Program in Physical and Chemical Biology


Program Scholars 2008

Fida Abuisneineh
Investigation of LMNA Gene Mutations and their Affects on Gene Expression in E161K Dermal Fibroblast Cells
Faculty Mentor: Elizabeth McNally

The study of LMNA mutations has resulted in the identification of a rare group of genetic disorders that disrupt the nuclear lamina of the nuclear envelope. Such defects of the nuclear lamina are known as laminopathies, and they are associated with a variety of clinical symptoms, including cardiac muscular dystrophy, lipodystrophy, and progeria. There are currently two hypotheses proposed to explain the wide range of phenotypes associated with LMNA mutations: the mechanical fragility hypothesis and the gene regulation read more...

Kevin Dalton
A Genetic, Biochemical, and Structural Analysis of Chromosomally-encoded Toxin/Antitoxin Systems
Faculty Mentor: Sean Crosson

The parDE toxin/antitoxin (TA) proteins form a plasmid-addiction system which stabilizes low copy number plasmids in bacterial populations by facilitating post-segregational death of daughter cells lacking the plasmid. Recently, gene pairs homologous to the parDE system have been identified on several bacterial chromosomes. I will examine these chromosomally encoded TA proteins using a combination of biochemical and genetic analyses.

Michael Jackson
Investigating the Structure and Function of a Newly Evolved Gene (Spx) in Drosophila
Faculty Mentor: Manyuan Long

The goal of this project is to investigate the structure and function of a newly evolved gene known as Spx. By analyzing collected sequence data we may gain a better understanding about the structure of Spx, which is a D. Melanogaster specific chimeric gene, and if its regulatory sequence and the recruited region were previously originated from an existing gene. Given that there is a lack of understanding of the phenotypic and functional evolution of read more...

Paul Kim
Characterization of Rdh54/Tid1 DNA Loop Extrusion and Stripase Activity via Atomic Force Microscopy
Faculty Mentor: Doug Bishop

Homologous recombination factor Rdh54/Tid1 is a repair protein specific to meiotic recombination. Rather than operating as a DNA helicase however, there is evidence that Rdh54 function encompasses a much broader range of activity including stabilizing nucleoprotein filaments, operating as a motor protein that translocates on duplex DNA, aiding in the search for homology, and acting as a DNA stripase by dissociating helical filaments read more...

Alexander Muir
Identification and Confirmation of Eyes absent (Eya) Phosphatase Substrates
Faculty Mentor: Ilaria Rebay

Eyes absent (Eya) was initially characterized as a transcriptional coactivator belonging to the Drosophila retinal determination gene network. More recently, it has been demonstrated that Eya also has protein tyrosine phophatase (PTP) activity, and this enzymatic activity is necessary for normal development of the Drosophila eye. The discovery of a bifunctional transcription factor suggests a novel degree of complexity to this transcriptional network, such that a single factor may interface with developmental signals read more...

Issra Rashed
In Depth Look: Usefulness and Practicality of the Organic Chelate Bis(acetylacetonato)oxovanadium(IV) as an Uncompetitive Inhibitor of Protein Tyrosine Phosphatase-1B
Faculty Mentor: Marvin Makinen

Protein tyrosine phosphatases (PTPs) regulate important cellular processes and are, therefore, the object of a wide variety of inhibitor design studies for potential therapeutic application. Since there are over 100 protein tyrosine phosphatases identified in the human genome, finding or developing a specific inhibitor unique to any single phosphatase is difficult to achieve: this is especially due to similarities in active site structure. In the case of human read more...

Jonathan Sellon
Cellular Mechanosensation: Correlating Cytoskeletal Protein Expression to Varying Substrate Stiffness
Faculty Mentor: Margaret Gardel

Cell migration requires generation of mechanical forces in the actin cytoskeleton based on actin filament (F-actin) polymerization and myosin-II-mediated forces to the extracellular matrix, creating focal adhesions sites. The exact manner through which cytoskeletal proteins are recruited to create these focal adhesions in response to internal and external stresses is larger unknown. This study aims to demonstrate the levels of various cytoskeletal read more...

Nora Yucel
Design of an enhanced, organophosphate neurotoxin detection and remediation system in Saccharomyces cerevisiae
Faculty Mentor: Stephen Kron

Organophophates (OPs) are highly toxic compounds used as pesticides and chemical ware-fare agents (CWAs) around the world. As a result, much research has been done to create efficient, eco-friendly and economically feasible systems of OP detection and biodegradation. The aim of this proposal is to develop a highly efficient whole-cell S. cerevisiae sensor and biocatalyst for the detection and remediation of the model organophosphate compound paraoxon and its degradation products. A library of S. cerevisiae genes induced in the presence of paraoxon and paraoxon-hydrolysis compiled Schofield, et al. will be used in conjunction with organophosphate hydrolase (OPH) isolated from Flavobacterium sp. for read more...

Wenjing Zong
Mechanisms of formin-mediated actin assembly
Faculty Mentor: David Kovar

Actin filaments partake in various cellular activities. The mechanism with which cells coordinate actin filament assembly during such activities is important for our understanding of the cell and may lead to potential advancement in cancer therapy. Recent studies have found that a protein called formin mediates the assembly of actin in all types of eukaryotic cells including fission yeast. There are three formins in fission yeast that are each required for a different cellular process Cdc12p-cytokinesis, For3p-polarized read more...