Individual Student Views - 2001

Sara Zimmer
Stern Lab
BMCB Field (entered program fall 2001)

From: St. Cloud, MN
Undergraduate: Michigan Technological University; Dual BS (Biological Sciences and Chemical Engineering)

Statement

I spent several years focused on a ski racing career before returning to research full time. The faculty at Cornell seemed to welcome the diversity of my experience when I applied and interviewed, and I appreciated the fact that they were utilizing ideas and technologies from various disciplines in their own work. Furthermore, I really feel the program supports me as I strive to become a better scientist while simultaneously becoming a first-time mother.

Research

Current research indicates that regulation of gene expression goes far beyond transcriptional control, including post-transcriptional alterations of RNA. The focus in the Stern lab is chloroplast gene expression, where relative levels of mRNAs are primarily regulated at post-trancriptional steps. I have identified several genes that are likely to participate in these steps, by modifying or cleaving RNA. I am silencing them in the versatile alga Chlamydomonas reinhardtii, as well as overexpressing one of them and performing biochemical assays. My thesis work is centered on determining what role these proteins have in both the processing and turnover of chloroplast RNAs. I am especially interested in understanding how polyadenylation promotes degradation of mRNAs and how my candidate genes affect this step in the degradation pathway.

Meetings/Outreach

Zimmer S. L. and Stern D. B. (poster) Identification of enzymes mediating polyadenylation in the mRNA decay pathway in Chlamydomonas reinhardtii chloroplasts. FASEB Summer Conference, Post-transcriptional Control of Gene Expression: Mechanisms of mRNA Decay, Colorado. 2006.

Publications

Merchant S. S., Prochnik S. E., Vallon O., et al (2007). The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science. 318:245-50.

Yehudai-Resheff S., Zimmer S. L., Komine Y., Stern D. B (2007). Integration of chloroplast nucleic acid metabolism into the phosphate
deprivation response in Chlamydomonas reinhardtii. Plant Cell 19:1023-38.

Awards

Graduate student poster award, FASEB Summer Conference. 2006.

Kristin Burns
Begley Lab
BMCB Field (entered program fall 2001).
GRADUATED August 2006, presently a postdoctoral fellow at the NIH.

From: Pennsylvania
Undergraduate: Franklin and Marshall College, BA (Chemistry) in 2001

Statement

The introductory eight-week lab course is one reason why I chose the BMCB Graduate Program. The Field System brings together labs from Chemistry, Nutrition, Microbiology, etc., so it was beneficial for us to get an introduction to a variety of techniques to prepare us for our rotations and future lab work. The Graduate Program also provides students with terrific training -- student seminars, Friday seminars and progress reports are just a few examples of this training.

Research

Pyridoxal-5-phosphate (PLP, vitamin B6) is an essential cofactor in all living systems. It plays an important role in amino acid and carbohydrate metabolism and has recently been implicated in singlet oxygen resistance. The biosynthesis of PLP in Escherichia coli has been well studied. This pathway, however, is restricted to a relatively small number of bacteria. Most bacteria, archaebacteria, fungi, and plants contain the highly conserved SNZ and SNO family of genes which have been implicated in PLP biosynthesis. My project involves the identification of the substrates for the SNZ and SNO family of proteins in Bacillus subtilis, reconstituting the biosynthesis, and analyzing the reaction mechanism.
I am interested in studying Mycobacterium tuberculosis in my post-doc, with the hope of uncovering interesting biosynthetic pathways and chemistry.

Publications

• Burns, Kristin E.; Baumgart, Sabine; Dorrestein, Pieter C.; Zhai, Huili; McLafferty, Fred W.; Begley, Tadhg P. (2005) Reconstitution of a New Cysteine Biosynthetic Pathway in Mycobacterium tuberculosis. Journal of the American Chemical Society 127: 11602-11603.
• Burns, Kristin E.; Xiang, Yun; Kinsland, Cynthia L.; McLafferty, Fred W.; Begley, Tadhg P. (2005) Reconstitution and Biochemical Characterization of a New Pyridoxal-5'-Phosphate Biosynthetic Pathway. Journal of the American Chemical Society 127:3682-3683.
• Park, Joo-Heon; Burns, Kristin; Kinsland, Cynthia; Begley, Tadhg P. (2004) Characterization of two kinases involved in thiamine pyrophosphate and pyridoxal phosphate biosynthesis in Bacillus subtilis: 4-amino-5-hydroxymethyl-2-methylpyrimidine kinase and pyridoxal kinase. Journal of Bacteriology 186:1571-1573.

Conference Presentations

• Enzymes, Coenzymes and Metabolic Pathways Gordon Research Conference, July 2005. Reconstitution and biochemical characterization of a new Pyridoxal-5-phosphate biosynthetic pathway, Kristin E. Burns, Yun Xiang, Cynthia L. Kinsland, Fred W. McLafferty and Tadhg P. Begley.
• 228th American Chemical Society National Meeting, August 2004. A new cysteine biosynthetic pathway in Mycobacterium tuberculosis, Kristin E. Burns, Sabine Baumgart, Pieter C. Dorrestein, Huili Zhai, Fred McLafferty and Tadhg P. Begley.

Honors

Research highlighted in Chemical and Engineering Latest News, August 31, 2005. TB's Novel Path To Cysteine: Route's chemistry suggests it may play a role during tuberculosis infection, by Amanda Yarnell. (http://pubs.acs.org/cen/news/83/i36/8336cysteine.html)

Award of Excellence, Vincent du Vigneaud Memorial Symposium, May 2005
Weill Medical College

Danso Ako-Adjei
Vogt lab
G&D Field (entered program fall 2001)
Graduated May 2007. Presently Postdoc, Emory University

From: born in Ghana, grew up mostly in New York City.
Undergraduate: Carleton University, Ottawa ON Canada; BS (Biology/Biotechnology) in 2001

Statement

I had always been interested in science, but not until my first undergraduate genetics course was I certain of my interests in molecular biology. After learning a bit about retroviruses and working at the Aaron Diamond AIDS Research Center in New York City, I became even more interested in virology. I decided to come to Cornell because of the flexibility afforded by the Graduate Field system. It also didn't hurt that Ithaca is absolutely beautiful.

Research

Our lab is interested in the mechanisms underlying retroviral assembly. A single structural protein, Gag, drives assembly by means of protein-RNA-, protein-protein- and protein-lipid interactions. The two retroviruses we focus on are the classic chicken virus Rous sarcoma virus (RSV) and human immunodeficiency virus type 1 (HIV-1). In my project I have created chimeric RSV/HIV-1 Gag proteins as tools to better understand assembly and morphogenesis.

Publications

Ako-Adej D, Johnson MC, and Vogt VM. (2005). The retroviral capsid domain dictates virion size, morphology, and co-assembly of Gag into virus-like particles. J Virol 79:13463-72.

Johnson MC, Ako-Adej D, and Vogt VM. (2005). The C-terminal half of TSG101 blocks Rous sarcoma virus budding and sequesters Gag into unique non-endosomal structures.
J Virol 79:3775-86.

Conference Presentations

Ako-Adjei D, Johnson M, Vogt VM.The retroviral CA domain dictates virion size, morphology and the co-assembly of Gag into virus-like particles." International Retrovirus Meeting, Cold Spring Harbor, NY (May 2005). (Poster)

Ako-Adjei D, Johnson M, Vogt VM.Assesment of retroviral size and morphology determinants via RSV/HIV chimeras." International Retrovirus Meeting, Cold Spring Harbor, NY (May 2004). (Poster)

Ako-Adjei D, Johnson M, Vogt VM.Electron microscopic analysis of virus particles assembled from RSV/HIV chimeric Gag proteins." International Retrovirus Meeting, Cold Spring Harbor, NY (May 2003). (Poster)

Abbie Saunders
Lis Lab
G&D Field (entered program fall 2001)
Graduated May 2007. Presently Postdoc, Cornell University

From: Gloucestershire, England.
Undergraduate: University of Nottingham; BS (Genetics) in 2001

Statement

I wanted to undertake my graduate study in the USA because the five year (as opposed to three year) program in the States gives greater opportunities for teaching, taking classes and learning how to write Grant applications. I chose Cornell because of its great reputation for being a top research and teaching institution, and because there were several labs at Cornell working on the area that I was most interested in (mechanisms of gene expression). The visitation weekend sealed my decision to come to Cornell, after I received a terrifically warm reception and immediately made a great bunch of friends. Another great bonus for Cornell was the setting in a small, friendly town with plenty of arts, entertainment and outdoor activities to take advantage of. I was also particularly excited about being within a 30 minute drive of a ski resort.

Research

The Lis lab studies the mechanism of transcription activation at the Drosophila heat inducible gene, hsp70. I primarily focus on examining the recruitment and localization of various transcription factors along the hsp70 gene, and my research makes use of a range of biochemical and genetic techniques. I am attempting to make fly lines carrying temperature sensitive alleles of factors that I'm interested in, and I am also making use of a drug that inhibits the activity of particular factor as a tool to study the factor. Additionally I am involved in the development of new technologies with which to study the distribution of factors along the gene.

Awards

Outstanding Graduate Teaching Assistant in the Department of Molecular Biology and Genetics (May 2003).

class="h2"Publications

Adelman, K., Marr, M. T., Werner, J., Saunders, A., Ni, Z., Andrulis, E. D. and Lis, J. T. (2004) Efficient Release From Promoter-Proximal Stall Sites Requires Transcript Cleavage Factor TFIIS. Molecular Cell 17:103-112.

Belotserkovskaya, R., Saunders, A., Lis, J. T. and Reinberg, D. (2004) Transcription Through Chromatin: Understanding a Complex FACT. Biochimica et Biophysica Acta 1677: 87-99.

Saunders, A., Werner, J., Andrulis, E. D. et al. (2003) Tracking FACT and the RNA Polymerase II Elongation Complex Through Chromatin in Vivo. Science 301: 1001-1140

Boehm, A. K., Saunders, A., Werner, J. and Lis, J. T. (2003) Transcription Factor and Polymerase Recruitment, Modification, and Movement on dhsp70 In Vivo in the Minutes following Heat Shock. Molecular and Cellular Biology 23: 7628-7637.

Conference Presentations

Saunders, A., Kim, S., Filippone, L., Spector, A. and Lis, J. T. (March 2005) Utilizing Yeast for the Creation of Drosophila Fly Lines Carrying Temperature Sensitive Alleles of Factors Involved in hsp70 Transcription. Poster abstract for the 46th Annual Drosophila Research Conference.

Workshop Talk at the March 2003 KeystoneEnzymology of Chromatin and Transcription meeting, Sante Fe, New MexicKinetic Analysis of the Transcription Apparatus on Drosophila hsp70.