Mbaye Diop
Stony Brook University (SUNY)
Junior Year
Biochemistry Major
 
Faculty Advisor:
Dr. Nicole Sampson
Department of Chemistry
 
Research Mentor:
Xinxin Yang
Department of Chemistry
 
Crystallization of 3?-Hydroxysteroid Dehydrogenase from Mycobacterium tuberculosis
Mbaye Diop (1), Xinxin Yang (2), Suzanne Thomas (2), Natasha Nesbitt (2), and Nicole Sampson (2)
 
New approaches are needed to combat Mycobacterium tuberculosis (M. tb). Multi-drug resistant and extremely drug-resistant forms of M. tb (MDR-TB and XDR-TB) have emerged and show resistance to front and second-line-tuberculosis drugs such as rifampicin and isoniazid. Experiments have shown that M. tb's oxidation of cholesterol is crucial for its intracellular survival in the host and is correlated with the pathogen's acquiring virulence. A first and key step in the cholesterol metabolic pathway is M. tb's ability to oxidize 3?-hydroxysterols (i.e. cholesterol) to 3-ketosteroids by the enzymatic activity of 3?-hydroxysteroid dehydrogenase (HSD). In this work, we attempt to understand and determine the molecular structure of HSD. To crystallize HSD, we first heterologously expressed and purified the protein; then, we set up various crystallization conditions using the hanging-drop method. Understanding and determining the molecular structure of HSD will guide drug discovery in pathways that are primarily utilized when the pathogen resides in the host environment. Antibiotics that target these pathways would be effective against all forms of TB including MDR/XDR TB.
 
(1) Department of Biochemistry, Stony Brook University, Stony Brook, NY
(2) Department of Chemistry, Stony Brook University, Stony Brook, NY

Maleshia Jones
University of Maryland, Baltimore County
Freshman Year
Mechanical Engineering Major
 
Faculty Advisor:
Dr. Lin-Shu Wang
Department of Mechanical Engineering
 
Research Mentor:
Jean Christian Brutus
Department of Mechanical Engineering
 
Testing Intercooler Effectiveness for Turbo-Expansion Cooling Applications
Maleshia Jones (1), Jean Christian Brutus (2), Lin-Shu Wang (2)
 
In the 1950s, expansion cooling was introduced as a way to reduce the charge air temperature with an expansion device upstream the intake manifold of internal combustion engines. In previous studies, it has been shown that expansion cooling in turbocharging systems is limited by the effectiveness of intercoolers. Intercoolers reduce the charge air temperature before the expansion device. Simulations have shown that expansion cooling requires intercooler effectiveness to be higher than 80%. In this study, the effectiveness of an air-air and a liquid-air intercooler were compared. A test bench was developed to gather temperature and pressure drops, as well as mass flow rates. Under the conditions of 125°F inlet charge air temperature, and mass flow of 5 lb/min, the "charge"-air-ambient-air intercooler effectiveness typically ranged between 60-70%, whereas the "charge"-air-water intercooler effectiveness ranged between 87-90% and the combined "water-cooled test bench" effectiveness ranged between 65-67%. The test bench operating conditions were different from real operation conditions of an internal combustion system. More importantly, the water-cooled test bench effectiveness depends on the effectiveness of the second water-ambient-air heat exchanger. Further study of the combined "water-cooled test bench" effectiveness at real conditions of higher temperatures and pressures and equipped with a high-performance second water-ambient-air heat exchanger is to be conducted.
 
(1) Department of Mechanical Engineering, University of Maryland, Baltimore County, Baltimore, MD
(2) Department of Mechanical Engineering, Stony Brook University, Stony Brook, NY

Kevin Knockenhauer
Stony Brook University (SUNY)
Junior Year
Biochemistry Major
 
Faculty Advisor:
Dr. Sanford Simon
Departments of Biochemistry and Pathology
 
Other Research Mentor:
Elizabeth Roemer, Department of Pathology
Katarzyna Sawicka, Department of Biomedical Engineering
 
Encapsulation within Nanofibers Confers Stability to the Protective Antigen Protein in a Transdermal Anthrax Vaccine
Kevin E. Knockenhauer (1), Katarzyna M. Sawicka (2), Sanford R. Simon (1,3)
 
The current vaccination paradigm for the prevention of anthrax is insufficient to deal with a potential, widespread epidemic. To solve this issue, we propose a self-administrable vaccine comprised of a solid-state nanofibrous membrane containing encapsulated protective antigen (PA), a binding protein secreted by Bacillus anthracis. Polyvinylpyrrolidone (PVP) nanofibers, produced by the technique of electrospinning, are utilized as our transdermal delivery vector because the high surface area to volume ratio that they afford maximizes contact between the encapsulated antigen of interest and the skin; in turn increasing local concentration gradients of PA when the hygroscopic PVP is solubilized via transepidermal water loss. Previous studies have confirmed the retention of PA immunoreactivity and functionality after the voltage-intensive electrospinning process. The study described here aimed to compare the retention of PA immunoreactivity and functionality in our nanofibrous membrane to PA in solution over a several month period in varying conditions, since it is theorized that encapsulation within nanofibers may confer protein stability. The percent of immunoreactivity retained in the nanofibrous membrane was significantly larger than that in solution over a 30 day period at -20°C and 4°C. Encapsulated PA retained a significantly higher level of functionality than PA in solution over a period of 59 days at 4°C.
 
(1) Department of Biochemistry, Stony Brook University, Stony Brook, NY
(2) Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY
(3) Department of Pathology, Stony Brook University, Stony Brook, NY

Tabassum Majid
University of Maryland, Baltimore County
Junior Year
Interdisciplinary Studies Major
 
Faculty Advisor:
Dr. Lorne Mendell
Department of Neurobiology and Behavior
 
Research Mentor:
Dr. Vanessa Boyce
Post-Doctoral Research Associate
 
Examining measures of plasticity in the motor cortex of spinalized rats: a preliminary study
Tabassum Majid (1), Vanessa Boyce PhD (2), Brenda Anderson PhD (3), Lorne Mendell PhD (2)
 
Adult spinalized cats treated with neurotrophic factors, brain-derived neurotrophic factor (BDNF) and neurotrophin 3 (NT-3), display improved treadmill locomotion. Untreated adult rats thoracically spinalized as neonates can exhibit stepping; in these rats cortical stimulation of hindlimb areas can activate trunk muscles, suggesting plasticity in motor cortex projections to the spinal cord. Thus, we examined anatomical parameters indicative of motor cortical plasticity in rats (control, adult spinalized, adult spinalized treated with BDNF, neonatally spinalized rats capable of consistent plantar weight supported stepping (steppers), and neonatally spinalized rats incapable of consistent stepping (non-steppers)).
 
Kinematic analysis of stepping indicated that adult spinalized rats could not step despite treatment, and that some neonatally spinalized adults spontaneously recovered stepping ability. We optimized a rapid Golgi staining protocol to investigate the cytoarchitecture of the motor cortex. Cortical thickness measurements indicated increased thickness of motor cortex hindlimb representation in all injury groups compared to controls. Staining with immunohistochemical markers for glial cells (GFAP), neurotrophic factors (BDNF, NT-3), neurons (NeuN), and proliferation (Ki67) revealed no distinct differences between groups. Future directions in this preliminary study include further optimization of Golgi staining of pyramidal cells, more animals per group, and extension of these studies to the cerebellum.
 
(1) Interdisciplinary Studies Department, University of Maryland, Baltimore County, Baltimore, MD
(2) Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY
(3) Department of Psychology, Stony Brook University, Stony Brook, NY

Melissa Ochoa-Trochez
The City College of New York (CUNY)
Senior Year
Biology Major
 
Faculty Advisor:
Dr. Jian Cao
Departments of Medicine and Pathology
 
Research Mentor:
Antoine Dufour
Department of Chemistry
 
The Role of the Hemopexin Domain of Membrane Type -1 Matrix Metalloproteinase in Cell Migration
Melissa Ochoa (1), Antoine Dufour (2, 3), and Jian Cao (2)
 
Membrane Type 1-Matrix Metalloproteinase (MT1-MMP) has been found to be upregulated in various forms of cancer. We previously demonstrated that MT1-MMP enhanced cell migration and invasion, however, this mechanism is not yet fully understood. To identify critical domains required for MT1-MMP enhanced cell migration, we generated mutant MT1-MMP constructs by swapping different domains of MT1-MMP with that of MMP-2. Swapping the PEX domain failed to result in MT1-MMP induced cell migration. These results support that the PEX domain of MT1-MMP is important in cell migration. We mutated each of the outer ?- strands (blades 1-4) of the PEX domain in order to identify the regions required for the migratory role of MT1-MMP. These four mutants of the MT1-MMP PEX domain were transfected into COS-1 cells and MT1-MMP activity was assayed through gelatin zymography and western blotting. Mutations of blades 1 and 4 failed to activate proMMP -2. Furthermore, mutants were tested in a transwell chamber migration assay showing that blades 1 and 4 of the MT1-MMP PEX domain play critical roles in enhancing the migration of COS-1 cells. We conclude that the PEX domain is essential for the ability of MT1-MMP to enhance COS-1 cell migration, suggesting an interesting target for future drug design that could impact inhibition of cancer cell invasion and metastasis.
 
(1) Department of Biological Sciences, The City College of New York, New York, NY
(2) Division of Hematology/Oncology, Stony Brook University, Stony Brook, NY
(3) Department of Chemistry, Stony Brook University, Stony Brook, NY

Vern Perera
University at Albany (SUNY)
Sophomore Year
Chemistry Year
 
Faculty Advisor:
Dr. Howard Sirotkin
Department of Neurobiology and Behavior
 
Employing Zinc Finger Nucleases to Understand the Mechanistic Activity of REST Corepressor Complexes
Vern Perera (1), Fatma Kok (2), Howard Sirotkin (2)
 
In neurogenesis, REST governs the transition from pluripotent stem cells to neural progenitors and mature neurons by the repression of neural genes. This repression is characterized by the acquisition of neural cell fates during embryonic stem cell differentiation. Here, we employ the use of zinc finger nucleases (ZFNs) in an effort to understand the mechanism of neural gene repression in the zebrafish model in vivo by targeting REST. ZFNs were designed using an algorithm provided by ZiFiT to target the REST gene in the zebrafish genome, and mRNAs encoding these ZFNs were injected into 1-cell stage embryos. Crossing fish containing certain ZFN arrays generated small mutations in embryonic DNA induced by frameshift mutations due to non-homologous end joining. Although generated at low yield, a large deletion was also observed using 181 site PCR primer pairs that maintained the reading frame of the DNA. We reasoned that this deletion halts activity of the mSin3-REST corepressor complex located at the N-terminus repressor domain of REST and, therefore, inactivates REST. Thus, the mechanistic properties of the mSin3 corepressor complex and its role in neurogenesis may be understood using ZFN-induced mutagenic lesions. Furthermore, this shows that ZFN technology is a plausible adaptation for gene knockouts in biological systems.
 
(1) Department of Chemistry, University at Albany, Albany, NY
(2) Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY

Laura Senatus
Brooklyn College (CUNY)
Junior Year
Biology Major
 
Faculty Advisor:
Dr. Orlando Schärer
Departments of Pharmacological Sciences and Chemistry
 
Research Mentor:
Barbara Orelli
Department of Pharmacological Sciences
 
Generation of Mutations in the N-terminus of XPF to Study the Role of ERCC1-XPF in DNA Interstrand Crosslink Repair
Laura Senatus (1), Barbara Orelli (2), Orlando D. Schärer (2)
 
Nucleotide Excision Repair (NER) is a DNA repair pathway that enables cells to eliminate bulky, helix distorting lesions caused by different environmental agents. A key factor in the process is ERCC1-XPF, a structure-specific endonuclease that makes the incision 5' to a lesion in NER. ERCC1 has additional roles in the repair of interstrand crosslinks (ICLs) that are less well understood. The goal of our project was to generate mutants in XPF that render cells specifically sensitive to ICL-forming agents. It has been shown that tagging XPF with GFP on its N-terminus appears to make cells sensitive to ICL forming agents but not to UV irradiation. In addition, a point mutation in the Drosophila XPF homolog Mei-9 disrupts the interaction with a protein called Mus312, which has a role in ICL repair. This data suggest that the N-terminal region of XPF might interact with one or more factor involved in ICL repair. We generated three different XPF constructs: one carrying a HA-tag at the N-terminus, a second having the first 4 amino acids of the protein deleted and a third one carrying a point mutation in the highly conserved residue G314 equivalent to the mutation found in Mei-9. The mutated XPF genes were cloned into the pWPXL lentiviral vector and human XP-F cells were transduced with the different lentiviruses. The cells expressing the mutant XPF proteins will be tested for their sensitivity to UV irradiation and ICL-forming agents. These N-terminus alterations would also be predicted to abolish ICL specific functions.
 
(1) Department of Biology, Brooklyn College, Brooklyn, NY
(2) Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY

Shayna Vega
University at Albany (SUNY)
Junior Year
Biology Major
 
Faculty Advisor:
Dr. James Konopka
Department of Molecular Genetics and Microbiology
 
Research Mentor:
Dr. Lois Douglas
Post-Doctoral Research Associate
 
The Role of Stress Response Gene HSP30 in Candida albicans
Shayna Vega (1), Lois M. Douglas (2), James B. Konopka (2)
 
Candida albicans (C.albicans) is the most common human fungal pathogen. Although it is normally found in the gastrointestinal tracts of humans as a benign part of the flora it can cause lethal systemic infections in individuals with a compromised immune system. Approximately 40% of these patients die from the infection, even with current antifungal therapy. Another problem in treating C. albicans infections is that it can easily mutate and become drug resistant. To help identify new drug targets and to improve current antifungal therapy, we are studying the function of plasma membrane proteins. Plasma membrane proteins carry out critical roles in cell regulation and their position on the outer surface of the cell makes them easily accessible to drugs. In order to better understand plasma membrane function, we are studying heat shock protein 30 (Hsp30), a stress-inducible regulator of the plasma membrane Hydrogen ATPase. We are investigating whether the regulator of stress response Hsp30 is important for C. albicans virulence by analyzing the phenotypes of an HSP30 deletion mutant (hsp30?) under various stress conditions that mimic those that are present in a human host. We have observed that the hsp30? cells were more sensitive to cell wall stress, suggesting that the mutant cells will be less able to infect a host. They were also defective in growth under poor nutrient conditions; this may be an indication of impaired growth following phagocytosis by macrophage cells. We also noted that they were less able to grow invasively into agar, suggesting that they will be less able to grow invasively into tissues to promote the spread of infection. Lastly, the mutants were also more sensitive to the antifungal drug Fluconazole. These phenotypes suggest that Hsp30 will be important for virulence and represents a potential new drug target. Ultimately, our goal is to better define plasma membrane organization in order to improve drug action and identify novel drug targets.
 
(1) Department of Biological Sciences, University at Albany, Albany, NY 12222
(2) Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11794

 
Akua Bonsra-Roach
Ph.D. student in Molecular and Cellular Pharmacology
 
Graduate School Preparation and Development Instructor

 
Al Herrera-Alcazar
Ph.D. student in Social and Health Psychology
 
Graduate School Preparation and Development Instructor

 
Rocio Ng
Ph.D. Student in Ecology and Evolution
 
Research Methods Instructor

 
Cindy Leiton
Ph.D. student in Molecular and Cellular Pharmacology
 
Research Methods Instructor

 
Andrew Ally
Undergraduate student in Computer Science
 
Residential Liaison Officer

 
Doreen Hopkins
Ph.D. student in Sociology
 
Graduate Assistant and Activities Coordinator