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Steve Potter. Biomedical Engineering.
Phone: 404 385-2989
Email: steve.potter@bme.gatech.edu
Institution: Georgia Tech-Emory
Location: Off-campus (but accessible via shuttle, e.g., Grady or VA Hospitals)
Availability: Spring,Summer,Fall
Lab Positions: 2
Project Description: See http://neuro.gatech.edu for ideas about projects in our lab.
Student Requirements: Depends on project. All backgrounds considered.
Accepts 1st year students? Y
Accepts 2nd year students? Y
Suggested Reading (References):
(1) See http://neuro.gatech.edu/groups/potter/publications.html
Techniques used in this lab: Depends on project, but may include optical microscopy, multi-electrode electrophysiology, cell culture, computer programming, mechanical design, and others.
Additional Comments: http://neuro.gatech.edu/groups/potter/people.html
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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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Christopher Beck. Biology.
Phone: 404-712-9012
Email: cbeck@biology.emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Spring,Fall
Lab Positions: 0
Project Description: Students would examine the effects of sex ratio on variation in spermatophore production by males and reproductive behavior in males and females in insects.
Additional Project Information: Effects of age on mate choice decisions. Energy allocation during tadpole development.
Student Requirements: background in ecology, evolution, or animal behavior is helpful, but not essential
Accepts 1st year students? Y
Accepts 2nd year students? Y
Techniques used in this lab: behavioral assays, automated behavioral data collection, statistical analysis
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Rachelle Spell. Biology.
Phone: 404-727-5828
Email: rachelle.spell@emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Spring,Summer,Fall
Lab Positions: 0
Project Description: Th student will perform site-directed mutagenesis to genes involved in the regulation of recombination in the model system of budding yeast.
Student Requirements: Background in introductory biology, genetics
Accepts 1st year students? Y
Accepts 2nd year students? Y
Techniques used in this lab:
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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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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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Arthur English. Cell Biology.
Phone: 404-727-6250
Email: art@cellbio.emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Spring,Summer,Fall
Lab Positions: 2
Project Description: After peripheral nerve injury, axons are capable of regeneration but restoration of function is universally poor. This is often blamed on a progressive loss of the ability of cells in the distal stumps of injured nerves to promote regeneration. We have discovered that electrical stimulation or exercise will stimulate the growth of regenerating axons in peripheral nerves in a manner that does not depend on cells in their environment. Using transgenic mice we will investigate whether these methods can be used to promote axon regeneration when the repair of the damaged nerve is delayed.
Additional Project Information: Electrical stimulation and treadmill exercise has been shown to increase the growth of regenerating axons. It is speculated that these methods exert their effects by enhancing activity in spinal neural networks. Using electrophysiological recordings from intact rats, we will study the magnitude of simple spinal reflexes after electrical stimulation or/and treadmill exercise.
Student Requirements: The most successful students are those who are rising seniors. Younger students who are rising juniors who are especailly highly motivated also work well. Background in biology and chamistry is a must.
Accepts 2nd year students? Y
Suggested Reading (References):
(1) Groves, ML., McKeon, R., Werner, E., Nagarsheth, M., Meador, W., English, A.W., Axon regeneration in peripheral nerves is enhanced by proteoglycan degradation. Exp. Neurol. 195: 278-292, 2005.
(2) English, A.W., Meador, W., Carrasco, D.I., Neurotrophin 4/5 is required for the early growth of regenerating axons in peripheral nerves. Eur J Neurosci, 21: 26242634, 2005.
(3) English, A.W., Enhancing axon regeneration in peripheral nerves also increases functionally inappropriate reinnervation of targets. J. Comp. Neurol. 490: 427-441, 2005.
(4) English, A.W., Schwartz, G., Meador, W., Sabatier, M.J., and Amanda Mulligan Electrical stimulation promotes peripheral axon regeneration by enhanced neuronal neurotrophin signaling. J. Neurobiol. In Press, 2007.
(5) Pol-Rodriguez, M.M., Schwartz, G. and English, Arthur W. Post-Translational Phosphorylation of the Slow/b Myosin Heavy Chain Isoform in Adult Rabbit Masseter Muscle. J. Mus. Res. Cell Motil. 22: 513-519, 2002.
Techniques used in this lab: survival surgery, confocal microscopy, electromyography
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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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Jeff Boatright. Ophthalmology.
Phone: 404 778-4113
Email: jboatri@emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Spring,Summer,Fall
Lab Positions: 0
Project Description: Dr. Boatright is a graduate of Brown University (Sc.B. in Neural Sciences and Experimental Psychology) and Emory University (Ph.D. in Pharmacology and the Neurosciences Training Program). He joined the faculty of the Department of Ophthalmology in 1999, conducting research on the regulation of retinal gene expression funded by an independent R01 grant from the National Institutes of Health National Eye Institute (NIH NEI). This research expanded into using endogenous DNA repair mechanisms treat genetic mutations that lead to blindness, work also funded by an independent NEI R01. In a separate project, Dr. Boatright uses in vivo pharmacological approaches to explore the effects of atypical, endogenous compounds on animal models of retinal degeneration and glaucoma. This work is funded by the Foundation Fighting Blindness, NIH National Center for Complementary and Alternative Medicine (NIH NCCAM), and a Merit Award from the Veterans Administration.
Additional Project Information: Dr. Boatright is founding and current Editor-in-Chief of Molecular Vision, a peer-reviewed journal dedicated to the dissemination of research results in molecular biology, cell biology, and the genetics of the visual system. The journal is rated second in a field of 14 competing journals and is routinely used as an Open Access exemplar by the National Library of Medicine and The National Institutes of Health Library. The journal is supported by Knights Templar and through initiatives generated in the Department of Ophthalmology.
Student Requirements: We can start from scratch.
Accepts 1st year students? Y
Accepts 2nd year students? Y
Techniques used in this lab:
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Ivan Rasnik. Physics.
Phone: 404-727-4039
Email: irasnik@physics.emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Spring,Summer,Fall
Lab Positions: 2
Project Description: In our lab we study biological systems using single molecule techiques. Currently we are studying several proteins that interact with DNA trying to understand their molecular mechanisms. For example we are looking at a helicase ( a protein that separates DNA or RNA strands) from the Hepatitis C virus, that is essential for virus replication. We are also looking at mismatch repair proteins, that correct errors during the replication process that if go uncorrected may result in cancer and other genetic disorders. By looking at the function of proteins, one at a time we can look at details that are impossible to observe looking at average behavior.
Additional Project Information: We will work towards the development of new approaches to formation of supported lipid bilayers. Present techniques rely on the bilayer formation on a surface, this approach has severe limitations in the applicability of this artificial membranes for membrane protein studies. We will start by exploring the possibilities of patterned surfaces to create lipid bilayers with minimal surface interaction. The physical properties of the lipid bilayers will be studied by single molecule fluorescnce studies of lipids and protein difussion.
Student Requirements: All the techniques we use can be learn if there is dedication and willing to learn. Undergraduate students start working with posdocs or graduate students till they master the technqiues and become independent.
Accepts 1st year students? Y
Accepts 2nd year students? Y
Suggested Reading (References):
(1) Rasnik, I., S. Myong, W. Cheng, T. M. Lohman and T. Ha (2004). Journal of Molecular Biology 336(2): 395-408
(2) Murphy, M. C., I. Rasnik, W. Cheng, T. M. Lohman and T. J. Ha (2004). Biophysical Journal 86(4): 2530-2537
(3) Ha, T., I. Rasnik, W. Cheng, H. P. Babcock, G. H. Gauss, T. M. Lohman and S. Chu (2002). Nature 419(6907): 638-41.
(4) Rasnik, I., McKinney, S. A., Ha T., Accounts of Chemical Research 38 (7): 542-548.
(5) S. Myong, I. Rasnik, C. Joo, T. M. Lohman and T. Ha . In Press, Nature (October 2005).
Techniques used in this lab: Our lab is highly interdisciplinary, the students will be exposed to a variety of techniques, depending on their specific interests they will use a substet of: fluorescence, spectrophotometry, gel purification, general chemistry lab procedures (buffer preparations etc.), surfaces cleaning protocols for single moelcule experiments, covalently polymer coating of glass surfaces, preparation of unilamelar vesicles, formation of supported lipid bilayers, single molecule fluorescence techniques (confocal, total internal reflection), programming (data acquisition, Labview, C++), programming (data analyses, IDL, Matlab, C++)
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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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iain Shepherd. Biology.
Phone: 404-727-2632
Email: ishephe@emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Spring,Summer,Fall
Lab Positions: 2
Project Description: Investigating the in vivo function of zebrafish orthologues of known Hirschsprung disease causing genes.
The enteric nervous system (ENS) is the largest most complicated subdivision of the peripheral nervous system and is completely derived from neural crest stem cells (NCSC). My lab is interested in determining what genes are involved in the specification of the NCSC that form the ENS. We are also interested in determining what molecules are involved patterning the migration of NCSC in the intestine and if these same molecules are involved in patterning the axonal projections of the differentiated ENS neurons in the intestine. These studies are of clinical importance due to pediatric conditions that perturb the normal development of the ENS such as Hirschsprung Disease (HSCR).
Taking advantage of the zebrafish model system we are investigating how known HSCR linked genes, such as Sip1, cause their ENS phenotypes. We have previously shown that the neurotrophic factor GDNF and its receptor complex are absolutely required for normal ENS development in zebrafish as in mouse and human. Using similar techniques we are investigating the function of other known HSCR genes in zebrafish ENS development. These studies are investigating the many unanswered questions as how these known HSCR genes actually cause their ENS phenotypes when mutated.
A student undertaking this type of project would typically carry out a detailed expression analysis of a HSCR associated gene by RT-PCR and wholemount in situ hybridization. This part of the project would involve a significant amount of microscope work. A student would also be involved in perturbing the gene's function in vivo by microinjection of different molecular reagents.
Additional Project Information: Identification and characterization of different zebrafish enteric nervous system (ENS) neuronal subtypes.
The enteric nervous system (ENS) is the largest most complicated subdivision of the peripheral nervous system and is completely derived from neural crest stem cells (NCSC). My lab is interested in determining what genes are involved in the specification of the NCSC that form the ENS. We are also interested in determining what molecules are involved patterning the migration of NCSC in the intestine and if these same molecules are involved in patterning the axonal projections of the differentiated ENS neurons in the intestine. These studies are of clinical importance due to pediatric conditions that perturb the normal development of the ENS such as Hirschsprung Disease (HSCR).
To aid in the analysis of zebrafish ENS mutant we are interested in identifying different ENS neuronal subtypes. A summer student on this project would screen antibodies to identify ones that recognize subsets of zebrafish ENS neurons. After identifying zebrafish cross-reacting antibodies a student would undertake a detail characterization of the spatial and temporal expression pattern of these markers in the developing ENS. The project will involve significant amounts of microscope work.
Student Requirements: Studenst should be Juniors or Seniors. Students need to have completed a genetics course. Preference will be given to those that have taken a Developmental BIology course.
Suggested Reading (References):
(1) Jacy Pietsch, Brett Jakaitis, Derek Stensby, Sarah Dohle, William Talbot, David W. Raible, and Iain T. Shepherd
(2) Shepherd, I. T., Pietsch, J., Elworthy, S., Kelsh, R. N. and Raible, D. W. (2004). Roles for GFR{alpha}1 receptors in zebrafish enteric nervous system development. Development 131, 241-249.
(3) Shepherd, I. T., Beattie, C. E. and Raible, D. W. (2001). Functional analysis of zebrafish GDNF. Dev Biol 231, 420-35.
(4) Elworthy, S., Pinto, J. P., Pettifer, A., Cancela, M. L. and Kelsh, R. N. (2005). Phox2b function in the enteric nervous system is conserved in zebrafish and is sox10-dependent. Mech Dev 122, 659-69
(5) Amiel, J. and Lyonnet, S. (2001). Hirschsprung disease, associated syndromes, and genetics: a review. J Med Genet 38, 729-39.
Techniques used in this lab:
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Donna Maney. NBB/Psychology.
Phone: office: 7-7470
Email: dmaney@emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Spring,Fall
Lab Positions: 2
Project Description: Study #1: We are interested in the neurogenomics of social behavior, and are currently working with a model in which variation in aggression and parenting behavior segregates with a structural rearrangement of chromosome 2. In collaboration with researchers in Human Genetics, we are in the process of mapping this rearrangement and identifying candidate genes we believe contribute toward aggression and parenting behavior. This project involves quantitative real-time PCR and in situ hybridization to quantify expression of candidate genes.
Additional Project Information: Study #2: We are interested behavioral neuroendocrinology, particularly how hormones mediate plasticity in the brain. One of the best ways to study brain plasticity is to look at seasonal animals, such as hamsters or songbirds, which change their behavior and brain morphology dramatically according to season and hormone levels. In the spring, when estrogen levels are high, females respond to male courtship cues by initiating courtship--but when estrogen levels are low in the fall, they don't. We are interested in how estrogen acts in the brain to cause such a big change in behavior. We are working with female songbirds that are treated with either estrogen or placebo and quantifying their behavioral and neuronal responses to auditory cues.
Student Requirements: If doing a wet lab project, completion of a chemistry lab is required (knowledge of pH, molarity, experience with balances and glasswashing). If doing image analysis only, then experience with programs such as Excel and Photoshop is helpful.
Accepts 1st year students? Y
Accepts 2nd year students? Y
Suggested Reading (References):
(1) Maney, D. L. (2008). Endocrine and genomic architecture of life history trade-offs in an avian model of social behavior. General and Comparative Endocrinology, 157, 275-282.
(2) Maney, D. L., Goode, C. T., Lake, J. I., Lange, H. L., and OBrien, S. (2007). Rapid neuroendocrine responses to auditory courtship signals. Endocrinology 148: 5614-5623.
(3) LeBlanc, M. M., Goode, C. T., MacDougall-Shackleton, E. A., and Maney, D. L. (2007). Estradiol modulates brainstem catecholaminergic cell groups and projections to the auditory forebrain in a female songbird. Brain Research 1171: 93-103.
(4) Maney, D. L., Cho, E., and Goode, C. T. (2006). Estrogen dependent selectivity of genomic responses to birdsong. European Journal of Neuroscience 23:1523-1529.
(5) Maney, D. L., Erwin, K. L., and Goode, C. T. (2005). Neuroendocrine correlates of behavioral polymorphism in white-throated sparrows. Hormones & Behavior 48:196-206.
Techniques used in this lab: Immunohistochemistry, in situ hybridization, autoradiography, real-time PCR, image analysis, behavioral quantification.
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Subhabrata Sanyal. Cell Biology.
Phone: 404-727-3758
Email: ssanya2@emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Summer
Lab Positions: 1
Project Description: The fundamental goal of the laboratory is to understand molecular and cellular changes that underlie learning and memory. We use the fruit fly, Drosophila as a model system to investigate signaling networks that operate in neurons during long-term neural plasticity. Essentially, long-term changes require synthesis of new proteins either through translation of pre-existing mRNA at synaptic sites or through activation of transcription. We have established that conserved signaling cascades such as those mediated by cAMP, PKA and MAPK operate in our model system to cause long-term change. These signaling cascades finally impinge on transcription factors, such as AP1 and CREB to drive expression of plasticity genes . Among several broad questions in the field that interest us are studying signaling cross-talk during plasticity and the identification and functional validation of target genes. A unifying aim is to ascertain how these genes regulate learning and memory in intact organisms, thus uncovering conserved principles of learning across species.
The project involves a screen to isolate targets of AP1 activation in neurons using a powerful forward genetic approach. We will utilize the fact that expression of a dominant negative Fos transgene in the eye causes rough and reduced adult eyes. That this phenotype is due to perturbation of endogenous AP1 activity is shown by rescuing this phenotype by co-expressing wild type AP1. We plan to use this background in a classical modifier screen by assaying a collection of mutant lines in this background. A downstream effector or an upstream activator can potentially alter the eye phenotype observed in Fbz animals. This is a powerful yet easy screen and transposon tagging makes gene identification simple and fast. Finally, since there is an observable AP1 phenotype at the neuromuscular synapse, future target validation will be straightforward.
Student Requirements: Juniors and Seniors only, course in genetics favored.
Suggested Reading (References):
(1) Sanyal S, Sandstrom DJ, Hoeffer CA, Ramaswami M.
AP-1 functions upstream of CREB to control synaptic plasticity in Drosophila.
Nature. 2002 Apr 25;416(6883):870-4.
(2) Hoeffer CA, Sanyal S, Ramaswami M.
Acute induction of conserved synaptic signaling pathways in Drosophila
melanogaster.
J Neurosci. 2003 Jul 16;23(15):6362-72. Erratum in: J Neurosci. 2003 Aug
27;23(21):7966.
(3) Sanyal S, Narayanan R, Consoulas C, Ramaswami M.
Evidence for cell autonomous AP1 function in regulation of Drosophila
motor-neuron plasticity.
BMC Neurosci. 2003 Sep 11;4:20.
(4) Sanyal S, Consoulas C, Kuromi H, Basole A, Mukai L, Kidokoro Y, Krishnan KS,
Ramaswami M.
Analysis of conditional paralytic mutants in Drosophila sarco-endoplasmic
reticulum calcium ATPase reveals novel mechanisms for regulating membrane
excitability.
Genetics. 2005 Feb;169(2):737-50. Epub 2004 Nov 1.
Techniques used in this lab: Fly genetics, molecular biology (cloning, RNA in situ etc.), immunohistochemistry, confocal imaging
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William Lewis. Pathology.
Phone: 404-712-9005
Email: wlewis@emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Spring,Summer,Fall
Lab Positions: 3
Project Description: The project would be focused on determining mitochondrial toxicity associated with NRTI antiretroviral therapy used to treat HIV/AIDS. Using transgenic cardiac-targeted murine models, outcomes are assessed using various molecular tools, including Real-time PCR, sequencing, Southern Analysis, gene copy determination, and Western Blotting. Results from 2x2 animal studies will help determine mechanisms of mitochondrial (mt) DNA depletion and NRTI toxicity.
Student Requirements: It is expected that the student has a basic understanding of biological systems and some experience handling pipettor transfer of microliter volumes with some precision. A level of maturity and interest in the research field is also expected.
Accepts 2nd year students? Y
Suggested Reading (References):
(1) Lewis et al, AIDS, 2006, 20:675-684
(2) Lewis et al, Lab Invest, 2005, 85:182-192
Techniques used in this lab: Students will develop proficiency in standard molecular biological techniques including isolation of DNA from tissues, set up of PCR reactions, Western blots, and/or analysis of data.
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Katherine Boss-Williams. Psychiatry.
Phone: 404 712-9771
Email: kwilli4@emory.edu
Institution: Emory
Location: Off-campus (but accessible via shuttle, e.g., Grady or VA Hospitals)
Availability: Spring,Summer,Fall
Lab Positions: 0
Project Description: A student will may perform but is not limited to, stereotaxic surgery, perfusion, immunohistochemistry, histology, drug administration and implantation of minipumps. Also, may conduct behavioral and/or pharmacological experiments using small rodents as subjects. These may include, but are not limited to, testing rats on the Morris Water Maze, the Elevated Plus Maze, monitoring ambulation via a computer-assisted program. The operation of electrical equipment, PCs experimental apparatus, animal handling, testing of subjects, recording of results, and graphing and analyzing data.
Student Requirements: Extremely well organized is a must
Accepts 1st year students? Y
Accepts 2nd year students? Y
Techniques used in this lab: stereotaxic surgery, perfusion, immunohistochemistry, histology, drug administration and implantation of minipumps, testing rats on the Morris Water Maze, the Elevated Plus Maze, monitoring ambulation via a computer-assisted program, animal handling, recording of results, graphing and analyzing data.
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Frans de Waal. Yerkes Primate Center.
Phone: 7-7898
Email: dewaal@emory.edu
Institution: Emory
Location: Other
Availability: Summer
Lab Positions: 2
Project Description: Projects on social behavior and social cognition of primates. Capuchin monkeys near Emory campus, Yerkes Main Ctr.
Student Requirements: anthro, psych, biol
Accepts 2nd year students? Y
Suggested Reading (References):
(1) See www.emory.edu/LIVING_LINKS
for lots of references to our work.
Techniques used in this lab:
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Jaap de Roode. Biology.
Phone: 4047272340
Email: jderood@emory.edu
Institution: Emory University
Location: On Campus (Emory main campus)
Availability: Spring,Summer,Fall
Lab Positions: 2
Project Description: Our lab works on the evolution and ecology of parasites, using parasites of monarch butterflies and rodent malaria as model systems. Projects will involve carrying out experiments with parasites of monarch butterflies, and include maintenance of larvae, adult butterflies and larval food plants.
Student Requirements: No particular experience is required, as long as the student has a keen interest in the research we do, and is meticulous and careful; we maintain sterile techniques to which the student has to conform.
Accepts 1st year students? Y
Accepts 2nd year students? Y
Suggested Reading (References):
(1) De Roode, J. C., Pansini, R., Cheesman, S.J., Helinski, M.E.H., Huijben, S. Wargo, A.R., Bell, A.S., Chan, B.H.K., Walliker, D. & Read, A.F. 2005. Virulence and competitive ability in genetically diverse malaria infections. Proceedings of the National Academy of Sciences of the United States of America 102, 7624-7628.
(2) " De Roode, J.C., Gold, L.R. & Altizer, S.A. (2007) Virulence determinants in a natural butterfly-parasite system. Parasitology 134(5): 657-668.
(3) " De Roode, J.C., Pedersen, A.B., Hunter, M.D. & Altizer, S. (2008) Host plant species affects virulence in monarch butterfly parasites. Journal of Animal Ecology 77, 120-126.
Techniques used in this lab:
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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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Steven Nilsen. Biology.
Phone: 770-784-4678
Email: spnilse@emory.edu
Institution: Oxford College of Emory
Location: Off-campus (but accessible via shuttle, e.g., Grady or VA Hospitals)
Availability: Spring,Summer,Fall
Lab Positions: 4
Project Description: "Investigations into the role of recently evolved morphological features in sexual selection"
As with most animals, sexual selection in Drosophila goes on through multiple contests. Males must successfully court females. Females can reject males based on the quality of their courtship songs and other nuances of the courtship ritual. Males also compete for access to females by defending territories that are presumed to attract fecund females. Males compete using innate patterns of aggression with varying levels of intensity and winners are thought to gain better access to available females. Thus both courtship and territorial behaviors are potential sources for sexual selection.
A recently evolved morphological characteristic in Drosophila males is the sex comb. Only two sub-groups show this feature, which is a row of modified bristles at the third or second and third tarsal segments of the male forelimbs. As the name suggests, the sex combs are thought to be used during copulation. However, preliminary findings show that species in the same sub groups that have sex combs also display aggressive behaviors not yet seen outside of those sub groups. This implicated a role for sex combs in aggression as well as the presumed role for sex combs in courtship has yet to be tested.
In collaboration with Artyom Kopp, who has characterized the evolution of the sex combs and implicated their importance to courtship, students will work with me to study how sex combs are used in copulation and aggressive behavior. We will analyze these behaviors using a variety of species that show different sex comb morphologies. Morphological variance will be compared with quantitative behavioral indexes designed to correlate the development of sex combs with with either altered aggression, courtship or both.
Additional Project Information: "Investigating the role of the gene fruitless in feeding behavior."
The gene fruitless codes for a transcription factor in the sex determination cascade of Drosophila, which is specifically expressed in a dozen neural sub-populations of male flies. These neurons are thought to collectively masculinize behavioral patterns. Thus far, courtship behavior and aggressive behavior are shown to be under the control of fruitless. However, feeding behavior, which is also sexual dimoprhic has not yet been shown to interact with fruitless.
Interested students can expand upon preliminary findings on feeding in fruitless mutants that are supportive of an involvement for fruitless in feeding. Students would use the recently developed CAFE protocol to measure feeding and ask weather the lifespans of control and experimental cohorts.
Investigating the rate of adaptation to altered living conditions in innate social behavioral patterns
Inbred strain of Dorosphila have been inbred for approximately 80 years under very dense culturing conditions. The population density of these cultures and living conditions do not mimic wild habitat. Thus, cultured Drosophila offer an excellent opportunity to investigate adaptation to new environmental parameters.
Interested students will make detailed behavioral comparisons between Drosophila recently isolated from the wild and Drosophila cultured for long periods of time. Aggressive behavior, because of its pattern complexity and sensitivity to socialization, will serve as an excellent marker for adaptation. New comparisons will expand existing unpublished data for publication.
Student Requirements: Students at any level whom have taken Bio141 (introductory biology) and are enrolled in or have taken Bio142 (advanced topics in genetics and molecular biology) will be at a significant advantage. Students with coursework in neuroscience, brain and behavior (NBB) will be at an additional advantage. No previous lab experience is required.
Accepts 1st year students? Y
Accepts 2nd year students? Y
Suggested Reading (References):
(1) Nilsen SP, Chan Y-B, Huber R, and Kravitz EA (2004) Gender-selective patterns of aggressive behavior in Drosophila melanogaster. Proc Natl Acad Sci USA 101(33):12342-12347.
(2) Vrontou E., Nilsen SP, Demir E, Kravitz EA, Dickson E (2006) fruitless splicing determines sex-specific patterns of aggression in Drosophila. Nature Neuro. 9:14691471
(3) Chen S, Lee AY, Bowens NM, Huber R, Kravitz EA. (2002) Fighting fruit flies: a model system for the study of aggression. Proc Natl Acad Sci USA. 2002;99:56645668.
(4) Yurkovic A, Wang O, Basu AC, Kravitz EA (2006) Learning and memory associated with aggression in Drosophila melanogaster. Proc Natl Acad Sci U S A. 103(46):17519-24
(5) Barmina O, Kopp A. (2007) Sex-specific expression of a HOX gene associated with rapid morphological evolution. Dev Biol. 311(2):277-86
Techniques used in this lab: Drosophila culturing
Drosophila anatomical characterization
Behavioral assays with Drosophila
aggression
courtship
feeding
Drosophila lifespan analysis
Behavior analysis
Additional Comments: I will eventually have a web page, but development of one is currently of low priority.
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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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Gretchen Neigh. Psychiatry & Behav Sci.
Phone: 404-727-9022
Email: gmccand@emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Spring,Summer,Fall
Lab Positions: 1
Project Description: Approximately 20% of the geriatric population manifests a neurobehavioral syndrome that is believed to be of vascular origin and consists of mild cognitive impairment, depression and anxiety. One possible cause for this syndrome is multiple minute strokes throughout the brain. Because of the inherent limitations of human research, my lab is using a rat model to determine if experimentally-induced multiple minute ischemic lesions produce behavioral changes similar to those documented in the geriatric human population. Data to date have demonstrated that induction of these lesions produces anxiety-like and depressive-like behaviors in young adult rats. The available project involves comparing behavioral outcomes between young adult and aged adult rats. In addition, the student would begin to analyze the differences in brain damage that occur from these lesions in a young versus an aged rat.
Student Requirements: The student should be familiar with working in a laboratory and have experience working with animals.
Accepts 1st year students? Y
Accepts 2nd year students? Y
Suggested Reading (References):
(1) Neigh, G.N., Kofler, J., Meyers, J.L., Traystman, R.J., Bergdall, V., La Perle, K., DeVries, A.C.
(2004) Cardiac arrest/cardiopulmonary resuscitation increases anxiety-like behavior and
decreases social interaction. Journal of Cerebral Blood Flow and Metabolism 24:372-382.
Neigh, G.N., Kofler, J., Meyers, J.L., Traystman, R.J., Bergdall, V., La Perle, K., DeVries, A.C.
(2004) Cardiac arrest/cardiopulmonary resuscitation increases anxiety-like behavior and
decreases social interaction. Journal of Cerebral Blood Flow and Metabolism 24:372-382.
(2) Neigh, G.N., Glasper, E., Kofler, J., Traystman, R.J., Mervis, R., Bachstatter, A.,
DeVries, A.C. (2004) Cardiac arrest/cardiopulmonary resuscitation selectively
alters formation of spatial memory and abates dendritic spines of CA1 pyramidal cells.
European Journal of Neuroscience 20:1865-1872.
(3) Neigh, G.N., Glasper, E.R., Zhang, N., Plotsky, P.M., Nemeroff, C.B., DeVries, A.C. (In prep)
Cardiac arrest and cardiopulmonary resuscitation increases CRF R1 receptor binding and alter
HPA axis responsivity.
Techniques used in this lab: behavioral testing - elevated plus maze, anhedonia, open field
histology - tissue preparation, cutting, staining
stereology - systematic assessment of tissue damage
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Nicole Gerardo. Biology.
Phone: 727-0394
Email: nicole.gerardo@emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Spring,Summer,Fall
Lab Positions: 4
Project Description: My lab uses an integrative approach to study the dynamics of microbial disease ecology and evolution. We use field surveys, molecular genetics, and laboratory experiments to understand the adaptive mechanisms by which hosts and microbes interact. Our goal is to gain a broader understanding of how host and parasite responses shape the evolution of disease by developing study systems in which we can manipulate species interactions in order to elucidate adaptive mechanisms and the genetics behind those mechanisms. To address such questions, we utilize insectmicrobe associations amenable to long-term laboratory maintenance and experimental manipulation. One of our main lines of research focuses on the interaction between aphids, their bacterial symbionts and pathogens that invade the aphid host. Aphids, small plant-feeding insects, contain several bacteria that shape their ecology. Some of these bacterial symbionts are known to protect aphids from parasitoid wasps and fungal pathogens. We currently know little about whether these bacteria protect aphids against other microbial invaders. One project in my lab for an undergraduate would be to test whether these bacterial symbionts protect aphids from bacterial pathogens. Experimental work could be coupled with molecular work (i.e., PCR, gel electrophoresis, quantitative PCR) to understand how the presence of these microbial invaders affects the number of symbiotic bacteria within the host.
Additional Project Information: Other research projects include:
1. screening milkweed aphids for bacterial symbionts and pathogens. This project would couple molecular analyses with classic microbiological techniques.
2. Using assays of cellular immune responses to characterize responses to viral and fungal pathogen
3. testing whether different aphid genotypes have different responses to the same fungal or bacteria pathogen. This work would couple experimental work, molecular analyses and microbiology.
Student Requirements: No previous experience or coursework is required. An interest in evolutionary biology and insects is a must. There will be opportunities to learn molecular techniques (DNA extraction, PCR, real-time PCR) as well as opportunities to conduct experimental projects. Students must be motivated, willing to ask questions and able to pay attention to detail. Younger students who might be interested in working in the lab for several years are strongly encouraged to apply.
Accepts 1st year students? Y
Accepts 2nd year students? Y
Techniques used in this lab:
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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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Graeme Conn. Biochemistry.
Phone: 404-727-5965
Email: gconn@emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Spring,Summer,Fall
Lab Positions: 1
Project Description: Our lab uses a multidisciplinary approach incorporating microbiological, biochemical and biophysical methods, including structural biology, to investigate the biological functions of important protein and nucleic acid (RNA) molecules. Current major areas of study center on: 1) viral non-coding RNAs and the mechanism(s) by which they counter host cell defenses (e.g. the protein kinase PKR or RNAi); 2) bacterial resistance to antibiotics arising from modification of their ribosomal RNA drug binding sites; and 3) the structure and ligand binding properties of the human sweet taste receptor. Defined short-term project(s) are available in any of these areas of our work. For example, in the antibiotic resistance project we are studying the thiostrepton-resistance enzyme (Tsr) and also a large family of aminoglycoside-resistance enzymes where many enzymes are uncharacterized. A student project could therefore begin with a completely new resistance enzyme gene that must be incorporated into an expression plasmid, and protocols determined for expressing, purifying and providing initial characterization of the protein. Alternatively, with a better characterized protein such as Tsr, a project can be developed that focuses on methods for analyzing the enzyme function (e.g. mutagenesis and functional assays) or structure (e.g. protein/ RNA crystallization). The availability of many possible projects will allow the goals be tailored to best match the students scientific interests and provide the maximum opportunity for training in the desired experimental approaches (see techniques below).
Student Requirements: Project can be tailored to suit student experience level and background. There are no specific requirements but projects would be best suited to students studying or planning to study chemistry, biochemistry or related subjects. Radiation training may be required for some projects for more senior/ experienced student researchers.
Accepts 1st year students? Y
Accepts 2nd year students? Y
Suggested Reading (References):
(1) Wahid, A.M., Coventry, V.K., and Conn, G.L. (2009) Investigation of two alternate structures in the Adenovirus VA RNAI Apical Stem reveals differential PKR binding and inhibition properties. Nucleic Acids Res. 37(17), 5830-5837.
(2) Wahid, A., Coventry, V.K. and Conn, G.L. (2008). Systematic deletion of the Adenovirus VA RNAI Terminal Stem reveals a surprisingly active RNA inhibitor of PKR. J. Biol. Chem. 283(25), 1748517493.
(3) Savic, M., Tomic, T.I., Macmaster, R., Vasiljevic, B. and Conn, G.L. (2008). Identification and characterisation of key residues for cofactor binding and catalytic activity in the aminoglycoside antibiotic resistance methyltransferase Sgm. J. Bacteriol. 190(17), 5855-5861.
(4) Dunstan, M.S., Hang, P., Zelinskaya, N.V., Honek, J. and Conn, G.L. (2009). Structure of the thiostrepton-resistance methyltransferase and its interaction with cofactor and ribosomal RNA. J. Biol. Chem. 284, 17013-17020.
(5) Nie, Y., Vigues, S., Hobbs, J.R., Conn, G.L. and Munger, S.D. (2005). T1R2 and T1R3 taste receptor subunits make distinct contributions to the detection of sweet stimuli. Current Biology, 15, 1948-1952.
Techniques used in this lab: The techniques used will depend on the details of the project but will include many of the following examples (see references for further details).
Molecular biology: polymerase chain reaction (PCR), site-directed mutagenesis, restriction digest, DNA ligation, etc.
Protein/ RNA sample preparation: bacterial culture, plasmid DNA isolation, recombinant protein expression, protein purification using chromatographic methods, RNA in vitro transcription and purification.
Functional/ biochemical assays of protein/ RNA activity, e.g.: measurement of antibiotic resistance, enzyme activity/ inhibition assays, protein-RNA binding assays, protein crystallization, etc.
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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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Carlos Moreno. Pathology and Laboratory Medicine.
Phone: 404-712-2809
Email: cmoreno@emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Spring,Summer,Fall
Lab Positions: 1
Project Description: In this project the student will test the hypothesis that two microRNA genes regulate predicted target genes in response to Wnt signaling. We have preliminary data that two microRNA genes are induced by Wnt treatment of prostate cancer cells. The predicted target genes are components of the Wnt pathway, suggesting a negative feedback loop. The student will test whether these microRNAs repress expression of the computational predicted target genes.
Student Requirements: Biology and Cell Biology
Accepts 2nd year students? Y
Suggested Reading (References):
(1) P. Liu, S. Ramachandran,, M. Ali-Seyed, C.D. Scharer, N. Laycock, W. B. Dalton, H. Williams, S. Karanam, M. W. Datta, D. L. Jaye, and C. S. Moreno. 2006. SOX4 is a Transforming Oncogene in Human Prostate Cancer Cells. Cancer Research, 66(8):4011-4018.
(2) CD McCabe, DD Spyropoulos, WD Martin, and CS Moreno. 2008. Genome-wide Analysis of the Homeobox C6 Transcriptional Network in Prostate Cancer, Cancer Research, 68(6):1988-96.
(3) CD Scharer, CD McCabe, M Ali-Seyed, MF Berger, ML Bulyk, and CS Moreno. 2009. Genome-wide Promoter Analysis of the SOX4 Transcriptional Network in Prostate Cancer Cells. Cancer Research, 69(2):709-717.
(4) CS Moreno, 2010. The SOX4 and HOXC6 Transcriptional Networks in Prostate Cancer Progression: Crosstalk with the Wnt, Notch, and PI3K Pathways, American Journal of Pathology, in press.
Techniques used in this lab: DNA preparation, PCR, Mammalian Tissue Culture, Transfection, Immunoprecipitation, Western Blotting
Additional Comments: The focus of the lab is understanding developmental pathways and regulatory gene networks important in cancer progression. We focus on transcription factors and microRNAs.
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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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Uriel Kitron. Environmental Studies.
Phone: 404-727-4253
Email: ukitron@emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Spring,Summer,Fall
Lab Positions: 4
Project Description: Opportunities exist for students to work under the umbrella of an extensive West Nile virus (WNV) and mosquito ecology research project in the greater Atlanta area. Student projects can focus on the role of bird hosts, mosquito vectors, and/or local environmental conditions impacting mosquito biology and WNV disease transmission around Atlanta. The primary field tasks that students will be trained to perform involve the trapping and processing birds and mosquitoes as well as the collection of water samples from potential mosquito breeding sites. Students will also gain laboratory experience, including processing avian blood samples, identifying and processing captured mosquitoes, and analyzing chemical determinants of water quality. Additionally, students will participate in bi-weekly paper discussion seminars aiming to encourage inquiry and further understanding of topics related to vector-borne disease epidemiology.
Student Requirements: Although no prior experience is necessary, we are looking for reliable, committed, and hard-working students who have the ability and willingness to conduct independent fieldwork, as well as work as part of a team. Students with an interest in learning about bird and mosquito ecology as well as various sampling methods will be preferred.
Accepts 1st year students? Y
Accepts 2nd year students? Y
Suggested Reading (References):
(1) Chaves, L.F., et al., Combined sewage overflow enhances oviposition of Culex quinquefasciatus in urban areas. Journal of Medical Entomology. 2009. 46: p. 220-226.
(2) Calhoun, L.M., et al., Combined Sewage Overflows (CSO) are major urban breeding sites for Culex quinquefasciatus in Atlanta, Georgia. American Journal of Tropical Medicine and Hygiene, 2007. 77(3): p. 478-484.
(3) Hamer, G.L., et al., Rapid amplification of West Nile virus: The role of hatch-year birds. Vector-Borne and Zoonotic Diseases, 2008. 8(1): p. 57-67.
(4) Loss, S.R., et al., Avian host community structure and prevalence of West Nile virus in Chicago, Illinois. Oecologia, 2009. 159: p. 415-424.
(5) Gibbs, S.E.J., et al., West Nile virus antibodies in avian species of Georgia, USA: 20002004. Vector-Borne and Zoonotic Diseases, 2006. 6(1): p. 57-72.
Techniques used in this lab: In the field, students will be trained to trap and process birds and mosquitoes and collect water samples from potential mosquito breeding sites. In the lab, students will proces avian blood samples, identify and process captured mosquitoes, and analyze chemical determinants of water quality.
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Thomas Gillespie. Environmental Studies.
Phone: 404-727-7926
Email: thomas.gillespie@emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Spring,Summer,Fall
Lab Positions: 4
Project Description: Research opportunities are available for interested undergraduates as part of a larger study focusing on interactions among anthropogenic environmental change; biodiversity; and the ecology and emergence of pathogens of people, wildlife, and domestic animals from Africa and Latin America. The research projects would involve microscopic analysis of samples from wildlife populations for gastrointestinal pathogens and statistical analysis of the results.
Student Requirements: We are looking for Freshman and Sophomores who may be willing to continue research into the school year. We are looking for hard-working and committed students interested in the fields of conservation science, wildlife medicine, and public health.
Although no prior experience is necessary, we are looking for reliable, committed, and hard-working students who have the ability and willingness to conduct semi-independent labwork, as well as work as part of a team.
Accepts 1st year students? Y
Accepts 2nd year students? Y
Suggested Reading (References):
(1) Gillespie, T.R., C.L Nunn, and F.H. Leendertz. (2008) Integrative approaches to the study of primate infectious disease: implications for biodiversity conservation and global health. Yearbook of Physical Anthropology. 51:53-69.
(2) Gillespie, T.R. (2006) Non-invasive assessment of gastro-intestinal parasite infections in free-ranging primates. International Journal of Primatology 27:1129-1143.
(3) Kowalewski, M., J.S. Salzer, J.C. Deutsch, M. Rano, M.S. Kuhlenschmidt, and T.R. Gillespie. (In Press) Black and Gold Howler Monkeys (Alouatta caraya) as Sentinels of Ecosystem Health: Patterns of Zoonotic Protozoa Infection Relative to Degree of HumanPrimate Contact. American Journal of Primatology (Speical Issue: Is Primate Conservation Essential to Ecosystem Conservation?)
(4) Gillespie, T.R., D. Morgan, J.C. Deutsch, M.S. Kuhlenschmidt, J.S. Salzer, K. Cameron, T Reed, and C. Sanz. ( In Press) A legacy of low impact logging does not elevate prevalence of potentially pathogenic protozoa in free-ranging chimpanzees and lowland gorillas in the Republic of Congo. EcoHealth.
Techniques used in this lab: Students would learn classical and/or immuno-fluorescent techniques for the detection and identification of gastrointestinal pathogens. In addition students will be trained in the categorization and identification of various pathogens. Students will learn basic microscopy skills, tools for statistical data analysis, and basic laboratory procedures.
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