Undergraduate Research Opportunities in Biochemistr

The overall goal of the Center for Biochemistry and Biophysics CBB, a unit of the Department of Chemistry at SUNYA, is to attract more researchers, to strengthen existing programs and to develop research programs on biological, bioorganic, biomaterial or bionanotechnological problems.

Research interests: Using mass spectroscopy to investigate macromolecular complexes, protein-nucleic acid interactions in viruses, high-resolution mass spectrometry, and RNA-based drug therapeutics.

My lab is interested in the following questions: How is ribosome composition altered in cells during stress and during a viral infection? How does ribosome composition regulate how much and which proteins are synthesized? Are ribosomes in cancer cells different from ribosomes in healthy cells? Cab we use ribosome modifications to identify novel biomarkers for early cancer detection?

Research interests: analytical chemistry, physical chemistry, biochemistry, laser spectroscopy.

We study the molecular structure, function, and mechanism of proteins or complexes related to bacterial or viral infection and host response, using crystallography, biochemistry, and molecular biology. Current projects include bacterial and viral superantigens, signaling proteins involved in apoptosis and stem cell regulation, and rational drug design against key viral enzymes.

Our laboratory is interested in understanding the structure-function relationship and the mechanism of regulation of glutamate ion channel receptors. These receptors mediate rapid synaptic neurotransmission and are indispensable in the brain function, such as memory and learning. Abnormal receptor activity, however, has been implicated in various neurological diseases and disorders

The focus of Dr. McDonough's laboratory is gene regulation in the context of bacterial pathogenesis, or the means by which bacteria cause disease. The team is primarily interested in two well-known pathogens: Mycobacterium tuberculosis, the bacterium that causes TB, and Yersinia pestis, the etiologic agent of bubonic and pneumonic plague. The lab uses a variety of techniques in their studies with both pathogens, ranging from molecular genetics and biochemistry to bioinformatics, proteomics and fluorescence microscopy.

Areas of interest: DNA binding and bending proteins, role of DksA in cellular response to nutritional stress, role of Fis in E. coli, genes subject to Fis regulation, and mechanisms of Fis regulation

The Pager lab is interested in the interaction and mechanisms by which RNA viruses subvert the cellular RNA metabolism pathways. We are particularly intrigued by how flaviviruses such as hepatitis C virus and Dengue virus commandeer the host’s mRNA storage and decay machinery to successfully establish an infection.

The parasite Trypanosoma brucei is a blood-borne pathogen that causes both human and zoonotic disease. T. brucei and related trypanosomatids are early eukaryotes and successful pathogens. Currently no preventative therapies are available and treatment is difficult, despite our knowledge of several unique biological processes with the potential to be exploited as drug targets. One such unusual process is RNA editing. RNA editing is found in many organisms including plants, yeast, humans and other mammals, although the mechanisms of editing are distinct. Within the trypanosomatids RNA editing is achieved by the insertion of non-encoded uridines or the deletion of encoded uridines. In the most extreme cases over 50% of the mature mRNA is the result of post-transcriptional editing. Editing takes place exclusively in the mitochondria, where it is required in order to generate mature mRNAs competent for translation into the correct proteins, and is carried out by a large ribonucleoprotein complex. Our work focuses on the biochemistry of editing by this multiprotein complex. We have identified a protein, RNA-Editing Associated Protein-1 (REAP-1), which specifically recognizes RNAs requiring editing. Evidence suggests that REAP-1 acts as a recruitment factor to deliver RNAs to the editing complex. REAP-1 is one of only two proteins that have been identified as components not of the core catalytic complex but of a larger (35-40S) complex believed to function in vivo. Through a combination of genetic and biochemical approaches, current work in the lab involves understanding how REAP-1 specifically recognizes and binds to its RNA targets, identifying other proteins with which REAP-1 interacts and determining how REAP-1 influences editing complex assembly and regulation of RNA editing.

The underlying theme of studies in the Musah research lab is in the mechanisms by which the redox versatility of sulfur is exploited by Nature to solve challenging issues in the chemical biology of plants and some viruses. The development of spectroscopic and mass spectrometric tools and methods that can be used to probe reactions involving organosulfur species are also of interest, as the tracking of organosulfur reaction intermediates presents unique challenges not often encountered with other elements.

The goal of the Rangan Laboratory is to understand how a stem cell fate is initiated, maintained and terminated. Stem cells have the capacity to both self-renew and differentiate. Improper differentiation or self-renewal of stem cells can result in a loss of homeostasis, which has been implicated in human afflictions such as cancer and degenerative diseases.

Our research group focuses on the areas of bioelectronics and bionanotechnology. These approaches, often combined with biomolecular engineering, are a rapidly emerging field aimed at development biology-inspired intelligent sensing systems. Our multidisciplinary research approach combines fundamental studies with forward-looking engineering efforts. Some of the projects our group is interested in stem from the fields of biochemistry, analytical science and biotechnology. We are exploring the biorecognition of different characteristics, such as, ethnicity and gender of forensic subjects. These are based on biological markers, detection of toxic compounds such as organophosphates and biochemical steganographic and encryptic systems or "smart" biofuel cells and actuators.

Research interests: Structural studies of protein-protein interactions involved in cellular signal transduction, structural studies of endocytic proteins and their interactions, development of novel NMR methodologies to effectively study large bio-complexes

Areas of interest: molecular and cellular biology of transcription and signal transduction, aptamer-mediated multi-pathway control in living cells and organisms, and drug discovery and development for cancer

Research interests: Structure/function relationships of nucleic acids, RNA-targeted drug discovery, Novel RNA-based antimicrobial targets, Roles of modified nucleosides in tRNA, Nuclear magnetic resonance (NMR) of RNA, RNA-RNA and RNA-protein interactions