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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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Paul Spearman. Pediatrics.
Phone: 404-727-5642
Email: paul.spearman@emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Summer
Lab Positions: 1
Project Description: HIV assembly: We seek to define the role of host cell molecules in the assembly of HIV particles, focusing primarily on factors that are engaged in the trafficking of Gag and Env glycoproteins, or in the budding process of HIV.
Student Requirements: Science knowledge base, especially chemistry and biology, will be necessary to understand concepts.
Accepts 1st year students? Y
Accepts 2nd year students? Y
Suggested Reading (References):
(1) Dong X, Li H, Derdowski A, Ding L, Burnett A, Chen X, Peters TR, Dermody TS, Woodruff E, Wang JJ, Spearman P: AP-3 directs the intracellular trafficking of HIV-1 Gag and plays a key role in particle assembly. Cell 2005, 120:663-674.
(2) Varthakavi V, Smith RM, Martin KL, Derdowski A, Lapierre LA, Goldenring JR, Spearman P: The pericentriolar recycling endosome plays a key role in Vpu-mediated enhancement of HIV-1 particle release. Traffic 2006, 7:298-307.
(3) Li H, Dou J, Ding L, Spearman P: Myristoylation is required for human immunodeficiency virus type 1 Gag-Gag multimerization in mammalian cells. J Virol 2007, 81:12899-12910.
Techniques used in this lab: Cloning, tissue culture, HIV replication, live cell confocal microscopy, protein analysis
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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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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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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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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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