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Richard Kahn. Biochemistry.
Phone: 404-727-3561
Email: rkahn@emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Spring,Summer,Fall
Lab Positions: 2
Project Description: My lab is primarily interested in cell regulation by GTP binding proteins. We employ a wide array of techiques, including protein purification, enzyme assays, protein structure determination (x-ray crystallography and NMR techniques), immunocytochemistry (primarily fluorescence based in mammalian cells), molecular biology, and protein expression studies in bacteria, yeast, and mammalian cells.
Student Requirements: Previous courses in biology, biochemistry, cell biology, molecular biology, genetics are all pluses but none are required. Previous experience in a research lab also helpful but not required.
Techniques used in this lab: see above; some combination of those listed
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Vincent Yang. Digestive Diseases.
Phone: 727-5638
Email: vyang@emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Spring,Summer,Fall
Lab Positions: 1
Project Description: The focus of our research interest is on understanding the molecular mechanisms that control proliferation and differentiation of the intestinal epithelial cells. In particular, our group has concentrated on the roles played by a number of Kruppel-like transcription factors in regulating these two important biological processes in the gut epithelium. One factor, called Kruppel-like factor 4 or KLF4, is a negative regulator of proliferation that mediates the functions of two important tumor suppressors, APC and p53. The other, called KLF5, is pro-proliferative and mediates the activities of important proto-oncoproteins including RAS and WNT. Our hypothesis that the two KLFs function in the larger network of tumor suppressor genes and oncogenes to regulate intestinal epithelial proliferation and differentiation. The knowledge derived from these studies may impact on the mechanism of gut development and tumorigenesis.
Student Requirements: Molecular Biology, Biochemistry, Genetics
Suggested Reading (References):
(1) Ghaleb, A.M., Nandan, M.O., Chanchevalap, S., Dalton, W.B., Hisamuddin, I. M., and Yang, V.W. (2005) Kruppel-like factors 4 and 5: the yin and yang regulators of cellular proliferation. Cell Research 15, 92-96.
(2) Nandan, M.O., Chanchevalap, S., Dalton, W. B., and Yang, V.W. (2005)Kruppel-like factor 5 promotes mitosis by activating the cyclin B1/Cdc2 complex during oncogenic Ras-mediated transformation. FEBS Letters 579, 4757-4762.
(3) Yoon, H.S., Ghaleb, A.M., Nandan, M.O., Hisamuddin, I.M., Dalton, W.B., and Yang, V.W. (2005) Kruppel-like 4 prevents centrosome amplification following g irradiation-induced DNA damage. Oncogene 24, 4017-4025.
(4) Ouko, L., Ziegler, T. R., Gu, L. H., Eisenberg, L. M., and Yang, V. W. (2004) Wnt11 signaling promotes proliferation, transformation and migration of IEC6 intestinal epithelial cells. Journal of Biological Chemistry 279, 26707-26715.
(5) Hisamuddin, I.M., Wehbi, M., Schmotzer. B., Easley, K., Hylind, L., Giardiello, F.M., and Yang, V.W. (2005) Genetic polymorphisms of flavin monooxygenase 3 in sulindac-induced regression of colorectal adenomas in familial adenomatous polyposis. Cancer Epidemiology Biomarkers & Prevention 14, 2366-2369.
Techniques used in this lab: Cell culture, PCR, Northern and Western blot, immunohistochemistry, transfection, DNA plasmid work
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Justin Gallivan. Chemistry.
Phone: 404-712-2171
Email: justin.gallivan@emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Spring,Summer,Fall
Lab Positions: 1
Project Description: Our lab is interested in harnessing the power of biological systems to solve problems in chemistry and materials science. The remarkable chemistry performed in living systems is ultimately directed by genes. We develop ways of cloning biosynthesis genes and we evolve these genes in the test tube to coax them to produce new compounds. This work is fundamentally interdisciplinary and students are exposed to a wide variety of techniques ranging from synthetic chemistry to molecular biology.
Student Requirements: All backgrounds are welcome to apply. Coursework in organic chemistry, biochemistry, or genetics is a plus, but is not required. Preference is given to students interested in a future career in science.
Accepts 1st year students? Y
Accepts 2nd year students? Y
Techniques used in this lab: Students can gain experience in molecular biology (cloning, PCR, directed evolution), synthetic organic chemistry, or a combination of the two areas.
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Lou Ann Brown. Pediatrics.
Phone: 404-727-5739
Email: lbrow03@emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Spring,Summer,Fall
Lab Positions: 2
Project Description: Background: Alcohol abuse has significantly increased in women of childbearing age resulting in a large population of premature infants with fetal alcohol exposure. Alcohol-induced oxidant stress and damage is best described in the developing brain, however, all developing organ systems are exposed to alcohol-induced oxidative stress. We have shown that maternal alcohol abuse increased the risk of early onset sepsis in the very low birth weight premature neonate. In utero exposure to pro-inflammatory cytokines increases the risk of adverse outcomes in the premature newborn such as chronic lung disease and sepsis. Bronchopulmonary dysplasia (BPD) results from chronic intrauterine exposure to pro-inflammatory cytokines that primes the fetal lung so that minimally injurious postnatal events provoke an exuberant pulmonary inflammatory response and potentiates lung injury.
In adults, chronic alcohol abuse depletes the antioxidant glutathione (GSH), induces chronic oxidant stress and a chronic pro-inflammatory state. This subsequently results in an exaggerated response to a second hit such as sepsis or trauma. As observed in adults, we do not believe that fetal alcohol exposure alone causes BPD. Rather, we postulate that alcohol-induced fetal GSH depletion results in a chronic pro-inflammatory state that places the very premature lung at a greater risk for injury when a second hit occurs. In animal models of in utero alcohol exposure, we are exploring fetal lung GSH depletion, chronic oxidant stress and a chronic pro-inflammatory state that subsequently delays lung maturation and increases the risk of lung injury when there is premature delivery. Furthermore, we propose that GSH precursors will attenuate that injury when given after delivery.
Student Requirements: Juniors and seniors only
Accepts 2nd year students? Y
Suggested Reading (References):
(1) T.W. Gauthier, X.D. Ping, F.L. Harris, M. Wong, H. Elbahesh, and L.A.S. Brown. Fetal alcohol exposure impairs alveolar macrophage functions via decreased glutathione availability. Pediatr. Res. 57: 76-81 (2005).
(2) L.A.S. Brown, F.L. Harris, X.-D. Ping and T.W. Gauthier. Chronic ethanol ingestion and the risk of acute lung injury: a role for glutathione availability? Alcohol 33: 191-197 (2004).
(3) M.H. Manar, M.R. Brown, T.W. Gauthier, and L.A.S. Brown. Association of glutathione-S-transferase P1 (GST-P1) polymorphisms with bronchopulmonary dysplasia. J. Perinatol. 24: 30-35 (2004).
(4) A. Pelaez, R.I. Bechara, P.C. Joshi, L.A.S. Brown and D.M. Guidot. Granulocyte/macrophage colony-stimulating factor treatment improves alveolar epithelial barrier function in alcoholic rat lung. Am. J. Physiol. (Lung Cell Mol. Physiol.) 286: L106-L111 (2004).
Techniques used in this lab: Fluorescent microscopy; confocal microscopy; real time PCR; western blot analysis
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Judith Fridovich-Keil. Human Genetics.
Phone: 404-727-3924
Email: jfridov@emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Spring,Summer,Fall
Lab Positions: 1
Project Description: Studies of normal galactose metabolism and the impact of impaired galactose metabolism on patients with transferase- or epimerase-deficiency galactosemia. Projects range from genetic and biochemical studies in yeast to mammalian cell studies to work with patient cells and samples. Our goals are to understand the mechanism and implications of normal galactose metabolism in eukaryotes, as well as the pathophysiology of galactosemia. Our ultimate goal is to devise novel and improved treatments for patients with this family of metabolic disorders.
Student Requirements: Applicants should be self-motivated students seriously considering a career in biological or biomedical research. Student must have at least some (classroom or laboratory) prior exposure to genetics, biochemistry, and molecular biology.
Accepts 2nd year students? Y
Suggested Reading (References):
(1) Openo, KK, JM Schulz, CA Vargas, CS Orton, MP Epstein, RE Schnur, F Scaglia, GT Berry, GS Gottesman, C Ficicioglu, AE Slonim, RJ Schroer, C Yu, V Rangel, J Keenan, K Lamance, and JL Fridovich-Keil. Epimerase-deficiency galactosemia is not a binary condition. Am J Hum Gen. In press 10/2005.
(2) Schulz, JM, KL Ross, K Malmstrom, M. Krieger, and JL Fridovich-Keil (2005). Mediators of galactose sensitivity in UDP-galactose 4'-epimerase impaired mammalian cells. J. Biol. Chem. 280(14):13493-502.
(3) Wasilenko, J., M.E. Lucas, J.B. Thoden, H.M. Holden, and J.L. Fridovich-Keil (2005). Functional characterization of the K257R and G319E hGALE alleles found in patients with ostensibly peripheral epimerase deficiency galactosemia. Molecular Genetics and Metabolism 84(1):32-8.
(4) Henderson, J.M., A. Watson, R. Sanders, J.B. Thoden, H.M. Holden, and J.L. Fridovich-Keil (2004) Determinants of Function and Substrate Specificity in Human UDP-Galactose 4-Epimerase. J Biol Chem 279(31):32796-803.
(5) Mendelsohn, B.A., C.A. Vargas, A-M. Li, A. Watson, K. Riehman, and J.L. Fridovich-Keil (2003). Genetic and biochemical interactions between SCP160 and EAP1 in yeast. Nucleic Acids Research. 31(20):5838-47
Techniques used in this lab: modern molecular biology, recombinant DNA, yeast genetic and biochemical manipulations, enzyme assays
Additional Comments: Flower in the Crannied Wall
by Lord Alfred Tennyson
(1809-1892)
Flower in the crannied wall,
I pluck you out of the crannies,
I hold you here, root and all, in my hand,
Little flower -but if I could understand
What you are, root and all, and all in all,
I should know what God and man is.
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Vince Conticello. Chemistry.
Phone: 7-2779
Email: vcontic@emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Summer
Lab Positions: 1
Project Description: The conceptual design of synthetic nano-scale devices can derive much information from structural investigations of biologically derived supramolecular assemblies and, conversely, biological structural motifs present an attractive target for the synthesis of artificial nano-scale systems on the basis of relationships between sequence and supramolecular structure that have been defined for native biological assemblies. Our research utilizes the same structural guidelines as employed in biological systems for the design and construction of non-native, nano-scale materials that display the structural specificity and the chemically and spatially unique functional group presentation of native biomolecular assemblies. In this process, my research group attempts to provide the means to answer four basic questions: (1) Can synthetic protein materials be prepared to emulate and enhance the properties of native protein materials? (2) Can these proteins be designed rationally and synthesized using conventional chemical and molecular genetic approaches? (3) Can the structures be analyzed using characterization methods that enable a meaningful correlation between sequence design and supramolecular architecture? (4) Can we develop methods for encoding function within the polypeptides that would facilitate the use of these materials within directed applications?
Student Requirements: some introductory chemistry and biology courses-rising junior or senior with biology/chemistry major.
Techniques used in this lab: Gene cloning. Protein Expression. Protein characterization techniques including NMR spectroscopy and electron microscopy. Chemical synthesis.
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Samuel Dudley. Medicine/Cardiology.
Phone: 404-329-4626
Email: sdudley@emory.edu
Institution: Emory University
Location: Off-campus (but accessible via shuttle, e.g., Grady or VA Hospitals)
Availability: Summer
Lab Positions: 1
Project Description: Investigating the role of oxidative stress on sudden death risk using mice, pigs, or humans.
Additional Project Information: Investigating a new hypothesis about the role of oxidative stress in causing diastolic heart failure in mice or humans.
Student Requirements: No previous experience is required. A facility with biology, chemistry, and physics is desirable.
Suggested Reading (References):
(1) DUDLEY, Jr., S.C., N.E. HOCH, L.A. McCANN, C.HONEYCUTT, L.DIAMANDOPOULOS, T. FUKAI, D.G. HARRISON, S.I. DIKALOV, J. LANGBERG. Atrial Fibrillation Increases Production of Superoxide by the Left Atrium and Left Atrial Appendage: Role of the NADPH and Xanthine Oxidases. (2005). Circulation vol. 112, 1266-1273.
(2) 14. XIAO, H.D., S. FUCHS, D.J. CAMPBELL, W. LEWIS, S.C. DUDLEY, Jr., V.S. KASI, B.D. HOIT, G. KESHELAVA, H. ZHAO, M.R. CAMPECCHI, K.E. BERNSTEIN. Mice with cardiac Restricted Angiotensin Converting Enzyme (ACE) have Atrial Enlargement, Cardiac Arrhythmia and Sudden Death. 2004. Am. J. Pathol. 165:1019-1032.
Techniques used in this lab: Electrophysiology, animal handling and breeding, proteomics, molecular biology, electrocardiography (ECG), electron spin resonance, human trials.
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Dale Edmondson. Biochemistry.
Phone: 404 727-5972
Email: deedmon@emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Summer
Lab Positions: 1
Project Description: Expression of fish monoamine oxidase in Pichia pastoris and purification and characterization of the recombinant enzyme. This project is to probe the structure and function of a precursor form of human monoamine oxidases A and B.
Student Requirements: Chemistry or Biology majors
Accepts 2nd year students? Y
Suggested Reading (References):
(1) Binda, C., Newton-Vinson, P., Hubalek, F., Edmondson, D.E. and Mattevi, A. 2002 "Structure of Human Monoamine Oxidase B, a Drug Target for the Treatment of Neurological Disorders" Nature, Structural Biology 9, 22-26
(2) Edmondson, D.E., Mattevvi, A., Binda, C., Li, M., and Hubalek, F. (2004) Structure and Mechanism of Monoamine Oxidase, Currents in Medicinal Chemistr0
y 11, 1893-1993
(3) DeColibus, L., Li, M., Bibda, C., Lustig, A., Edmondson, D.E., and Mattevi, A. (2005) Structure of Human Monoamine Oxidase A : Relationship to the Structures of Rat MAO A and Human MAO B Proceeding of the National Academy of Sciences 102, 12684-12689
Techniques used in this lab:
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Periasamy Selvaraj. Pathology.
Phone: (404) 727-5929
Email: pselvar@emory.edu
Institution: Emory University
Location: On Campus (Emory main campus)
Availability: Spring,Summer,Fall
Lab Positions: 2
Project Description: Development of cancer vaccines using protein transfer.
Tumors modified by transfecting genes for immunostimulatory molecules such as B7 and cytokines are now considered as a potential therapeutic tumor vaccine. However, transfection is not always efficient and can be difficult with many cell types, especially freshly isolated tumor cells from patients. Moreover, transfection of genes requires the introduction of vectors of viral origin which is not desirable for human therapeutic purposes. Studies have shown that purified GPI-anchored cell surface proteins can be spontaneously incorporated into membranes by incubating the proteins with the cells or cell membranes (Protein Transfer). This unique property can be used to reconstitute cell surface expression receptors on cell membranes without the use of gene transfection. Using recombinant techniques, we have developed many immunostimulatory molecules including B7-1, IL-2, and IL-12 as GPI-anchored form. Currently we are working on mouse models of cancer to determine the efficacy of vaccine prepared using protein transfer technology. In the long-term the knowledge obtained from this study could be used to develop an effective cancer vaccine to treat cancer patients.
Additional Project Information: Structure and function on Fc receptors. Fc receptors for IgG (FcgR) are involved in phagocytosis, antibody-dependent cellular cytotoxicity, and removal of immune complexes from blood circulation. FcgR III (CD16) is expressed in macrophages, granulocytes and NK cells. CD16 on granulocytes is phosphatidyl inositol glycan (GPI) anchored whereas the CD16 expressed on NK cells and macrophages is polypeptide anchored. These two membrane anchor isoforms of CD16 differ in triggering signals for tumor cell cytotoxicity and phagocytosis. Further structure-function studies will be carried out on membrane isoforms of CD16. We have also identified that the avidity state of FcgRII is regulated by cell activation. Future studies will focus on the defining the molecular mechanisms involved in regulation of affinity of FcgRII molecule expressed on human neutrophils.
Student Requirements: Chemistry
Sophomore, Juniors, Seniors
Accepts 2nd year students? Y
Suggested Reading (References):
(1) Cimino, AM, Kim, AC, and P. SELVARAJ. Cancer Vaccine Development: Protein Transfer of Membrane-anchored Cytokines and Immunostimulatory Molecules. Immunol Res. 2004; 29:231-40
(2) Bumgarner, GW, Zampell, JC., Nagarajan, S, Poloso, NJ., Dorn, AS, D'Souza MJ, and P. SELVARAJ. Modified cell ELISA to determine the solubilization of cell surface proteins: Applications in GPI-anchored protein purification. J. Biochem. Biophys. Methods 2005; 64:99-109.
(3) SELVARAJ P, Fifadara NH, Cimino A, and Wang G. Functional Regulation of Human Neutrophil Fc gamma Receptors. Immunol Res. 2004 29:219-30
(4) Poloso NJ, Nagarajan S, Mejia-Oneta JM, SELVARAJ P. GPI-anchoring of GM-CSF results in active membrane-bound and partially shed cytokine. Mol Immunol. 2002; 38:803-16.
(5) Nagarajan S, Fifadara N, and P. SELVARAJ. Signal specific activation and regulation of human neutrophil Fc gamma receptors. J. Immunol 2005; 174: 5423-32.
Techniques used in this lab:
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Michael Koval. Pulmonary Medicine.
Phone: 404-712-2976
Email: mhkoval@emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Spring,Summer,Fall
Lab Positions: 1
Project Description: We use a combination of molecular, cell biology and physiological techniques to study how cells regulate intercellular communication pathways and roles for these pathways in health and disease. Research in my lab falls into three major categories: 1) Trafficking and assembly of membrane proteins at cell junctions, 2) Roles for intercellular communication in lung function and injury, 3) Interplay between cell adhesion and endocytosis
Additional Project Information: For more information and references please see: http://userwww.service.emory.edu/~mhkoval/
Student Requirements: Completion of first year chemistry preferred. Also, an interest in biomedical research and the ability to work independently are encouraged. Students are required to participate in general laboratory maintenance in addition to work on their project.
Accepts 2nd year students? Y
Suggested Reading (References):
(1) Daugherty, B.L., et al., Regulation of heterotypic claudin compatibility.
J Biol Chem. 282:30005-30013. (2007).
(2) Patel A.S., et al. Paracrine stimulation of surfactant secretion by extracellular ATP in response to mechanical deformation. Am J Physiol Lung Cell Mol Physiol. 289:L489-96. (2005).
(3) Daugherty, B.L., et al., Developmental regulation of claudin localization by fetal alveolar epithelial cells. Am J Physiol Lung Cell Mol Physiol. 287:L1266-73 (2004).
(4) Abraham V., et al. Heterocellular gap junctional communication between alveolar epithelial cells. Am J Physiol Lung Cell Mol Physiol. 280:L1085-93 (2001).
(5) Abraham V., et al. Phenotypic control of gap junctional communication by cultured alveolar epithelial cells. Am J Physiol. 276:L825-34 (1999).
Techniques used in this lab: Molecular biological approaches to create chimeric and mutant junction proteins to identify sorting and assembly motifs, Development of cultured cell models which mimic in vivo cell-cell interactions using established cell lines and primary lung epithelial cells, Quantitative fluorescence microscopy to examine protein expression, membrane trafficking and cell-cell communication
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Hui Mao. Radiology.
Phone: (404) 712-0357
Email: hmao@emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Spring,Summer,Fall
Lab Positions: 1
Project Description: Developing and characterization of novel MRI contrast agents for target specific cancer imaging in vivo and for other diagnostic imaging applications.
Additional Project Information: Metabolite profiling of biological samples, e.g, tissue, cells, using high resolution solid state NMR.
Student Requirements:
Accepts 1st year students? Y
Accepts 2nd year students? Y
Techniques used in this lab: magnetic resonance imaging, magnetic resonance spectroscopy, medical image process and analysis
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Douglas Falls. Cell Biology.
Phone: 404-727-0520
Email: dfalls@emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Spring,Summer,Fall
Lab Positions: 0
Project Description: Neurogenesis (more later)
Additional Project Information: Synaptogenisis (more later)
Student Requirements: any level (more later)
Accepts 1st year students? Y
Accepts 2nd year students? Y
Suggested Reading (References):
(1) Falls DL (2003) Neuregulins: functions, forms, and signaling strategies. Exp Cell Res 284:14-30.
(2) Falls DL (2003) Neuregulins and the neuromuscular system: 10 years of answers and questions. J Neurocytol 32:619-647.
(3) Coskun V, Falls DL, Lane R, Czirok A, Luskin MB (in preparation 2005) Subventricular zone neuronal progenitors undergo multiple divisions and retract their processes prior to each cytokinesis.
(4) Bonsall JM, Falls DL, Luskin MB (in preparation) Extracellular matrix and/or cell surface associated molecules restrict neuronal progenitors to the rostral migratory stream.
Techniques used in this lab:
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Pradip De. Hemat & ,Medical Oncol..
Phone: 4047783037
Email: pde@emory.edu
Institution: WCI; Emory
Location: On Campus (Emory main campus)
Availability: Summer
Lab Positions: 1
Project Description: Studying the signal-biology in the tumorogenesis of hormone positive breast cancer.
Additional Project Information: Studying the signal-biology in the tumorogenesis of HER2 over expressed breast cancer.
Student Requirements: Undergraduate
Accepts 1st year students? Y
Accepts 2nd year students? Y
Techniques used in this lab: Cell culture, Integrin directed cell movement, Kinase and GTP-ase assay,Hypoxia, RT-PCR.
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Shanthi Sitaraman. Medicine.
Phone: 404-727-2430
Email: ssitar2@emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Spring,Summer,Fall
Lab Positions: 1
Project Description: Characterization of the role of metalloproteinases in inflammatory bowel disease. We have shown that metalloproteinases cause worsening of colitis. The project will involve studying the effect of metalloproteinases in vitro intestinal cell lines using inflammatory, wound healing as read-out assays.
Additional Project Information: Elucidate the regulation and role of adenosine receptor in inflammatory bowel disease
Student Requirements: Previous laboratory experience preferred but not necessary
Accepts 1st year students? Y
Accepts 2nd year students? Y
Suggested Reading (References):
(1) Castaneda et. al. Targeted deletion of metalloproteinase attenuates colitis. Gastroenterology 2005
Techniques used in this lab: Western blot, zymography, cloning, PCR, bacterial assays, immunohistochemistry
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June Scott. Microbiology.
Phone: 404-727-0402
Email: scott@Microbio.emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Spring,Summer,Fall
Lab Positions: 2
Project Description: Regulation of gene expression in Streptococcus pyogenes
Additional Project Information: Mechanism of attachment of proteins to the surface of Streptococcus pyogenes
Student Requirements: Some knowledge of molecular biology from coursework; some lab experience using micropipettes
Accepts 2nd year students? Y
Suggested Reading (References):
(1) See http://www.microbiology.emory.edu/scott/index.htm
Techniques used in this lab:
Additional Comments: We have had undergraduates in the lab for many years. Several have co-authored papers. Those going to grad school find their experience in our lab helps them get accepted by the school of their choice and receive fellowships.
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Paul Doetsch. Biochemistry.
Phone: 404-727-0409
Email: medpwd@emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Spring,Summer,Fall
Lab Positions: 1
Project Description: Project would address some aspects of the interconnections between DNA repair and DNA damage tolerance systems in the management of DNA damage using a simple eukaryotic model system (yeast) in order to understand this process in higher organisms (i.e. humans) and its relationship to the development of cancer. Techniques would include genetic, biochmical and molecular biological experimental strategies.
Additional Project Information: We are also using the yeast model system and its genetic and biochemical dissectability to elucidate the mechanisms of action of anticancer drugs and to use isogenic strains of yeast as a potential rapid, inexpensive drug screening tool.
Student Requirements: General science background in biology or chemistry. Undergraduate genetics would be very useful but not absolute requirement.. Undergraduate biochemistry would be useful but not required.
Suggested Reading (References):
(1) Evert BA, Salmon TB, Song B, Liu JJ, Siede W, Doetsch PW. (2004) Spontaneous DNA Damage in Saccharomyces cerevisiae Elicits Phenotypic Properties Similar to Cancer Cells. J. Biol. Chem. 279: 22585-22594.
(2) Beljanski V, Marzilli L, Doetsch PW. (2004) DNA Damage Processing Pathways Involved in the Eukaryotic Cellular Response to Anticancer DNA Crosslinking Agents. Mol. Pharm. 65:1496-1506
(3) Doudican NA, Song B, Shadel GS, Doetsch PW. (2005) Oxidative DNA Damage Causes Mitochondrial Genetic Instability in Saccharomyces cerevisiae. Mol. Cell Biol. 25: 5196-5204.
(4) Salmon TB, Evert BA, Song B, Doetsch PW. (2004) Biological Consequences of Oxidative Stress-Induced DNA Damage in Saccharomyces cerevisiae. Nucleic Acids Res. 32: 3712-3723.
(5) O'Rourke T, Doudican NA, Zhang H, Eaton JS, Doetsch PW, Shadel GS. (2005) Differential Involvement of the Related DNA Helicases Piflp and Rrm3p in mt DNA Point Mutagenesis and Stability. Gene 354: 86-92.
Techniques used in this lab: Yeast genetic manipulatiions including strain construction, mutagenesis and recombination assays, and biochemical techniques such as protein purificatiion and Western blot analysis. Cell biological techniques such as fluorescence microscopy and cell sorting and analysis are also likely to be used.
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Keith Berland. Physics.
Phone: 404 712 9061
Email: kberland@physics.emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Spring,Summer,Fall
Lab Positions: 2
Project Description: A wide variety of undergraduate research opportunities are available in the biophotonics lab, ranging from the development of novel optical instrumentation to the application of high-sensitivity fluorescence measurements to investigate protein dynamics and interactions in living cells. Many of our research projects are highly interdisciplinary, and appropriate for students interested in physics, biophysics, biochemistry, and even cell biology. Students interested in instrumentation can participate in designing and building new optical devices, or in writing software for instrument control and data analysis. Interested students should contact the PI about specific current opportunities.
Student Requirements: Preferable to have a strong math background and or computer programming skills, but not specifically required. Molecular biology skills are also useful.
Accepts 2nd year students? Y
Suggested Reading (References):
(1) Observation Volumes and Gamma Factors in Two-Photon Fluctuation Spectroscopy. Biophysical Journal. Vol. 89, 2077-2090
(2) Characterizing Observation Volumes and the Role of Photophysical Dynamics in One-Photon Fluorescence Fluctuation Spectroscopy. Journal of Biomedical Optics Vol 10(4). 044015, 1-9
(3) Saturation Modified Point Spread Functions in Two-Photon Microscopy. Microscopy Research and Technique. Vol. 64, 135-141.
(4) High Sensitivity Detection of Specific DNA Molecules Using Dual-Color Two-Photon Fluorescence Correlation Spectroscopy. Journal of Biotechnology. Vol. 108, 127-136.
(5) Fluorescence Correlation Spectroscopy: A New Tool for Quantification of Molecular Interactions , Protein-Protein Interactions: Methods and Protocols (ed. H. Fu), Humana Press. Pp. 383-397.
Techniques used in this lab: Some reserach tools you may learn about and use in the lab include: Fluorescence Microscopy, Fluctuation Spectroscopy, Laser Physics, Two-photon microscopy, Nuclear Localization Signal Biophysics, Protein Conjugation, Amyloid Peptide Self-assembly, Biophysics of the Intracellular Environment
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David Pallas. Biochemistry/WCI.
Phone: 404-727-5620
Email: dpallas@emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Spring,Summer,Fall
Lab Positions: 0
Project Description: PP2A is an important phosphatase involved in the regulation of the cell cycle, of apoptosis, and of neuronal function. It has been implicated in both cancer and Alzheimer's Disease. An example of a project an undergraduate could carry out would be to investigate the mechanism of regulation of PP2A by methylation, phosphorylation, etc. Approaches could include shRNA knockdown of enzymes that regulate PP2A, cell biological approaches using time-lapse microscopy, immunological and biochemical monotoring of PP2A's modification and activity, and a variety of other possible genetic, cell biological, or biochemical approaches.
Student Requirements: Juniors and seniors only, unless there are exceptional circumstances where the student has taken a variety of college level biochemistry and related courses.
Techniques used in this lab:
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Dipali Sharma. Winship Cancer Institute.
Phone: 404-778-3265
Email: dsharma@emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Spring,Summer,Fall
Lab Positions: 2
Project Description: Selective estrogen receptor modulators, or SERMs, are a class of compounds that can act as estrogen receptor (ER) agonists in some tissues while acting as ER antagonists in others. SERMs are being evaluated and used to treat and prevent such diseases as breast cancer, osteoporosis and cardiovascular disease. The biochemical mechanisms underlying the tissue selectivity of SERMs, however, remain largely unknown. During past couple of years, several laboratories have identified many important co-regulatory molecules that play a central role in mediating the transcriptional activity of many nuclear receptors including ER. Our hypothesis is that the differential expression and interaction of these molecules accounts in part for the tissue-specific selectivity of selective ER modulators, such as tamoxifen and raloxifene.
Also, a major focus of our studies is directed towards understanding, at the cellular and molecular levels, the factors conferring estrogen-independence and antiestrogen resistance and those responsible for affecting estrogen responsiveness. Tamoxifen is the most common endocrine agent used at all stages of breast cancer. ER ? status has been used to identify breast cancer patients who are likely to respond to tamoxifen, but resistance nonetheless occurs in almost 50% of treated ER? positive breast cancer patients. We believe that this resistance could be because of dysregulation of ER interacting co regulatory proteins in breast cancer.
Student Requirements: Cell biology, Molecular biology, Biochemistry
Accepts 1st year students? Y
Accepts 2nd year students? Y
Techniques used in this lab: Cloning, mutagenesis, electrophoresis, transfection, Immunoprecipitaion, ChiP, Methylation Specific PCR, PCR, RT-PCR etc
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Danny Reines. Biochemistry.
Phone: 4047273361
Email: dreines@emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Summer
Lab Positions: 0
Project Description: We are working with yeast to understand a new gene regulatory circuit that controls transcription.
Student Requirements: lab courses or prior work in a lab would help,
biology/chemistry coursework useful for conceptual background
Accepts 2nd year students? Y
Suggested Reading (References):
(1) Kopcewicz KA, O'Rourke TW, Reines D.
Free in PMC
Metabolic regulation of IMD2 transcription and an unusual DNA element that generates short transcripts.
Mol Cell Biol. 2007 Apr;27(8):2821-9. Epub 2007 Feb 12.
(2) McPhillips CC, Hyle JW, Reines D.
Free in PMC
Detection of the mycophenolate-inhibited form of IMP dehydrogenase in vivo.
Proc Natl Acad Sci U S A. 2004 Aug 17;101(33):12171-6
(3) Smith KT, Coffee B, Reines D.
Free Full Text
Occupancy and synergistic activation of the FMR1 promoter by Nrf-1 and Sp1 in vivo.
Hum Mol Genet. 2004 Aug 1;13(15):1611-21. Epub 2004 Jun 2.
(4) Shaw RJ, Bonawitz ND, Reines D.
Free Full Text
Use of an in vivo reporter assay to test for transcriptional and translational fidelity in yeast.
J Biol Chem. 2002 Jul 5;277(27):24420-6. Epub 2002 May 2.
(5) Shaw RJ, Wilson JL, Smith KT, Reines D.
Free Full Text
Regulation of an IMP dehydrogenase gene and its overexpression in drug-sensitive transcription elongation mutants of yeast.
J Biol Chem. 2001 Aug 31;276(35):32905-16. Epub 2001 Jul 5.
Techniques used in this lab: Northern blotting, recombinant DNA assembly, cell transformation, introducing DNA into the genome via homologus recombination, PCR and RT-PCR, primer extension end mapping and others.
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Nael McCarty. Pediatrics.
Phone: 727-3654
Email: namccar@emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Summer
Lab Positions: 1
Project Description: Our lab has identified a peptide toxin inhibitor of CFTR, the chloride channel protein defective in Cystic Fibrosis. The summer project would entail the production of mutant forms of this toxin, which we call GaTx1, and performance of electrophysiological experiments to test the efficacy of inhibition by the mutant toxins. Students will learn: molecular biology, recombinant protein production, electrophysiology.
Student Requirements: Rising junior at least, having completed basic biology courses and had some wet lab experience.
Accepts 1st year students? Y
Accepts 2nd year students? Y
Suggested Reading (References):
(1) 25) Fuller, M.D., C.H. Thompson, Z.-R. Zhang, C. Freeman, B. Sarkadi, G. Szakacs, D. McMaster, R.J. French, J. Pohl, J. Kubanek, and N.A. McCarty (2007) State-dependent inhibition of CFTR chloride channels by a novel peptide toxin. J. Biol. Chem. 282:37545-37555.
(2) 23) Fuller, M.D., Z.-R. Zhang, G. Cui, and N.A. McCarty (2005) The block of CFTR by scorpion venom is state-dependent. Biophys. J. 89: 3960-3975.
(3) 22) Thompson, C.H., D.M. Fields, Olivetti, P.R., M.D. Fuller, Z.-R. Zhang, and N.A. McCarty (2005) Inhibition of ClC-2 Cl- channels by a peptide component of scorpion venom. J. Membr. Biol. 208: 65-76.
(4) 1) Thompson, C.H., P.R. Olivetti, M.D. Fuller, C.S. Freeman, D. McMaster, R.F. French, J. Pohl, J. Kubanek, and N.A. McCarty. Isolation of a peptide toxin inhibitor of ClC-2 voltage-gated chloride channels. (submitted)
Techniques used in this lab: Molecular biology (mutagenesis, sequencing, plasmid manipulation); recombinant protein production (biochemistry, HPLC); electrophysiology (patch-clamp)
Additional Comments: News release on this project: http://gtresearchnews.gatech.edu/reshor/rh-ws08/venom.pdf
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Gary Bassell. Cell Biology/Neurology.
Phone: 404-727-3772
Email: gbassel@emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Spring,Summer,Fall
Lab Positions: 2
Project Description: The objective of the project is to use cell and molecular biological methods to investigate defects in the development of nerve cells in a mouse model of an inherited neurological disease. The student will learn methods in: nerve tissue processing, nerve cell culture, immunocytochemistry and DNA/RNA analysis. At the end of the project, it is expected that the student will have analyzed for a possible impairments in the protein and mRNA composition of specific nerve and synapse populations. Throughout the project, the student will receive training in the required methods from a PhD neuroscientist. The student will also have opportunities to interact with graduate and undergraduate students.
Student Requirements: rising juniors and seniors only
Suggested Reading (References):
(1) Zhang et al. 2001. Neurotrophin induced transport. Neuron. 31.261-275.
(2) Zhang et al. 2003. Active transport of SMN. Journal of Neuroscience. 23. 6627-6637.
(3) Antar et al. 2004. Metabotropic glutamate receptor activation. Journal of Neuroscience.24.2648-2655
(4) Bassell and Kelic. 2004. Binding proteins for mRNA localization. Curr Opin Neurobiol.14.574-581.
(5) Antar and Bassell. 2003. Sunrise at the Synapse. Neuron. 37.555-558.
Techniques used in this lab: nerve tissue processing, cell culture, gel electrophoresis, PCR, immunohistochemistry, confocal microscopy
Additional Comments: Dr. Bassell has a long standing history of mentorship in undergraduate research.
You will learn a lot and also have fun in the process!
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EUGENE DEMCHUK. Division of Toxicology.
Phone: 770-488-3327
Email: edemchuk@cdc.gov
Institution: CDC/ATSDR
Location: Off-campus (personal vehicle required, carpool possible but not guaranteed)
Availability: Spring,Summer,Fall
Lab Positions: 2
Project Description: Autism Spectrum Disorder (ASD) is an increasingly common developmental disability in industrial nations. ASD is thought to result from gene-environment interactions. Despite research progress in identifying candidate genes associated with ASD, no clear etiology or causative marker has been found. If and when a genetic predisposition is identified, the next research question will be: What environmental trigger is responsible for the development or manifestation of the clinical phenotype? To address this question we develop a rapid-screening computational toxicology methodology which can be applied to large numbers of environmental pollutants (ligands) and a known or suspected biological target for autism. Starting with a model database of hypothesized chemical triggers and a set of critical-pathway genes, we screen the chemicals against known genetic variants using state-of-the-art molecular docking techniques. Top scored gene/chemical combinations potentially offer an educated choice for further in-depth analysis of gene-environment interactions using laboratory and/or epidemiological methods.
Additional Project Information: The Agency for Toxic Substances and Disease Registry (ATSDR) Computational Toxicology and Method Development Laboratory implements the full range of methods in support of ATSDR mission to protect human populations from exposure to environmental contaminants. These include benchmark dose, chemical-specific adjustment factor, physiologically-based pharmacokinetic, quantitative structure-activity relationship (QSAR), genetic-susceptibility- and meta-analysis modeling, and modeling the toxicity of chemical mixtures. Computational toxicology methods are used as an integrated systematic approach in the development of ATSDR Minimal Risk Levels to be used as health guidance values to protect populations exposed to toxic chemicals at hazardous waste sites. These methods are also used in the development of ATSDR Toxicological Profiles, to support environmental health consultations and prioritization of environmental chemical hazards, when experimental information is insufficient, and to improve study design, when filling the priority data needs as mandated by the Congress. Also, the Laboratory is engaged in the development of response strategies to new emerging chemical threats. We develop methods for assessing toxicological effects of potentially hazardous chemicals from their chemical structure alone. A need for analysis of this type is especially imminent during the times of emergencies, whether it is an accidental chemical release, major natural disaster, or terrorist threat in all situations when time is a critical element of public health response.
Student Requirements: chemistry, toxicology and/or physiology, statistics, biochemistry, basic understanding of principles in physics, basic math
Accepts 1st year students? Y
Accepts 2nd year students? Y
Suggested Reading (References):
(1) Demchuk, E.; Ruiz, P.; Wilson, J.D.; Scinicariello, F.; Pohl, H.R.; Fay, M.; Mumtaz, M.; Hansen, H.; De Rosa, C.T. Computational toxicology methods in public health practice . Toxicol. Mech. Method. 2008, 18, 119135.
(2) Snyder, J.A.; Demchuk, E.; McCanlies E.C.; Schuler, C.R.; Kreiss, K.; Frye, B.; Ensey, J.; Stanton, M.; Weston, A. Impact of negatively charged patches on the surface of MHC class II antigen-presenting proteins on risk of chronic beryllium disease . J. R. Soc. Int. 2008, 5, 749758.
(3) Demchuk, E.; Albin, B.C.; Fay, M.; Garrett, R.M.; Hansen, H. Structure-activity analysis of chemical health guidance values . Toxicologist (Suppl. to Toxicol. Sci.) 2006, 90, 186.
(4) Demchuk, E.; Yucesoy, B.; Johnson, V.J.; Weston, A.; Germolec, D.; De Rosa, C.T.; Luster, M.I. A statistical model to assess genetic susceptibility as a risk factor in multifactorial diseases: Lessons from occupational asthma . Environ. Health Persp. 2007, 115, 231234.
(5) Hnizdo, V.; Darian, E.; Fedorowicz, A.; Demchuk, E.; Li, S.; Singh, H. Nearest-neighbor nonparametric method for estimating the configurational entropy of complex molecules . J. Comp. Chem. 2007, 28, 655668.
Techniques used in this lab: Students may learn various computational toxicology techniques, including benchmark dose modeling, chemical-specific adjustment factor modeling, physiologically-based pharmacokinetic/pharmacodynamic modeling, (quantitative) structure-activity relationship -- (Q)SAR modeling, genetic-susceptibility- and meta-analysis modeling, modeling the toxicity of chemical mixtures and chemical-chemical interactions, molecular docking, protein homology structure modeling, and other.
Additional Comments: A brief description of the ATSDR Computational Toxicology lab can be found at http://www.atsdr.cdc.gov/dtem/programs/comptox/index.html
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Neeraj Saxena. Medicine/Digestive Dis..
Phone: 4047275623
Email: nksaxen@emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Summer,Fall
Lab Positions: 2
Project Description: Current research project focus on elucidation of the molecular mechanisms underlying links between obesity, adipocytokines and carcinogenesis. Specifically, to understand the suppressive role of Adiponectin in the Leptin induced growth and metastasis of human hepatocellular carcinoma.
Student Requirements: junior or senior with biology background
Accepts 1st year students? Y
Accepts 2nd year students? Y
Suggested Reading (References):
(1) Neeraj K. Saxena, LaTonia Taliaferro Smith, Brandi Brandon, Frank A. Anania and Dipali Sharma (2008). Bidirectional cross talk between leptin and IGF-1 signaling promotes invasion and migration of triple-negative breast cancer cells via transactivation of EGFR. Cancer Research. 2008, (68): 9712-9722.
(2) Neeraj K. Saxena, Paula M. Vertino, Frank A. Anania and Dipali Sharma (2007). Leptin induced growth stimulation of breast cancer cells involves recruitment of histone acetyltransferases and mediator complex to cyclin D1 promoter via activation of Stat3. The Journal of Biological Chemistry. 2007, 282(18): 13316-13325.
8. Neeraj K. Saxena, Paula M. Vertino, Frank A. Anania and Dipali Sharma (2007). Leptin
induced growth stimulation of breast cancer cells involves recruitment of histone acetyltransferases and mediator complex to cyclin D1 promoter via activation of Stat3. The Journal of Biological Chemistry. 2007, 282(18): 13316-13325.
(3) Neeraj K. Saxena, Dipali Sharma, Songbai Lin, Xiaokun Ding, Didier Merlin and Frank A. Anania. (2007). Concomitant activation of the JAK/STAT, PI3K/AKT and ERK signaling is involved in leptin mediated promotion of invasion and migration of hepatocellular carcinoma cells. Cancer Research. 2007, 67(6): 2497-2507.
(4) Songbai S. Lin, Xiaokun Ding, Neeraj K. Saxena, Lance L. Stein, and Frank A. Anania. (2006) Leptin increases Tissue Inhibitor of Metalloproteinase I (TIMP-1) gene expression by a dual Sp1/STAT3 mechanism. Molecular Endocrinology. 2006, 20(12): 3376-3388.
(5) Xiaokun Ding, Neeraj K. Saxena, Songbai lin, Amin Xu, Shanthi Srinivasan, and Frank A. Anania (2005). The role of leptin and adiponectin: a novel paradigm in adipocytokine regulation of liver fibrosis and stellate cell biology. American Journal of Pathology. 2005 June; 166(6): 1655-1669.
Techniques used in this lab: Cell culture, Transfection, Westren-blot, Cloning, plasmid-bacterial work, immunohistochemistry, RT-PCR,
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Gregg Orloff. none.
Phone: 404-727-0308
Email: gorloff@emory.edu
Institution: Emory
Location: Off-campus (but accessible via shuttle, e.g., Grady or VA Hospitals)
Availability: Spring,Summer,Fall
Lab Positions: 2
Project Description: CancerQuest (http://www.cancerquest.org) is an award-winning cancer education project designed to educate and empower cancer patients, caregivers, students and the general public.
We produce content, videos, animations, games, posters and other educational tools.
Students, depending on their interest and skills, could be involved in all aspects of the program including researching, science writing, video creating and editing, graphics, programming, etc.
Student Requirements: Some Biology background and an interest in education/outreach. Computer skills are not necessary but the student must have the desire to learn new programs.
Accepts 1st year students? Y
Accepts 2nd year students? Y
Suggested Reading (References):
(1) Breast Cancer: A Patient's Journey (DVD)
(2) COMPASS: Breast Cancer Edition (DVD)
(3) Gastrostomy Tubes (DVD)
Techniques used in this lab: Science writing, video editing, Flash, HTML (some), Web programming (if interested).
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Stefan Lutz. Chemistry.
Phone: 404-712-2170
Email: sal2@emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Spring,Summer,Fall
Lab Positions: 1
Project Description: We do a wide variety of protein engineering studies, tailoring these biocatalysts to work with unnatural substrates, to perform novel reactions, and to function in the laboratory environment (elevated reaction temperature, organic solvents etc.)
Student Requirements: classes in organic chemistry and biochemistry
Accepts 1st year students? Y
Accepts 2nd year students? Y
Techniques used in this lab: Gene cloning (molecular biology), working with bacteria and yeast (microbiology), protein purification & enzyme kinetics (biochemistry), organic synthesis, biophysical methods (spectroscopy, calorimetry,...)
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Byeongwoon Song. Pediatrics.
Phone: 404-727-1746
Email: bsong4@emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Spring,Summer,Fall
Lab Positions: 1
Project Description: We are interested in the cellular functions and potential antiviral activities of the tripartite motif (TRIM) family proteins.
The TRIM proteins contain a RING finger domain, one or two B-box domains, and coiled coil domain, and the RBCC structure is followed by a variety of C-terminal domains. The RING domain of many TRIM has been shown to have E3 ubiquitin ligase activity, whereas the B box and coiled coil domains may be involved in protein-protein interactions and homo/heterodimerization.
Some TRIM proteins were shown to be involved in a variety of cellular functions including cell proliferation, differentiation, development, oncogenesis, and apoptosis, but the functions of most TRIM proteins are not well understood. It has been reported that several TRIM proteins are up-regulated by type I interferons (IFN) suggesting potential innate immune functions, and it was shown that some TRIM proteins have an antiviral activity.
Using various biochemical and cell biology tools, we will determine the cellular functions and potential antiviral activities of TRIM family proteins.
Student Requirements: Junior or senior with Biochemistry or Molecular Biology coursework completed or in progress.
Suggested Reading (References):
(1) 13. Song B, Javanbakht H, Perron M, Park DH, Stremlau M and Sodroski J. Retrovirus restriction by TRIM5a variants from Old World and New World primates. J. Virol 2005; 79:3930-3937.
(2) 17. Stremlau M, Perron M, Lee M, Yuan L, Song B, Javanbakht H, Diaz-Griffero F, Anderson DJ, Sundquist WI, and Sodroski J. Specific recognition and accelerated uncoating of retroviral capsids by the TRIM5a restriction factor. Proc. Natl. Acad. Sci. USA 2006; 103:5514-5519.
(3) 19. Si Z, Vandegraaff N, Ohuigin C, Song B, Yuan W, Xu C, Perron M, Li X, Marasco WA, Engelman A, Dean M and Sodroski J. Evolution of a cytoplasmic tripartite motif (TRIM) protein in cows that restricts retroviral infection. Proc. Natl. Acad. Sci. USA 2006; 103:7454-7459
Techniques used in this lab: Plasmid DNA isolation, Cloning, Cell culture, Transfection, Western blotting, Immunoprecipitation, Immunostaining, ELISA, and Flow cytometry
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