Emmanual Adomfeh
University at Albany
Freshman Year
Chemistry Major
 
Faculty Advisor:
Dr. Gloria Viboud
Department of Molecular Genetics and Microbiology
 
Creation of a YopD mutant to study type III secretion system in Yersinia pseudotuberculosis
Emmanuel Adomfeh(1), Nikolai Cassanova(1), James Bliska(2) and Gloria I. Viboud(2)
 
Yersina pseudotuberculosis is a gram-negative bacteria closely related to Yersinia pestis, the causative agent of Black Death. However, Yersinia pseudotuberculosis causes a much milder type of infection, restricted to the mesenteric lymph nodes. Both species infect host cells by utilizing the Type III Secretion System (TTSS). The TTSS is a syringe-like apparatus that allows the bacteria to deliver protein effectors, known as Yersinia Outer Proteins (Yops), across the plasma membranes of the host cell. The action of translocated Yops hinders the immune defenses of the host cell by modulating different cellular pathways. YopD, along with YopB, mediates translocation by forming a channel for effector proteins to enter the host cell. This process is thought to be modulated by the host cell GTPase protein Rho. Thus, membrane damage caused by insertion of the translocation channel during infection is prevented by the inhibitory action of one of the effector Yops (YopE) on the host cell Rho GTPase. To determine whether YopD is involved in Rho activation, we created a yopD deletion mutant by allelic exchange. A suicide vector carrying a DNA fragment with homology to the upstream and downstream region of yopD was inserted into a YopE- mutant of Y. pseudotuberculosis by conjugation. The YopED- mutant (YP62) was obtained after two homologous recombination events. We also inserted a plasmid containing YopD by conjugation (YP62/pyopD) to complement the yopD gene deletion in YP62. To verify the phenotype of the YopED- mutant and the complemented strain, a Yersinia infection assay was performed in Hela cell. This mutant will be used in further studies to elucidate the mechanism of regulation of the TTSS.
 
(1)Department of Chemistry, University at Albany, Albany, NY
(2Department of Molecular Genetics and Microbiology, Center for Infectious Diseases, Stony Brook University, Stony Brook, NY

Alejandro Avilés
University of Puerto Rico-Humacao (Puerto Rico)
Junior Year
Microbiology Major
 
Faculty Advisor:
Dr. Josephine Aller
School of Marine & Atmospheric Sciences
 
Other Research Mentor:
Alexandra Valdés, Ph.D. Candidate
School of Marine & Atmospheric Sciences
 
Detection of Human Pathogens from Discharge of Wastewater Treatment Plant Effluent in Port Jefferson Harbor Waters, Sediment and Air
Alejandro Avilés(1), Alexandra Valdés(2) and Josephine Aller(2)
 
After wastewater treatment processing, the effluent product still contains measureable numbers of pathogenic organisms. These include bacteria and viruses that survived the different treatment stages. Many of these pathogens enter coastal waters potentially becoming the source of many illnesses. Both viruses and bacteria have been found in sediments, water and aerosol samples in the Port Jefferson Harbor. Viruses were concentrated from water samples using two filtration methods: Tangential Flow Filtration (TFF) and Adsorption-Elution (AE). Aerosols were analyzed after collection using the SKC BioSampler into glycerol. Organisms associated with bottom sediments were analyzed after resuspension with sterile seawater. Abundances of both bacteria and viruses were determined by total direct counts using epifluorescence microscopy following staining with SYBR-Gold. Reverse-Transcriptase Polymerase Chain Reaction (RT-PCR) was performed to detect the presence of enteroviruses, and the Readycult Coliform 100 test was used to detect the presence of total coliform bacteria. Viral-like particles (VLPs) in water ranged from 1.08 x108 to 1.374x109per mL, while bacteria ranged between 2.211 x106 to 4.394 x106 per mL. Though enteroviruses were detected in sludge samples none were detectable in Harbor water samples. The presence of total coliforms and E. coli were found when samples were taken at low tide but no coliforms were detected at high tide. Even though VLPs were present in the water we were unable to detect Enteroviruses at either of the two sampling sites. VLPs, bacteria, and eukaryotes were collected in aerosol samples although we did not determine whether they were natural marine organisms or possibly pathogens.
 
(1)Department of Microbiology, University of Puerto Rico-Humacao, Humacao, PR
(2)School of Marine & Atmospheric Sciences, Stony Brook, NY

Shantay Branton
Allen University (South Carolina)
Sophomore Year
Mathematics Major
 
Faculty Advisor:
Dr. Stephen Finch
Department of Applied Math & Statistics
 
Other Research Mentor:
Rose Saint Fleur, Ph.D. Candidate
Department of Applied Math & Statistics
 
Longitudinal Relationship Among Cognitive Score, Hippocampal and Brain Volumes in Late Onset Alzheimer’s Disease Participants
Shantay J. Branton(1) , Rose M. E. Saint Fleur(2), and Stephen J. Finch(2)
 
The Mental Mini State Examination (MMSE) is a widely used brief cognitive test for the screening of Alzheimer’s disease (AD). It is used to test the major domains of cognitive functions, including language, visual construction ability, and memory. Hippocampus plays a precise role in memory. It is thought to be critical for the consolidation of new memories, that is, the capacity to retain information over delays. We looked at whether there was homogeneity in the data set, whether APOE-4 allele has an association with group membership given that there is heterogeneity, and if the changes of other variables were associated with the changes in the MMSE Score. The SAS PROC TRAJ procedure was used to test for the presence of heterogeneity with and without the APOE-4 allele. The SAS PROC PLOT procedure was used to fit a basic scatter plot in the data to find any potential trend between the change in MMSE and the other variables. Our analysis indicates that there is heterogeneity in the data. However, APOE-4 allele was not associated with group membership. We also found that change in MMSE has a strong association with hippocampal volume and brain volume.
 
(1)Department of Mathematics and Natural Science, Allen University, Columbia, SC
(2)Department of Applied Mathematics and Statistics, Stony Brook, NY

Nikolai Cassanova
University at Albany (New York)
Sophomore Year
Biology Major
 
Faculty Advisor:
Dr. Gloria Viboud
Department of Molecular Genetics and Microbiology
 
Creation of Yersinia pseudotuberculosis YopD Mutation Library using Error Prone Polymerase Chain Reaction (PCR)
Nikolai Cassanova(1), Emmanuel Adomfeh(1), James Bliska(2) and Gloria I. Viboud(2)
 
Yersinia pseudotuberculosis is a gram negative bacteria that cause diseases in animals and humans. Yersinia produces a type three secretion system (TTSS) to deliver toxins into the host cell. The TTSS comprises a needle like structure, three “translocator” proteins (YopB, YopD and LcrV), and six “effector” proteins (YopE, YopH, YopJ, YopO, YopM, YopT) that act to disarm the host immune system. To identify residues in YopD that are required for translocation, we aimed to create a random YopD mutation library using error-prone Polymerase Chain Reaction (PCR). In the PCR reaction, the YopD gene encoded in the Yersinia expression plasmid pMMB67HE was used as a template, oligonucleotides complementary to regions flanking the yopD gene were used as primers, and an error-prone enzyme as a DNA polymerase. The PCR fragments of the mutated YopD gene are then used as megaprimers in a second PCR reaction to incorporate the mutation in pMMB67HE. A random YopD mutation library in the YopD gene of Y. pseudotuberculosis will be of great importance in future studies to understand how the TTSS translocon works. Such studies could potentially lead to the discovery of novel antimicrobials.
 
(1)Department of Chemistry, University at Albany, Albany, NY
(2)2Department of Molecular Genetics and Microbiology, Center for Infectious Diseases, Stony Brook University, Stony Brook, NY

Erica Green
Allen University (South Carolina)
Sophomore Year
Biology Major
 
Faculty Advisor:
Dr. Carol Carter
Department of Molecular Genetics & Microbiology
 
Other Research Mentor:
Dr. Min-Huei Chen and Dr. Lorna Ehrlich, Research Scientists; Dr. Gisselle Medina
Department of Molecular Genetics and Microbiology
 
The Relationship between HIV and the Cellular Protein Sprouty2Does Spry2 help in the release of virus-like particles?
Erica Green(1), Min-Huei Chen(2), Gisselle Medina (2), Lorna Ehrlich (2), And Carol Carter(2)
 
YA chimeric protein is created through the joining of two or more gene products. The relationship between the Human Immunodeficiency Virus (HIV) protein Gag and the cellular protein Sprouty (Spry) 2 was investigated by creating chimeric proteins consisting of an assembly-defective Gag mutant, P7L, fused to Spry2 or mutants of Spry2. P7L-Gag encodes a point mutation in the late domain, which inhibits the release of the virus. Spry2 seems to participate in the late stages of virus budding. The purpose of the experiment was to determine whether the cellular protein Spry2 helps the virus to exit from cells. This report describes construction of P7L fused to Spry2 in which the amino acid Arginine 252 had been mutated to Aspartic acid (R252D). Cultures of E. coli containing the plasmid encoding P7L-Gag-GFP or the Spry2 mutant were grown. The restriction enzyme BamH I was used to linearize (open) the P7L-Gag-GFP DNA and the polymerase chain reaction (PCR) was then used to amplify the Spry2 gene and to add BamH I restriction sites to its 5’ and 3’ ends. DNA analysis to ensure the presence of fragments of the correct size was done through examination of the reaction products in agarose gel. The anticipated result is to create P7L-Spry2-R252D-GFP, introduce it into mammalian cells (Cos-1), and determine through the use of the confocal microscope or by Western blotting, whether or not Spry2 will rescue the release of virus-like particles.
 
(1)Department of Biology, Allen University, Columbia, SC
(2)Department of Microbiology, Stony Brook University, Stony Brook, NY

Roy Irby
Savannah State University (Georgia)
Sophomore Year
Mathematics Major
 
Faculty Advisor:
Dr. Stephen Finch
Department of Applied Math & Statistics
 
Other Research Mentor:
Rose Saint Fleur, Ph.D. Candidate
Department of Applied Math & Statistics
 
Describing Heterogeneity in Patients with Late Onset Alzheimer’s Disease (LOAD)
Roy Anthony Irby, Jr(1), Rose Saint Fleur(2), Stephen J. Finch(2)
 
Data has been reported on 89 subjects with Late Onset Alzheimer Disease (LOAD). We used the Mini Mental State Exam (MMSE) and the Clinical Dementia Rating (CDR) sum of boxes as tools to classify patients with Alzheimer Disease (AD). The MMSE is a standard measure of cognitive state (High capability = 30, Low = 0). We defined a new variable D (decline in MMSE) as 30-MMSE. CDR is a score for staging instrument for dementia (no impairment = 0, severe impairment = 3). It characterized six domains of cognitive and functional performance. The CDR sum of boxes is a sum of the six subcategories of CDR. We applied a two stage analysis to determine whether the pattern was homogenous. HLM is a two-stage modeling scheme involving a within-subjects stage and a between-subjects stage. In stage one (the within-subjects stage), we used transformation on the independent variable (here time T) to fit a linear polynomial on the data using the formula D = aTp+b, where p is the power transform to fit a linear function. In stage two (the between-subjects stage), we fit a mixture model on p to test for the presence of heterogeneity. We applied the same technique on the CDR sum of boxes variable. Based on the result obtained using HLM, our null hypothesis of homogeneity should be rejected.
 
(1)Department of Mathematics, Savannah State University, Savannah, GA
(2)Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY

Uruj Kamal
Wesleyan University (Connecticut)
Junior Year
Neuroscience and Behavior Major
 
Faculty Advisor:
Dr. Howard Sirotkin
Department of Neurobiology & Behavior
 
Other Research Mentor:
Keith Gates, Ph.D. Candidate
Department of Neurobiology & Behavior
 
Effects of REST and sox2 Expression on Zebrafish Neural Development
Uruj Kamal(1), Keith Gates(2), and Howard Sirotkin(2)
 
REST and sox2 are involved in regulation of neural gene expression, which is key to central nervous system development. REST protein represses neural genes in non-neural tissue and neural precursors. Sox2 is a gene expressed in neural precursors, which are undifferentiated (proliferative) cells within the central nervous system. In situ hybridization on fixed embryos at different stages of development will lead to a better understanding of REST functioning during neural development. Comparing and contrasting these expression patterns to those of sox2 will reveal more information on REST function and can then be compared to other animals such as frog, chick and mouse.
 
We are also interested in seeing how REST expression is affected when signaling pathways involved in development are disturbed. Mutations in the mindbomb gene cause uncontrolled neurogenesis early in development due to disruptions in the Notch signaling pathway. We would like to trace differences in REST expression between these mutant mindbomb embryos and wildtype embryos. We have also been investigating retinoic acid (RA) regarding its role in promoting the differentiation of neural stem cells. Retinoic acid has been strongly linked to active neurogenesis. We will be investigating the effects of excess RA and blocking of RA with DEAB on REST and sox2 expression patterns.
 
(1)Department of Neuroscience, Wesleyan University, Middletown, CT
(2)Department of Neurobiology & Behavior, Stony Brook University, Stony Brook, NY

Jeremiah Miller
SUNY Potsdam (New York)
Sophomore Year
Biology, Psychology & Public Health Major
 
Faculty Advisor:
Dr. Brenda Anderson
Department of Psychology
 
Other Research Mentors:
Diane Kim, Ph.D. Candidate
Department of Psychology
 
Effects of Chronic Psychological Stress: A Rat Model
Jeremiah Miller(1), Diane Kim(2), Brenda J.Anderson(2)
 
Threats to physiological homeostasis result in stress. Physical stress refers to a direct threat to homeostasis. Psychological stressors refer to the anticipation of a threat to homeostasis. Chronic psychological stresses in humans produce adverse psychological effect, but the neural substrates are not well understood. To understand the neural consequences of psychological stress, without physical stress, we are testing a new rodent model of psychological stress. We sought to understand factors that chronic psychological stress in rats which cause deficit of spatial working memory. In humans, stress can impair working memory. In our model, male rats were handled and randomly assigned to stress tunnels (ST), control tunnels (CT), and non tunnels (NT). Animals in the stress tunnels were exposed to ferret’s dander odor which was paired with light; sound and air to simulate the threat of a predator attack. Stimuli were delivered randomly. The stress group and non-stress groups were kept in separate rooms. After 21 days, the rats were tested for spatial working memory, anxiety, learned helplessness, and defensive behavior. Chronic psychologically stressed rats were found to have deficits in spatial working memory and appear more anxious.
 
(1)Department of Psychology, SUNY Potsdam, Potsdam, NY
(2)Department of Psychology, Stony Brook University, Stony Brook, NY

Amber Ortega
New Mexico Institute of Mining and Technology (New Mexico)
Sophomore Year
Biology Major
 
Faculty Advisor:
Dr. Marian Evinger
Department of Pediatrics; Department of Molecular Pharmacology
 
Discovery of Nicotine’s Role in Inhibition of the AKT Pathway to Breast Cancer Using shRNA
Amber J. Ortega(1), Marian Evinger(2)
 
It was established that nicotinic receptors are present on human mammary cells and that nicotine activates the signal transduction pathway containing Akt, a protooncogene10 with regulatory roles in diverse cellular processes and cancer progression. Akt activity is elevated in ~70% of breast cancers11. Normal human mammary epithelial cells experience different levels of induction by nicotine from transformed MCF-7 cells, a model for human breast cancer. Based on our initial observations that nicotine may activate Akt signalling, we hypothesize that Akt kinase plays a key role in nicotine mediated signal transduction in human mammary cells. The objective of this study was to determine if inactivation of Akt would block nicotine stimulated events and behaviors of the MCF-7 cell line. We synthesized three siRNA sequences to construct shRNA expressing plasmids to inhibit Akt in human epithelial breast cells. Double stranded oligonucleotides containing inhibitory siRNAs designed to form hairpin structures for cleavage by cellular RNAi processing machinery were cloned into the pcDNA6/Super plasmid vector for propagation in Escherichia coli. After purification, plasmids were transfected into mammalian cells by Lipofectamine Plus with selection by antibiotic resistance. After 48h incubations, to permit maximal expression, MCF-7 cells will be incubated with nicotine and harvested for analysis of Akt mRNA and proteins. These experiments will provide important preliminary data to establish a role for nicotine in influencing mammary cell function and potentially contributing to establishment of cancer.
 
(1)New Mexico Institute of Mining and Technology, Socorro, NM
(2)Department of Pediatrics, Stony Brook University, Stony Brook, NY

Luisa Torres
University at Albany (New York)
Senior Year
Biochemistry Major
 
Faculty Advisor:
Dr. Bernadette Holder
Department of Biochemistry & Cell Biology
 
Other Research Mentors:
Dr. Ken-Ichi Takemaru, Department of Molecular & Cellular Pharmacology
Janet Chang, Ph.D. Candidate in Molecular Biology
 
Role of MESD and Chibby in Normal Mouse Development
Luisa Torres(1), Bernadette Holdener(2), Ken-Ichi Takemaru(2), and Janet Chang(2)
 
One approach toward understanding embryonic patterning is to study mutations that disrupt development. This study focuses on examining two genes previously shown to be essential for normal mouse embryogenesis.
 
Loss of mesd function (mesoderm development) blocks gastrulation and mesoderm differentiation in mice. Polarity defects likely result from improper localization of Wnt co-receptors LRP5/6, which are members of the low-density lipoprotein related receptors (LRP) family. Using immunohistochemistry, we suggest that localization of other members of the LRP family, such as LRP2, may also depend on MESD.
 
The second part of this study focuses on the small nuclear protein Chibby (Cby), an inhibitor of the Wnt/ß-catenin pathway. Perturbations to this pathway have been implicated in a variety of human diseases, especially cancer. Approximately 30% of mouse embryos lacking Cby die during development; but the exact stage at which this occurs is still unknown. By photographing embryos at 10.5 days after fertilization, we identified abnormal embryo morphology that might be associated with lack of Cby during embryogenesis, though we did not observe a consistent phenotype among the mutants. For future work, the exact stage of embryonic lethality will be determined by dissecting mice at later stages of development.
 
(1)Department of Biochemistry, University at Albany, Albany, NY
(2)Department of Biochemistry, Stony Brook University, Stony Brook, NY

 
Jamal Irving
Undergraduate Student in Computer Science
 
Residential Liaison Officer

 
Melissa Mark
Ph.D. Student in Ecology and Evolution
 
Writing to Win Instructor

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

 
Betty Noel
Ph.D. Student in Molecular Genetics and Microbiology
 
Research Methods Instructor

 
Sandra Tinta
Ph.D. Student in Computer Science
 
Activities Coordinator

 
Oladapo Yeku
MD/Ph.D. MSTP Program
 
Research Methods Instructor