Skye Fishbein ’12 Wins Fulbright

Skye Fishbein ’12 has received a Fulbright grant to perform research at Stellenbosch University in South Africa. Her research project will look at interactions between TB and HIV in patients with both (“A Study of the Synergy between Mycobacterial Infections and HIV in Capetown, South Africa”) . She also plans to volunteer with the Kick TB program, which empowers children with an awareness of TB/HIV through an integration of soccer and public health awareness. She graduated with a BS/MS  in biology and a minor in mathematics.

For more about the program and other Brandeis winner, see story at Brandeis NOW.

JBS Computer Science Product Showcase 2012

The JBS Computer Science Product Showcase will take place on Thursday 8/2/2012 in the main Auditorium of the Mandel Center from 2:00-4:00

Tim Hickey and Pito Salas will present a short overview of this year’s Justice Brandeis Semester in Web Applications and Social Networks, and then each of four student groups will present the product they created this summer. There are four products that involve a database-backed web application and possibly a mobile component as well. The products are listed below, with a little suggestion of their purpose:

  • Spy Game: a new genre of Augmented Reality phone games
  • WikiWitness: an archive for first person reports of historical events
  • LinkedIn for volunteers
  • Where’s My Lane: civic hacking for Boston bike commuters

The JBS program covered not only the technical aspects of how to create a database backed website that could efficiently handle hundreds of millions of records, but also covered the practice of computer science and software entrepreneurship. The students will give 10-15 minute presentations with 5-10 minutes of discussion.

Followup: story at BrandeisNOW

Natural Language Annotation for Machine Learning

From the Computer Science Department blog:

James Pustejovsky and his student Amber Stubbs have a new book “Natural Language Annotation for Machine Learning” out from O’Reilly Books and Media: “Systems exist for analyzing existing corpora, but making a new corpus can be extremely complex. To help you build a foundation for your own machine learning goals, this easy-to-use guide includes case studies that demonstrate four different annotation tasks in detail. You’ll also learn how to use a lightweight software package for annotating texts and adjudicating the annotations.”

ACA Symposium to honor Foxman

At the 2012 Meeting of the American Crystallographic Association, to be held in Boston starting this weekend, one of the highlights will be a session entitled “Transactions: Transformations and Structural Oddities in Molecular Crystals: In Honor of Bruce M. Foxman“. This session, organized to honor \Professor of Chemistry Bruce Foxman “for his contributions to the field of solid state chemistry and his dedication to teaching” on the occasion of his 7oth birthday. Foxman’s research over the years has involved solid state reactions and polymorphism of molecular crystals, and one of his greatest contributions to the field is a series of online tutorials, including one on Symmetry and Space Groups, another on Bruker’s APEX 2 software. and a third aimed at high school students. The symposium will be held in two parts on Sunday July 29, and Wednesday, August 1, at the ACA meeting in Boston.

Unraveling mutations in pediatric brain cancer

Medulloblastoma is the most common malignant brain tumor of childhood, with an overall mortality of 40 to 50 percent. Surviving children often have significant long-term cognitive and physical sequelae resulting from existing treatments. Therefore, identifying and understanding the genetic events that drive these tumors is critical for the development of more effective therapies.

In the 2 August issue of the journal Nature, Brandeis Biochemistry faculty member Daniel Pomeranz Krummel contributed his structural biological expertise in collaboration with colleagues at Children’s Hospital Boston, Dana-Farber Cancer Institute, Harvard University, the Broad Institute (MIT), Stanford and the Hospital for Sick Children in Toronto. The paper titled, “Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations,” unravels a landscape of mutations that are peculiar to medulloblastomas. This paper represents a landmark study of medulloblastomas. More specifically, Pomeranz Krummel’s collaborators noticed that a protein called DDX3X had numerous mutations in medulloblastoma. Pomeranz Krummel was able to create a structural model of DDX3X that provided insight into the functional significance of the critical mutations in children with medulloblastoma (below, image).

DDX3X is an ATP-dependent RNA helicase. RNA helicases are fascinating proteins that function to drive the restructuring of RNA and/or RNA-protein assemblies, and have proven to be of great importance in cancer biology and HIV research. Pomeranz Krummel’s long-standing interest is in RNA-protein interactions and application of methods to visualize the enzymes critical to processing of RNA in the human cell. Thus, thinking about the structure-function relationship of this RNA helicase DDX3X was a problem of much interest to Pomeranz Krummel. This collaboration involved forging links between basic and translational scientists, thus giving rise to promising new horizons of treatment options for children with medulloblastoma.



Mushroom tyrosinase and the HA tag: a new method for protein labeling

In a new paper in ChemBioChem, researchers from the Hedstrom lab describe a novel method for protein labeling that is versatile and selective.  The method involves the modification of HA tags (a short amino acid sequence commonly used as an epitope tag that contains several tyrosines) selectively in a variety of ways using mushroom tyrosinase. This cheap and versatile chemical biological tool can effect HA tag cleavage, aggregation, or functionalization by changing conditions. The method for dye-labeling HA-tagged proteins has been applied in both E coli and mammalian cell lysates.

Long MJ, Hedstrom L. Mushroom Tyrosinase Oxidizes Tyrosine-Rich Sequences to Allow Selective Protein Functionalization. Chembiochem : a European journal of chemical biology. 2012. (DOI: 10.1002/cbic.201100792)

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