a prodigious task:  RNAP must start at a particular base pair of DNA, but the cell contains millions of base pairs to choose from.  It has been proposed that gene-finding challenge is aided by a process termed ‘facilitated diffusion (FD).  In FD, RNA polymerase first binds to a random position on DNA and then slides along the DNA like a bead on a string until it encounters the target DNA sequence.

single-mol-testIn a recently published study in PNAS (1), biophysicists Larry Friedman and Jeffrey Mumm worked with Prof. Jeff Gelles in the Brandeis Biochemistry department to test key predictions of the FD model.  They used a novel light microscope that Friedman and colleagues invented and built at Brandeis, a microscope that can directly observe the binding of an individual RNA polymerase to a single DNA.  The scientists studied the σ54 RNA polymerase holoenzyme, an RNA polymerase found in most species of bacteria.  Surprisingly, none of the three predictions of the FD model that the experiments tested were found to be valid, demonstrating that target finding by the polymerase is not accelerated by sliding along DNA.  Friedman and colleagues instead propose that RNA polymerases are present in such large numbers that they can diffuse through the cell and efficiently bind to their target sites directly.  The absence of FD may explain how other proteins can bind to positions on the DNA that flank gene start sites and yet not interfere with RNA polymerase finding the gene.

Is this the end of the story? Not likely, given previous publications suggesting FD plays a role for some other DNA binding proteins. Using single-molecule techniques like those developed in the Gelles lab, scientists in next few years should give us a better idea if FD is very rare or very common. [editor: as a chemical engineer, I’m sad to see FD not have a role — it seemed like such a nice theory…]

Friedman LJ, Mumm JP, Gelles J. RNA polymerase approaches its promoter without long-range sliding along DNA.  Proc Natl Acad Sci U S A. 2013 May 29. [Epub ahead of print]

 

 

Dogic Lab Wins Andor Insight Award

The ‘Insight Awards‘  is a video contest showcasing research imagery from the physical and life sciences which utilize Andor technology to capture data.  This year, the Dogic Lab submitted a research video to the competition and garnered first prize in the Physical Sciences division for their video of Oscillating Microtubule Bundles.

From the competition notes:

Microtubules are a bio-polymer composed of the protein tubulin and are used extensively in the cell for cellular division, cell motility, and transportation of cargo within the cell. Here, we investigate the material properties of mixtures of microtubules, a depletion agent, and the molecular motor Kinesin. The microtubules, driven by Kinesin motors, spontaneously organize into bundles of microtubules that oscillate in a manner reminiscent of flagella and cilia found in biology. This engineered system will allow us to studying systems of self-propelled and self-organized matter that exist far from equilibrium in the field known as Active Matter.

We use standard fluorescent microscopy to image labeled microtubules in a thin, flow cell microscope chamber. An Andor Clara camera was used in conjunction with a Nikon Ti Eclipse microscope to capture this video.

Video and Entry by Stephen DeCamp.

For this, and more videos from the Dogic Lab, visit their YouTube page or their website at Brandeis University.

John Lowenstein (1926-2012)

Professor Gregory Petsko delivered the following tribute for John Lowenstein at Brandeis University Faculty Meeting late last year:

lowensteinJohn Lowenstein, who passed away from pancreatic cancer on November 3, 2012 at the age of 86, joined the Brandeis community in 1958 as a Senior Research Fellow, and became a member of the faculty two years later. From 1974-1995 he held the Helen Rubenstein Chair in Biochemistry; and he was also chair of the department in the 1990s.  John was not only a highly accomplished scientist; he was also an extraordinarily literate man, well versed in English, Russian and German literature, and a staunch devotee of opera, too. Even after his retirement in 2008, he continued to pursue his research interests and to work with students – he continued, in fact, to supervise an undergraduate until a few weeks before he died.

Those are the bare bones facts.  Let me tell you the story.  Many of you may know that John was one of the first members of the Biochemistry Department.  He came in the fall of 1958.  He’d been a Fellow at Oxford University, a position that allowed him a lot of independence, so when Mary Ellen Jones persuaded Nate Kaplan, the legendary founder of the department, to offer him a job, John already had the beginnings of a research program going.  He accepted the offer because America was, at that time, a better place for his wife, who was a clinician.  So he actually came here as an accompanying spouse (he once told me that he considered that a surprisingly liberated role for a man in the 1950s).  Before leaving England, he wrote to both the NIH and NSF to ask if it was OK for a foreigner to apply for a research grant; when they said it was, he wrote two different proposals, one to each of them.  He thought it was unethical to ask for salary on a grant, so he didn’t.  To his surprise, both grants were funded, so he ended up with full research support but no salary support.  Clearly, as we all know, Brandeis is a perfect choice for someone who wants to work without a salary!

Somebody then suggested he write a fellowship proposal, which he did, to the Helen Hay Whitney Foundation.  That was at the time, and still is, one of the most prestigious fellowships in the sciences.  Of course, he got that too, so when he finally showed up at Brandeis as, in essence, a postdoc, he had two grants and full salary support – more than most of the faculty!  Three weeks after he arrived, he started to lecture in Biochemistry on the 3rd floor of Kalman.  John once told me he was delighted that he was able to say that he had outlived that building!  Within 6 years of his arrivak, the Biochemistry Department was listed among the top 10 departments in the country, and it remained there until the mid-70s, when the practice of ranking departments stopped. 

After less than 2 years as a Whitney Fellow at Brandeis, John was already getting offers of faculty positions from other institutions for his work on nonenzymatic phosphate transfer by ATP, a very important process that he discovered.  Kaplan talked him out of considering most of them, but when one came from Tufts, Kaplan immediately promoted him to assistant professor.  By then, John had overcome his ethical objections to putting his salary on research grants…

purine nucleotide cycle

By the early 1970s, John had worked out the function of the important enzyme AMP-deaminase, the founding member of a family of enzymes that are very important in health and disease.  He then went on to do something only a handful of scientists have ever done: he discovered a metabolic pathway, the purine nucleotide cycle that AMP deaminase functions in.  This ought to be called the Lowenstein Cycle, but John once told me that if you discover something so important that you don’t have to name it after yourself, you’ve really done something special!

John always ran a small research lab but in many ways he ran the department for quite some time.  He had served on every possible departmental committee, popular and unpopular, sometimes all at the same time, or at least it seemed that way to him!  He was Chair of the Department in the early 1990s.  When I became chair of the department, a few years ago, I immediately sought out his advice.  He said, “Greg, my advice to you is to start drinking heavily.” 

He taught Biochem 101, the department’s signature graduate course, for many years, and then led the movement for the department to teach undergraduates.  Putting his money where his mouth was, he then taught the basic undergraduate course, Biochem 100 – sometimes two sections a day – until 2005. 

John had three sons; his middle son is a scientist at Johns Hopkins; the youngest is a professor of music, and his oldest is a businessman.  John was very, very proud of his family, but said to me on more than one occasion that the major place in his life, outside that family, was Brandeis.  It’s no accident that, for many years, John was the faculty member all the graduate students went to for advice.  He had a pilot’s license and used to fly sailplanes, but I think the students were quick to identify someone who was always good at keeping his feet on the ground. 

John once said that if he were independently wealthy he would still do what he does.  I was thrilled to hear that because it meant that, even after becoming emeritus, John would still be around a lot, and he was.  The best raconteur in the department, John had a warm, wise and often dryly funny story for every occasion.  It was part of the way he imparted his enormous common sense.  No one here meant more to me as a colleague, a friend, and a role model. He said to me that, when he retired, it meant the Biochemistry Department was going to gain in reputation, because he was going to have much more time for research… Few did it better, or with more style. 

On the occasion of his retirement, I asked John to sum up his years at Brandeis.  He just smiled and said, in his typical understated way, “I like to think I’ve been a cog in something worthwhile.”  We should all be such a cog!

Remembrances may be made to the American Jewish Joint Distribution Committee, www.jdc.org.

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