Biochemistry Senior Research Talks

It’s also the season for Senior Honors / Masters Thesis talks…


Annual Senior Research Talks
2009/2010 Biochemistry Honors and BS/MS Candidates

Friday, April  23, 11:30-1:30pm – G-zang 122

Clarence Friedman – BS/MS

Characterization of 1-d-deoxyxylulose reductoisomerase
Advisor: Dan Oprian

Stefan Isaac  – BS/MS

Functional Characterization and in silico Modeling of HlyU
Advisors:  Dagmar Ringe/Greg Petsko

Seth Lieblich BS/MS

Bacterial Gene Repressors
Advisor: Dagmar Ringe

Miranda Patton BS/MS

Mutation of the Active Site of IMP Dehydrogenase, to Find a Novel Mutant and Create a Hybrid GMP Reductase
Advisor:  Liz Hedstrom

Nat Lazar BS

We are superfamily: bioinformatic and biochemical analyses of protein evolution
Advisor:  Douglas Theobald

Kanchana Ravichandran BS

Formation of heterotetramers between the human isozymes of Inosine 5’-Monophosphate Dehydrogenase
Advisor:  Liz Hedstrom

Seth Robey BS

Streamlining C1C-0 Purification and Examining the pH Dependence of an Amino Acid Transporter
Advisor:  Chris Miller

Kenta Yamamoto BS

The Type-1 Insulin-Like Growth Factor in Cancer and Hematopoiesis
Advisor: Ruibao Ren

Everyone is welcome and encouraged to come.  Pizza will be provided.

PhD Defense Season

It’s the season for PhD defenses…

  • Apr 20: Megan Zahniser (Biochemistry), On the structure of Benzaldehyde Dehydrogenase, a Class 3 Aldehyde Dehydrogenase from Pseudomonas putida – 2pm, Rosenstiel Penthouse
  • Apr 21: Chris Hoefler (Biochemistry/Bioorganic Chemistry). Inhibitors of IMPDH: Tools for Probing Mechanism and Function – 3:40 pm, Gerstenzang 122
  • Apr 22: Tepring Piquado (Neuroscience), Language and the aging brain – Thu 4/22/2010, 2 pm, Volen 201
  • Apr 23: Suvi Jain (Molecular and Cell Biology), Regulation of DNA Double-Strand Break Repair by the Recombination Execution Checkpoint in Saccharomyces cerevisiae – 3:30 pm, Rosenstiel 118
  • Apr 29: Ben Cuiffo (Molecular and Cell Biology), Targeting RAS palmitoylation in hematological malignancies – 2 pm, Abelson 131

Prodrug activation by Cryptosporidium thymidine kinase

Xin Sun, a Biochemistry grad student from the Hedstrom Lab, discusses her recent paper in J. Biol. Chem.:

I get to say the word “diarrhea” within the first 1-2 sentences of
talking to a stranger about what I work on, and the look I get back is always amusing. We work on developing inhibitors against a human pathogen called Cryptosporidium parvum, a nasty little parasite that causes the aforementioned diarrhea. We specifically zoomed in on the parasite’s nucleotide synthesis pathways to look for potential drug targets. Our recent paper looked at the enyzme thymidine kinase from the parasite, and studied its role in activating a prodrug that we showed to be effective in reducing parasite load in both a cell culture assay,  and in a mouse model.

Chloride channels and antiport mechanism

In a new paper in Journal of General Physiology, Brandeis postdoc Hyun-Ho Lim and Professor Christopher Miller examine the detailed mechanism by which a chloride transporter protein works. In particular, this protein does a rather crazy thing: it stoichiometrically swaps a proton on one side of the membrane for two Cl- ions on the other, and countertransports them across the membrane.  In this work, the authors identify a special glutamate residue on the cytoplasmic side of the protein that is responsible for picking up protons on that side in order to carry out this “antiport” mechanism.  (That glutamate is indicated by the spacefilled residue with red oxygen atoms in this depiction of the dimeric protein.)

Actin "pointers" for EM labeling

Single particle electron microscopy reconstruction can be a powerful tool for determining the structure of large protein complexes. One limitation of the technique is the difficulty in coming up with specific labels for the protein that can be visualized with EM. In a new paper in RNA, postdoc Beth Stroupe and coworkers show that the use of the actin-nucleating protein Spire as a cloneable tag allows them to nucleate actin filaments that then “point” to the location of the tag in the complex seen in EM, and applied the technique to their studies of the C complex spliceosome.

Structural diversity of amyloid fibrils

Amyloid fibrils are associated with Alzheimer’s disease. In a recent study published in J. Mol. Biol., Nikolaus Grigorieff and coworkers used electron cyro-microscopy to study these structures and show that these fibrils coexisting in solution can be extremely polymorphic.

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