Biology mentors and mentees needed

The Biology Undergraduate Peer Mentorship Program is a new initiative by the Biology Department and was created by Biology UDR, Dipal Savla. In the program, junior and senior Biology mentors will provide guidance to freshmen and sophomores mentees who are considering majoring in Biology. Oftentimes, new biology majors have a broad range of concerns such as what courses to take, when to take them, how to get involved in research, selecting and applying to internships and other experiential opportunities, and balancing the biology major with other academic and extracurricular interests. Through the program, mentors will be able to use their experience as Biology majors to help mentees work towards their goals as early as the first day of their freshman year. The specifics of the mentor-mentee relationship are flexible — Mentors and mentees can communicate over email or meet in person depending on what they decide.

The program was created in response to the diverse range of interests students have within the biology major. For example, students who are double majoring in Biology and Neuroscience have very different goals for their biology major than students double majoring in Biology and Environmental Studies. Thus, they would have differing choices for courses and internships. The students best able to advise these students would be those who have worked through similar issues.

If you are a rising freshman or sophomore considering a major in biology, and would like to join this program as a mentee, please email Dipal Savla (dsavla@brandeis.edu) for more information and an application.

Sprout Grant Winners 2011

Entrepreneurship is alive and well at Brandeis.

Last week, fourteen teams of Brandeis scientists presented their research to a panel of industry experts to compete for funding from the Brandeis University Virtual Incubator Sprout Grant Program.  The Virtual Incubator seeks to nurture and support entrepreneurial scientists at Brandeis by providing education, mentoring, networking and seed grants to help move their discoveries from the laboratory to the market.

Judges were impressed by the team presentations. The teams ranged from biologists who have projects that could be ready for licensing as early as next year, to computer science / IT entrepreneurship students with a web application that already has 1200 users.

“We were overwhelmed by the phenomenal proposals we received” says Irene Abrams, Associate Provost for Innovation.  “The response was incredible – with only a few weeks notice, 23 teams applied for Sprout Grants and 14 presented their proposals to the panel of judges.  I was impressed by the level of creativity among the applicants, and by the hard work the teams put into the presentations.  We only had $50,000, so we had to turn down many excellent applications, which we would have funded if we had more money.”

The 2011 winning projects are:

  • Generation Of A Rapid And Efficient Protein Knockout System, Lead Scientist:  Erin Jonasson (with Satoshi Yoshida)
  • Identification Of Molecules For Stabilizing DJ-1, A Protein Involved In Parkinson And Alzheimer Diseases. Lead Scientist: Joey Salisbury (with Brian Williams, Ala Nassar, Jeff Agar and Greg Petsko)
  • Targeting Oncogenic Ras For Protein Degradation, A Novel Approach To Therapy. Lead Scientist: Rory Coffey (with Marcus Long, Ruibao Ren, and Liz Hedstrom)
  • Identifying Pharmacological Chaperones that Promote Survival in Mouse Models of ALS, Lead Scientist: Jared Auclair (with Joey Salisbury, Dagmar Ringe, Greg Petsko, and Jeff Agar)
  • A Novel, Low Cost, Highly Sensitive Form Of Suppression PCR, Lead Scientist: Ken Sugino (with Sean O’Toole and Sacha Nelson)
  • Zen.Do, Team: Bill DeRusha, Joshua Silverman, Jason Urton (Computer Science)

see also: Brandeis NOW

Physics students present research at 20th Annual Berko Symposium on May 16

On Monday, May 16, the Physics Department will hold the Twentieth Annual Student Research Symposium in Memory of Professor Stephan Berko in Abelson 131. The symposium will end with talks by the two Berko Prize winning students, undergraduate Netta Engelhardt and graduate student Tim Sanchez. The whole department then gathers for a lunch of cold cuts, cookies and conversation. “It’s a great way to close out the academic year,” said Professor of Astrophysics and Department Chair John Wardle. “We come together to celebrate our students’ research and hear what the different research groups are doing.”

The undergraduate speakers will describe their senior thesis honors research. This is the final step in gaining an honors degree in physics, and most of them will also be co-authors on a paper published in a mainline science journal. The graduate student speakers are in the middle of their PhD research, and will disucss their progress and their goals.

The prize winners are nominated and chosen by the faculty for making particularly noteworthy progress in their research. Graduate student winner Sanchez’ talk is titled “Reconstructing cilia beating from the ground up.” He works in Professor Zvonimir Dogic’s lab studying soft condensed matter. Undergraduate winner Engelhardt’s talk is titled “A New Approach to Solving the Hermitian Yang-Mills Equations”. She works with Professors Matt Headrick and Bong Lian (Math) on problems in theoretical physics and string theory. The schedule for Monday morning and abstracts of all the talks can be found on the Physics Department website.

Sanchez’ research very much represents the growing interdisciplinary nature of science at Brandeis. Here, a physicist’s approach is used to study a biological organism. Professor Zvonimir Dogic says of his work “He has made a whole series of important discoveries that are going to have a measurable impact on a number of diverse fields ranging from cell biology, biophysics, soft matter physics and non-equilibrium statistical mechanics.  His discoveries have fundamentally transformed the direction of my laboratory and probably of many other laboratories as well.”

Engelhardt’s research is much more abstract and mathematical, and concerns fundamental problems in string theory, not usually an area tackled by undergraduates. Professor Headrick says “Netta really, really wants to be a theoretical physicist, preferably a string theorist. She has a passion for mathematics, physics, and the connections between them.” He adds that she is utterly fearless in tackling hard problems. Netta has been awarded an NSF Graduate Research Fellowship based on her undergraduate work here.  Next year she will enter graduate school at UC Santa Barbara and will likely work with eminent string theorist Gary Horowitz, who has already supervised the PhD research of two other Brandeis physics alumni, Matthew Roberts ’05, and Benson Way ’08.

This Student Research Symposium is now in its 20th year. The “First Annual…..” (two words which are always unwise to put next to each other) was initiated in 1992 by Wardle to honor Professor Stephan Berko, who had died suddenly the previous year. Family, friends and colleagues contributed to a fund to support and celebrate student research in his memory. This provides the prize money which Netta and Tim will share.

Stephan Berko was a brilliant and volatile experimental physicist who was one of the founding members of the physics department. He was born in Romania in 1924 and was a survivor of both the Auschwitz and Dachau concentration camps. He came to the United States under a Hillel Foundation scholarship and obtained his PhD at the University of Virginia. He came to Brandeis in 1961 to establish a program in experimental physics and worked tirelessly to build up the department. Together with Professors Karl Canter (dec. 2006) and Alan Mills (now at UC Riverside) he established Brandeis as a world center for research into positrons (the anti-matter mirror image of ordinary electrons). In a series of brilliant experiments they achieved many “firsts,” culminating in election to the National Academy of Sciences for Steve, and, it has been rumored, in a Nobel Prize nomination for the three of them. Steve was as passionate about teaching as he was about research, and when he died, it seemed most appropriate to honor his memory by celebrating the research of our graduate and undergraduate students. During the coffee break on Monday, we will show a movie of Steve lecturing on “cold fusion,” a headline-grabbing but phony claim for producing cheap energy from 1989.

PSD-95 contributes to synaptic homeostasis

Most people probably take it for granted that our brains rarely experience extreme activity conditions such as epilepsy (hyperactivity) or catatonia (hypoactivity). But to neuroscientists this stability is quite puzzling, because our brain activity is constantly perturbed by both changes in the external world and by internal changes that result from learning and development. Over the past two decades, research pioneered by Brandeis neuroscientists has suggested that our brains solve this stability problem by using a set of “homeostatic” plasticity mechanisms that stabilize neural excitability. One of the best documented such mechanisms is known as homeostatic synaptic scaling, in which synaptic strengths are up- or down-regulated to compensate for external fluctuations in drive. This form of plasticity acts like a “synaptic thermostat” to maintain neural excitability within an optimal operational range. However, the molecular mechanisms by which changes in activity lead to bidirectional adjustments in synaptic strength are not fully understood. Now a recent paper published in the Journal of Neuroscience by Brandeis graduate student Qian Sun (PhD ’11) and Professor Gina Turrigiano shows that two abundant and well-studied synaptic proteins, PSD-95 and PSD-93 (or Postsynaptic Density-95 and 93), are critical for the expression of synaptic scaling.

PSD-95/PSD-93 are rock stars of the synaptic world. They are important synaptic proteins that act as “scaffolds” to organize other synaptic proteins, and are known to contribute to several non-homeostatic forms of synaptic plasticity such as long term potentiation and long term depression. This new study adds an additional critical function to the already complex role that the PSD-95 protein family plays in synaptic plasticity, by showing that PSD-95 mediates both scaling up and scaling down, but that these two directions of plasticity are mediated by distinct aspects of PSD-95 function. Taken together with other work, this study suggests that PSD-95/PSD-93 serve as critical synaptic organizers ~ synaptic conductors, if you will ~ that can mediate many forms of synaptic plasticity through distinct protein-protein interactions within the synapse. This study provides a glimpse into the complexity of the synaptic machinery, and sheds important new light into the mechanisms of homeostatic synaptic scaling.

Mapping hydrogens in chymotrypsin structures with neutron diffraction

In a new paper “Time-of-flight neutron diffraction study of bovine γ-chymotrypsin at the Protein Crystallography Station” published in this month’s edition of the journal Acta Cryst F, Biochemistry grad student Louis Lazar and co-workers from the Petsko-Ringe lab report progress on their project to determine exact hydrogen positions in proteins using neutron diffraction.

Neutron diffraction was chosen, as opposed to X-ray diffraction, because one can visualize hydrogen species directly using neutrons, while it is extremely difficult and in most cases impossible to do so using X-ray diffraction. They chose the protein γ-chymotrypsin in order to determine hydrogen positions, as it fills the necessary requirements to be suitable for a neutron diffraction experiment. These requirements include a very large crystal size (> 1 mm3), moderately sized unit cell axes (no dimension greater than 100 Å), and it must be very stable as well as well-characterized. γ-chymotrypsin is the stereotypical serine protease, cleaving C-terminal to aliphatic and aromatic residues and containing a catalytic triad of serine, histidine, and aspartate. This information on hydrogen placement can then be applied to improve computational methods in which said placement is paramount, such as molecular modeling and rational drug design.

The paper details the collection of neutron data at pD (pH*) 7.1, with the help of the scientists at the Los Alamos National Laboratory. In particular, from the initial maps, they note that the catalytic histidine is doubly protonated, while the serine and aspartate making up the catalytic triad do not show density for the presence of deuterium. In order to complete the study of γ-chymotrypsin, data at a variety of pH values must be collected; data at pD (pH*) 5.6 has already been collected (Acta Cryst F65, 317-320), and data at pD (pH*) 9.0 will be collected in the future.

see also: full text of article (Brandeis users)

A molecular function of Zillion Different Screens protein explained

In a recent paper in Journal of Cell Biology entitled “Spatial regulation of Cdc55-PP2A by Zds1/Zds2 controls mitotic entry and mitotic exit in budding yeast“, Brandeis postdoctoral fellow Valentina Rossio and Assistant Professor of Biology Satoshi Yoshida reveal a molecular function of a mysterious protein Zds1.

The Zds1 protein in yeast  was identified some years ago in “a zillion different screens” for cell cycle mutants, stress response mutants, RNA metabolism mutants, etc., but the molecular function of the protein remained a mystery for more than 15 years. Rossio revealed that Zds1’s key target is a protein phosphatase 2A (PP2A) complex. She showed that Zds1 controls nucleocytoplasmic distribution of PP2A complex, and that this regulation is critical for cells to know when to enter and to exit from mitosis (picture below; cells lacking Zds proteins adopt an abnormal shape because of problems in mitosis). Rossio thinks all the other complicated phenotypes associated with ZDS1 can also be explained by PP2A regulation and is currently studying mechanistic details about the Zds1-PP2A interaction.

See also the accompanying commentary “Proteins keep Cdc55 in its place

Beckman Scholarships and URP Awards for Summer 2011

Beckman Scholars and Undergraduate Research Program Winners

Summer 2011

Beckman Scholars

The 2011 Beckman Scholars are:

Frank Scangarello (mentor: Suzanne Paradis, Biology)
Multivalent Metalloproteases Inhibitors to Increase Small Molecule Avidity and Selectivity to Study Semaphorin4D-Cleavage Mediated Synaptic Nerve Development

Zhequan Xu (mentor: Christine Thomas, Chemistry)
Novel Catalyst Design for Green Fuels

URP Recipients

(only students from the Division of Science are included in this list)

Heather Bernstein ’12 (Language & Linguistics; Neuroscience) with Prof. Stephen Van Hooser
Stimulus Therapy & its Implications for Rehabilitation: Using Channelrhodopsin-2 to determine spike time-dependent plasticity in neurons of the primary visual cortex in postnatal ferrets at eye opening

James En Wai Chin ’14 (Chemistry) with Prof. Lizbeth Hedstrom
IMP dehydrogenase nucleic acid association (How do IMPDH mutants affect IMPDH nucleic acid binding?)

Nimrod Deiss-Yehiely ’12 (Biology) with Prof. Sacha Nelson
A mouse model for Infantile Spasms involving TTX

Scott Finkelstein ’12 (Biology) with Prof. Paul Miller
Comparative Success of Strategies in a Continuous Iterated Prisoner’s Dilemma

Jessica Friedman ’13 (Biochemistry) with Prof. Tom Pochapsky
Insights into Substrate Recognition in Cytochrome P450cam

Julie Miller ’12 (Neuroscience) with Prof. Stephen Van Hooser
Roles of Inhibitory Neurons in Cortical Development

Anna Slavina ’12 (Psychology) with Prof. Art Wingfield
Selective syntactical attention among bilingual speakers

Sophie Travis ’13 (Biochemistry) with Prof. Dagmar Ringe
In vitro characterization of VPS35

Akash Vadalia ’12 (Biology; HSSP) with Prof. Angela Gutchess
Cross-Cultural Differences in the Specificity of Memory for Objects and Contexts

Alison White ’13 (Psychology) with Prof. Art Wingfield
Monitoring the Capacity of Short Term Memory

Abigail Zadina ’13 (Psychology) with Prof. Michael Rosbash
Huntington’s Disease: Insights into Mechanisms Involving Circadian Systems

Summer science classes at Brandeis

Enrollment for Summer School 2011 at Brandeis is open now (Session I starts on May 31). A number of science classes are being taught, from General Chemistry to Molecular Biotechnology. There is more information at the new Summer School Blog, including a story about Justin Dore, who is teaching a couple of the courses.

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