Georgina Bermudez Stony Brook University Junior Biomedical Engineering Faculty Mentor: Dr. Janet Andersen, Assistant Professor of Biomedical Engineering Laboratory of Dr. Nancy Reich Department of Pathology
The Response of Cells to Viral Infection The focus of our study is to investigate the role of Interferon Regulatory Factor 3 (IRF3) and a select set of Interferon Stimulated Genes (ISGs) in apoptosis or cell death. IRF3 is a transcription factor that increases the production of interferon after viral infection. Interferon is produced by the body's immune system in response to viral infections and it induces the expression of a different set of ISGs in nearby cells that produces antiviral products. In addition, IRF3 can induce the transcription of a select set of ISGs independent of interferon by forming the transcription factor complex called double-stranded RNA activated factor 1 (DRAF1). To study the effects of IRF3 and this set of ISGs in the absence of viral infection, we are generating an Inducible Mammalian Expression System, using the human cell line HEC 1B. Using the Inducible Expression System may enable us to manipulate the specific genes involved to combat viral diseases.
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	Willie Caraballo City College Junior Electrical Engineering Faculty Mentor: Dr. Thomas Robertazzi, Assistant Professor Department of Electrical Engineering
The Equilibrium State Transition Flow Patterns Statistical performance evaluations have become our primary tool for designing multifaceted communication and information processing systems. One important aspect of this field is "Queuing Theory"−mainly the study of queues. Typically, a queue is defined as a form of a waiting line that exists due to the difference between the arrival rate and the service rate of a system. This branch of mathematics is mainly concerned with flows of probability flux within a system of queues. In this research, the main goal to is to discover certain patterns within a system of queues, of non-product form solution, that will help facilitate the obtainment of an alternative computational algorithm for equilibrium state probability in the near future.
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	Jamilla Dick Medgar Evers College Junior Environmental Science Faculty Mentor: Dr. Sultan Hameed, Professor Marine Science Research Center
Criteria Pollutant Trends in New York City Criteria pollutants are those for which the United States Environmental Protection Agency (USEPA) has established National Ambient Air Quality Standards (NAAQS). These include standards for Carbon Monoxide (CO), lead (Pb), nitrogen dioxide (NO2), ozone (O3), particulate matter (PM) and sulfur dioxide (SO2). Over the past twenty years the Department of Environmental Conservation (DEC) and the EPA have continuously monitored these six criteria pollutants, especially after many programs designed to reduce their ambient concentrations have been put into place. This research uses air concentrations of the criteria pollutants that are collected at various monitoring sites in New York City to show how the pollutant trends have changed. The air quality trends compiled based on the information collected over the ten-year period from 1988 to1998 are of great importance. Significant changes in the pollutant concentrations can be determined and measured to correct and understand their sources. Thus pollution levels could be reduced and maintained at acceptable standards. In this work we will try to determine: (i) how and why do pollutant concentrations and type vary (ii) why changes for pollutants in certain locations are similar or different, and (iii) the statistical properties of these trends.
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	Lakesha Farmer Grambling State University Junior Biology Faculty Mentor: Dr. James Konopka, Associate Professor Research Mentor: Dr. Amy Warenda, Post Doc Department of Microbiology
Factors that Promote True Hyphal Growth in Candida Albicans The budding yeast Candida albicans is an opportunistic human pathogen capable of growing in a variety of forms. The polymorphic fungus can grow in a round yeast form, called a blastospore, or in two filamentous forms: true hyphae and pseudohyphae. Microscopically, cells with true hyphal growth and pseudohyphal growth have very similar phenotypes. To distinguish the difference two, GFP (green fluorescent protein) is used to tag Cdc 10, one of the four septin proteins (Cdc 3, 10, 11, 12) found in yeast cells. Septin proteins are highly homologus, filament forming proteins that organize other proteins in all eukaryotes. The septin-GFP proteins localize as a ring at the neck of pseudohyphal cells and on the tip or towards the middle of the germ tube of true hyphae allowing easy classification of the two filamentous morphs. There are several factors that contribute to true hyphal growth: temperature, pH, cell density, nutrients, and serum concentration. In lab, factors that mimic a mammalian host such as growth at 37°C, neutral pH, and the presence of blood serum, tends to promote true hyphal growth. Reports vary of the amount of serum necessary to promote true hyphal growth. This study attempts to investigate the relationship between the amount of serum in the media and the percentage of true hyphal cells generated. It also investigates if the amount of serum affects the overall hyphal lengths. Additionally, cells are being tested to see how the absence of sugar (dextrose) affects true hyphal growth. Overall, it appears that higher percentages of serum in the media increase the percent of true hyphal cells and germ tube length. Results also show that the absence of sugar in the media increases the percent of true hyphae and filamentous growth.
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	Frances Fernandez Hunter College Junior Biochemistry Faculty Mentor: Dr. James Bliska, Associate Professor Department of Microbiology, Centers for Molecular Medicine
Purification of Translocator Proteins from Yersinia Yersinia pseudotuberculosis is a bacterium that causes an infectious disease characterized by mesenteric lymphoadenitis. Yersinia uses the type III secretion system to inject bacterial effectors (Yops) into the host cell through the use of a small needle like projection extended from its surface. Three Yop proteins, YopB, YopD, and LcrV, are required for the translocation of the other Yops across the membrane. They are thought to form a pore in the target cell membrane that allows effectors to enter and disturb the target cell. This work involves the purification of YopB, YopD, and LcrV to determine the effect of each individual protein on the target cell. In order to purify the proteins, genes coding for these proteins are cloned in plasmids under the control of bacteriophage T7 RNA polymerase transcription, which is induced by the use of IPTG. The pET 28a plasmid allows the cloning of a gene next to a sequence that codes for a poly-histidine tag. When T7 RNA polymerase is induced, the majority of the cell´s resources are diverted to the transcription of the His-tagged fusion proteins. Conditions for growth, temperature and induction time are analyzed to obtain the maximum amount of soluble protein.
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	Zoe Gibson Fort Valley State University Junior Biology Faculty Mentor: Dr. Daniel Bogenhagen, Professor Department of Molecular Pharmacology
Purification of Mitochondrial DNA; Protein Complexes from the Fission Yeast S. Pombe Schizosaccharomyces pombe is a fission yeast having characteristics similar to those of other, more complex eukaryotes. In our lab mtDNA (mitochondrial DNA) nucleoids, consisting of mtDNA and all other proteins associated with it, including the DNA binding protein, mtTFA (mitochondrial transcription factor A) have been purified from Xenopus oocytes. These studies will determine whether or not this nucleoid can be purified from S. pombe. This may be possible because S. pombe´s mtDNA is similar in size to human and Xenopus mtDNA and it undergoes the normal eukaryotic cell cycle. Although no protein equivalent to the Xenopus DNA binding protein mtTFA has been identified in S. pombe, two HMG Box proteins have been found to be possible homologs to mtTFA. We will determine if either of these proteins is associated with mtDNA. S. pombe has recently had its genome sequenced. It has been discovered that its genome is much smaller than that of any other eukaryote whose genome has been sequenced, containing only 4,824 protein-coding genes. This is advantageous because it makes it much simpler to study all of the proteins that bind to mtDNA.
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	Timothy Nwobosi St. John´s University Junior Biology Research Mentor: Dr. Daniel Bogenhagen, Professor Department of Molecular Pharmacology
An Investigation into Whether the Ethanol Metabolite Acetaldehyde Cross-Links Mitoshondrial DNA to Proteins as Mitoshondrial Trasncription Factor a (MTTFA) Previous experimental work has shown that mitochondrial DNA in mouse liver is selectively degraded after acute intoxication with ethanol. The mechanism involves detoxification of ethanol to acetaldehyde, an intermediate in the conversion to ethyl acetate. The central hypothesis here is that N2-ethylidene-dG, a Schiff base and the most abundant intermediate of acetaldehyde adduction, may react with adjacent proteins such as mtTFA (mitochondrial transcription factor A) also called TFAM in mammals or abf2 in yeast. The mtTFA protein is an HMG (high mobility group) box protein that binds to the minor groove of mtDNA where it is accessible to the N2 adduct. The DNA-protein complex formation was monitored, using an electrophoretic mobility shift assay. SDS polyacrylamide gel electrophoresis was used to observe cross-linking of protein to DNA. The covalent cross-linking of protein to DNA would explain the negative effect of acetaldehyde on mtDNA transcription and replication. In replication of DNA via DNA polymerase, the protein (e.g. mtTFA) interferes with the replication and transcription by influencing the access of DNA damaging agents to mtDNA or by directly cross-linking to sites of DNA damaged residues.
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	Mary Osisami Stony Brook University Senior Biology Faculty Mentor: Dr. Dafna Bar-Sagi, Professor Department of Microbiology
The Regulation of HSPRY2 Subcellular Localization Receptor tyrosine kinase (RTK) signaling is involved in cell migration, growth and differentiation. However, high levels of RTK activity can lead to oncogenic transformation. Sprouty, a protein first identified in a genetic screen in Drosophila, is an inhibitor of the RTK /RAS/ MAP kinase pathway. Four mammalian homologues of Sprouty have been identified, hSpry1-4; among these hSprouty2 has the highest homology to Drosophila Sprouty. Recent studies in our lab have shown hSpry2 localizes to the endosome, however, the mechanism that regulates this sub cellular localization and function has yet to be identified. We are interested in characterizing the region(s) responsible for hSpry2 targeting to the endosome, since this would give insight into how it is regulated and how it functions. HA-tagged hSpry2 and a series of truncation mutants were expressed in COS-1 cell and analyzed by immunofluorescence microscopy. In this study we have identified two regions responsible for hSpry2 localization to the endosome.
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	Chanda Louis Oton City College Freshman Civil Engineering Faculty Mentor: Dr. Perena Gouma, Assistant Professor Department of Materials Science
The Development of Biosensors Generally the concentration of organic compounds and inorganic ions in the body represent the efficiency of the metabolic functions of the organs. Thus in clinical diagnosis, it is imperative to know and be able to detect what these compounds are, and their concentration levels. Our primary concern is to be able to easily and effectively detect urea. Urea is a nitrogenous ((NH 4) 2 CO 3 ) substance found in excess in perspiration and urine. It undergoes a process called the urea cycle, a five-enzyme cycle, which works to detoxify ammonia. The first four enzymes are comprised from arginine biosynthesis; the fifth enzyme is argininosuccinate. In the urea cycle disorder there is a deficiency in any of the five enzymes, which allows for the accumulation of ammonia. An overabundance of ammonia can lead to irreversible brain damage. Because of its irreversibility, preventive techniques have become favorable. Currently we are developing a new technique that will allow for us to detect urea, by measuring the concentration of ammonia, using resistor biosensors, which are comprised of a ceramic matrix and biological components that react with enzymes. When the analyte reacts with the enzyme it releases ammonia, allowing for measurement of the ammonia.
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	Stanley Pyram Bronx, New York Stony Brook University Junior Mechanical Engineering Research Mentor: Dr. Hui Zhang, Assistant Professor Department of Mechanical Engineering
Polyethylene The purpose of this research is to determine the effects of spray parameters on surface roughness and "splat" morphologies. The roughness analysis of spray polyethylene (spray at different conditions for example air fuel ratio, standoff distance, speed, etc.) was done using an instrument called Newview 200. Newview 200 is a three-dimensional Surface Profilers (Zygo) that characterizes and quantifies surface texture, step heights and critical conditions. With this instrument three-dimensional surface topography was obtained and used to determine which spray parameters have the greatest influence on surface roughness. In addition the analysis of single splats of polyethylene onto aluminum was done using a microscope to find how the morphology (i.e. shapes and sizes) of single splats of polyethylene are affected by processing conditions.