Sprout Grant Winners Announced

19 06 2013

Winners of the 2013 Sprout Grant competition held by the Brandeis Office of Technology and Licensing have been announced. Sprout grants support research that is “novel, patentable and [has] commercial potential“, and encourage students to think about new and different ways to apply their basic science for practical good. Each team applying for a grant must be led by a Brandeis student or postdoc (noted in asterisks below), who were responsible for presenting their proposals to the review panel.

Teams that received funding.

  • Marcus Long (*), Ann Lawson, Lior Rozhansky ’15, and Liz Hedstrom: $20,000 to develop novel inhibitors of deubiquitinating enzymes;
  • Michael Heymann (*), Achini Opathalage, Dongshin Kim, and Seth Fraden: $5,500 for its development of CrystalChip;
  • Michael Spellberg (*), Calla Olson, Marissa Donovan, and Mike Marr: $10,000 to develop a tool to purify Calmodulin-tagged recombinant proteins;
  • Julian Eskin (*) and Bruce Goode: $2,000 for work on a rapid and efficient kit to purify actin;
  • Eugene Goncharov ’13 (*), Yuval Galor ’15,  and Alex Bardasu ’15: $2,500 towards development of their iPhone app LineSaver, which collects data on local hotspots and gives users an estimated wait-time for restaurants, clubs and tourist attractions.

You can read more at BrandeisNOW



Simulations Say Viral Genome Lengths are Optimal for Capsid Assembly

14 06 2013

Viruses are infectious agents made up of proteins and a genome made of DNA or RNA. Upon infecting a host cell, viruses hijack the cell’s gene expression machinery and force it to produce copies of the viral genome and proteins, which then assemble into new viruses that can eventually infect other host cells. Because assembly is an essential step in the viral life cycle, understanding how this process occurs could significantly advance the fight against viral diseases.

In many viral families, a protein shell called a capsid forms around the viral genome during the assembly process. Capsids can also assemble around nucleic acids in solution, indicating that a host cell is not required for their formation. Since capsid proteins are positively charged, and nucleic acids are negatively charged, electrostatic interactions between the two are thought to be important in capsid assembly. Current questions of interest are how structural features of the viral genome affect assembly, and why the negative charge on viral genomes is actually far greater than the positive charge on capsids. These questions are difficult to address experimentally because most of the intermediates that form during virus assembly are too short-lived to be imaged.

hagan-capsid-sim

Snapshots from a computer simulation in which model capsid subunits (blue) assemble around a linear, negatively charged polymer (red). Positive charges on the capsid proteins are shown in yellow.

In a new paper in eLife, Brandeis postdoc Jason Perlmutter, Physics grad student Cong Qiao, and Associate Professor Michael Hagan have used state of the art computational methods and advances in graphical processing units (on our High Performance Computing cluster) to produce the most realistic model of capsid assembly to date. They showed that the stability of the complex formed between the nucleic acid and the capsid depends on the length of the viral genome. Yield was highest for genomes within a certain range of lengths, and capsids that assembled around longer or shorter genomes tended to be malformed.

Perlmutter et al. also explored how structural features of the virus — including base-pairing between viral nucleic acids, and the size and charge of the capsid — determine the optimal length of the viral genome. When they included structural data from real viruses in their simulations and predicted the optimal lengths for the viral genome, the results were very similar to those seen in existing viruses. This indicates that the structure of the viral genome has been optimized to promote packaging into capsids. Understanding this relationship between structure and packaging will make it easier to develop antiviral agents that thwart or misdirect virus assembly, and could aid the redesign of viruses for use in gene therapy and drug delivery.

Perlmutter JD, Qiao C, Hagan MF. Viral genome structures are optimal for capsid assembly. eLife 2013;2:e00632



Brandeis Café Science held this Monday, June 3 with Prof. Bulbul Chakraborty

2 06 2013

sandStrolling on the beach we notice that our feet create dry spots around them.  The sand around the leopard’s feet flows while it speeds along the desert.  Close to the ocean, we often notice dark striations on the sand.  These phenomena are so familiar to us that we hardly ever pause to wonder their origin.  The surprising fact is that we do not really understand why sand behaves the way it does.

Join us THIS Monday, June 3, at 6:00pm at the Elephant Walk in Waltham for our next Brandeis Café Science! Professor of Physics Bulbul Chakraborty will take you on a journey through the world of granular matter: matter made out of large objects for which gravity is important and temperature is not.  This is stuff that we see around all around us but know very little about.

For the last five years Prof. Chakraborty has been working on developing a theory of granular materials that can predict their collective behavior. How do sand grains assemble into sand dunes and what causes them to avalanche?  Her research has led to a new paradigm for the emergence of solid-like properties.  Prof. Chakraborty will take you along on her journey to the discovery of this new paradigm as she asks you the questions that she asked herself.



Class of 2013 Physics Majors Announce Their Plans

14 05 2013

cohn_suman2

Eight of our graduated physics majors have announced their future plans:

Aaron Chevalier will work at the Broad Institute in Cambridge, Mass as an Associate Computational Biologist.

Rebecca Cohn will attend George Washington University in Washington, D.C. to pursue a Master of Education in secondary education.

Michal Dichter
will begin a PhD program at the University of New Mexico in Albuquerque, N.M., possibly in geophysics.

Aaron Chevalier


Valerie Marchenko
will begin her PhD in physics at Brown University, Providence, R.I.

Adam Ollanik
will pursue a PhD in physics at Tulane University, New Orleans,La.


Asher Preska Steinberg
will work towards a PhD in chemical physics at California Institute of  Technology.

Prasanna Suman
will work in computer programming for the summer.

Tianyun Wu
will begin a Master of Science in computation for design and optimization at MIT, Cambridge, Mass. helen4



Asher Preska Steinberg ’13 receives NSF Graduate Fellowship

10 05 2013

steinbergAsher Preska Steinberg ’13, who majored in both chemistry and physics at Brandeis, has been awarded a National Science Foundation Graduate Research Fellowship in materials research.  The fellowships, which are awarded based on a national competition, provide three full years of support for Ph.D. research and are highly valued by students and institutions.

At Brandeis, Asher worked on his senior thesis in chemistry with Professor Milos Dolnik as part of the Epstein Group. They studied the growth dynamics of Turing patterns in photosensitive reaction-diffusion systems. As part of the 2011 NYU MRSEC Research Experiences for Undergraduates (REU) program Asher worked with Paul Chaikin to study active colloids, and they recently published an article in Science entitled “Living Crystals of Light-Activated Colloidal Surfers”. The article received attention from the press, including the LA Times, Wired, and Ars Technica.  Last summer Asher participated in the Columbia EFRC Research Program for Undergraduates (RPU) and studied silver plasmonic nanoparticles with Louis Brus.

Asher will be attending California Institute of Technology this coming fall in the field of Chemical Physics.



Senior Honors Thesis Defenses for Physics Majors, Thursday May 9

8 05 2013

Senior physics majors will present their honors thesis defenses Thursday,
May 9 from 1:30pm to 4:00pm in Abelson 229.  Light refreshments.

Schedule:

1:30pm – 2:00pm, Michal Dichter
Advisers: Profs. Aparna Baskaran and Bulbul Chakraborty
“Signatures of Incipient Jamming in Collisional Hopper Flows”

2:00pm – 2:30pm, Walter Simons-Rose
Advisers: Profs. Aparna Baskaran and Jane’ Kondev
“The Effects of Confinement in Determining Chemical Rates”

2:30pm – 3:00pm, Adam Ollanik
Advisers: Profs.  Seth Fraden, Zvonimir Dogic and Jane’ Kondev
“Techniques in Microfluidics”

3:00pm – 3:30pm, Aaron Chevalier
Advisers: Profs. David Roberts and John Wardle
“Search for twisted polarization in arcsecond scale Quasar jets”

3:30pm – 4:00pm, Valerie Marchenko
Advisers: Profs. John Wardle and Richard Fell
“Testing the iC/CMB Model for X-ray Emission: Constraining the Orientation
of Extragalactic Jets”

 

Poster 2013



The Genetics Training Grant hosts a panel discussion and lunch focused on careers outside academia

3 05 2013

This past Monday, April 29th, students and post-docs, eager to learn more about careers outside of academia, had the opportunity to hear from, and question, panelist who have successfully harnessed their PhD experience to excel in non-academic careers. The event, hosted by the Genetics Training Grant, brought together panelists from several different fields, including scientific publishing, pharmaceutical research, consulting, and intellectual property law. The panelists were Priya Budde, Reviews Editor, The Journal of Cell Biology; Sadanand Vodala, Research Scientist, ARIAD Pharmaceuticals; Derek Buhl, Principal Scientist, Pfizer Neuroscience; Peter Bak, Consultant, Back Bay Life Science Advisors; and John Garvey, Partner, K&L Gates LLP. Each panelist spoke about their background in academia, how they made the transition to their current position, and fielded numerous questions from the audience both during the panel and at the networking lunch that followed.

The panelists gave the audience a sense of what their specific careers entail, and how skills they had acquired during their PhDs were highly relevant to their current work. Some of the transferable skills mentioned included critical thinking and the ability to quickly synthesize information and distill what is most important and interesting about a given scientific finding. These skills enabled them to be highly effective in their jobs, whether efficiently evaluating scientific manuscripts as an editor, or determining the crux of a client’s research as a consultant or intellectual property lawyer.

Having completed their transition from academia to the business world, panelists were able to highlight some of key cultural and practical differences associated with working in a profit-driven industry. While Derek described his lab at Pfizer as largely mimicking an academic environment (minus the need to perpetually write grants), he and other panelists noted that, unlike academia, business evaluations are based almost exclusively on having achieved specific pre-determined goals. On the upside, for those who exceed expectations in business, there are lots of opportunities to move up the ladder. Other differences that panelists encountered in their non-academic professions included firmer deadlines, higher dressing standards, and less flexible hours.

While the majority of the discussion was specific to the panelists’ career paths, much of the advice applied to career searches in general. The importance of good networking was emphasized. Job seekers were encouraged to make the most of their networks – and their network’s network as well. Each panelist explained how he or she had acquired their job through a combination of effective networking, being proactive, and in some cases, luck. Panelists were quick to point out, though, that time and effort invested were positively correlated with “luck.”

Panelists stressed that effective networking required quickly following through with contacts, and being prepared to impress key contacts with excellent questions that demonstrate your research on a given company. They encouraged the audience to be proactive, and if needed persistent, in reaching out to people whose work they find interesting. Several panelists also emphasized the benefits of acquiring job-related experience. They noted this was a good way to both boost your resume and get a better sense of whether a given profession is the right fit for you. For example, John Garvey recommended joining a consulting or biotech club, and/or taking a business class. Getting involved in job-related activities is also excellent ways to establish good contacts for networking.

Overall the panelist presented several attractive alternatives to a traditional academic career. By carefully analyzing his or her personality, strengths, and working style, each of them had found a rewarding career that effectively utilized their scientific background/training. Priya, the editor, described how she enjoyed being able to see where scientific fields are going and staying up to date with the latest scientific breakthroughs. Derek, the pharmaceutical researcher, explained how it was gratifying for him to be working directly to develop drugs that could benefit people. John, the lawyer, explained how his work solving business problems was important because it helped provide pharmaceutical companies with the financial resources to bring new life-saving drugs to market. The general take-home message from all of the panelists was that, using the right career strategies, one can effectively use one’s PhD as a launching point to successfully pursue many different avenues outside of academia. Those interested in getting a better sense of what career might be a good fit for them are encouraged to visit http://myidp.sciencecareers.org and fill out the survey.

What do Brandeis life science PhD students go on to do?



Brandeis-India Science Scholars Applications Due May 10

29 04 2013

We are excited to be offering the opportunity for undergraduate students to study courses in Biological Sciences, Chemical Sciences, Electrical Sciences, Mathematical and Physical Sciences, Mechanical Sciences, and Computer Sciences at the Indian Institute of Science, the premier science research and education institution in India, beginning in Spring 2014.

Please visit the Brandeis-India Science Scholars website for additional information and to access the application. Additional funding opportunities are available for this program through the Brandeis-India Initiative and the Physics Department.  More information about these opportunities is available in the financial section on the program website.

Application deadline: May 10th, 2013

Please feel free to contact Amber Thacher in the Office of Study Abroad with any questions about the program or application process.  athacher @t brandeis dot edu






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