Research Scientist Molecular Biology

Ramya Kolli

************@*****.*** +1-347-***-**** Durham, NC 27708

SUMMARY

• Dedicated Research Scientist with efficient technical and analytical skills demonstrated by multiple projects in academic, government and industry positions.

• Collaborative execution of multi-omics projects in environmental exposure studies, especially focusing on chemical mixtures and farming communities prevalent with chronic kidney disease.

• Design and execution of research projects pertinent to breast and bladder cancer and in vitro exposure models.

• Multiple peer-reviewed publications with academia and the federal government. EDUCATION

• Ph.D.: Toxicology, Pharmaceutical and Biomedical Sciences University of Georgia Athens, GA Dec 2017

• Master of Science: Biotechnology

New York University Brooklyn, NY Jan 2011

• Bachelor of Technology: Biotechnology

Sathyabama University Chennai, India Apr 2008

EXPERIENCE

Research Scientist

Duke University Durham, NC Sept 2022 – current

• Nicholas School of the Environment

• Successfully executed and completed Proteomics analysis of urine samples with the Duke core facility, leading to significant insights into chronic kidney disease of unknown etiology

(CKDu).

• Published first-ever urinary proteome on CKDu.

• Ongoing validation of mechanisms of CKDu from proteomic data in zebrafish as a kidney disease model.

• Ongoing development of first-of-its-kind human urinary mitochondrial mutational study using Duplex Sequencing.

Postdoctoral Fellow

Duke University Durham, NC Sept 2021 – Sept 2022

• Nicholas School of the Environment

• Planning and execution of Proteomics analysis of urine samples leading to significant insights into the mechanism and progression of CKDu. The knowledge applicable to ongoing development of zebrafish kidney disease model.

• Co-authored a review on CKDu.

Postdoctoral Fellow

NIEHS Durham, NC June 2018 - Feb 2021

• Epigenetics and Stem Cell Biology Laboratory.

• Designing and planning Bladder cancer patient sample analysis of fixed tumor tissue using NanoString gene expression analysis technology.

• Performed data analysis and visualization using nSolver, GSEA and IPA, followed by data interpretation and manuscript preparation.

• Planning and executing high-throughput Epigenome analysis in the Breast Cancer cohort population with a team of Biologists and Staff Scientists.

• Validated breast cancer EWAS (epigenome-wise association study) data using targeted gene bisulfite sequencing. Prepared NGS libraries for Illumina MiSeq run.

• Analyzed data using command line Linux-based Bismark tool and basic R packages.

• Published the findings in Epigenetics 2019.

Student Services Contractor

US EPA Athens, GA January 2014 - December 2017

• National Exposure Research Laboratory, Office of Research and Development.

• Collaborated with the UGA’s Aquatic Biotechnology and Environmental Laboratory to set up a zebrafish exposure system.

• Developed omics techniques using zebrafish hepatocytes in vitro.

• Maintained adult zebrafish line and performed time-dependent exposure studies.

• Effectively designed, lead and completed zebrafish exposure project involving epigenetic mechanisms, estrogen and feminization, the fruits of which became the second part of my doctoral dissertation.

• Performed NGS DNA methylation analysis on extracted liver DNA and qPCR analysis on RNA.

• Publication underway.

Graduate Student Researcher

University of Georgia Athens, GA August 2012 - December 2017

• Interdisciplinary Toxicology Program, Dept of Pharmaceutical and Biomedical Sciences.

• Designed and successfully completed in vitro mechanistic study involving epigenetic alterations, p21 expression and water disinfection byproduct bromate, as first part of doctoral dissertation.

• Molecular techniques used included plasmid DNA isolation, restriction digestion, ligation, cloning and qPCR; analyzed histone modifications using chromatin immunoprecipitation.

• Developed targeted gene bisulfite sequencing approach for DNA methylation analysis.

• Learned and Performed data analysis using Bismark bisulfite mapper, a Linux-based Bowtie platform. Performed additional analysis using other Bioinformatics tools like Geneious, Sequencher, BLAST and Clustal.

• Designed a VirtualMachine for the targeted NGS data analysis and made the code available to fellow students and researchers in the UGA Toxicology program website.

• Published the findings and analysis in ToxSci 2019 and PeerJ 2019. Published previous findings in ToxSci 2014 and CBI 2016.

Cell Culture Associate

ABS Inc, Client-Merck & Co North Wales, PA May 2012 - August 2012

• Merck Research laboratories.

• Handled aseptic production and banking of various cell lines for timely and on-demand supply, both adherent and suspension cultures.

• Worked with TripleFlask and HYPERFlask cell culture vessels for scheduled cell-deliveries to perform assays with high-throughput screening Robots.

Research Assistant

NYU-Poly Brooklyn, NY October 2009 - May 2012

• Department of Chemical and Biological Sciences.

• Lead the cell biology laboratory.

• Supervised and trained undergraduate and graduate students for thesis research.

• Designed research and training, executed cytotoxicity studies with mammalian cell lines

(fibroblasts and PC-12 cells), using whole cell-based sensors and MTT assays.

• Designed and used cell sensors in Potentiometric studies for real time drug screening and biomaterial interactions.

• Published the findings in Electroanalysis 2015 and a book chapter in Electrochemical Processes in Biological Systems 2015.

Visiting Student Volunteer

Jawaharlal Nehru Center for Adv Scientific Res Bangalore, India March 2009 - July 2009

• Evolutionary and Integrative Biology Unit.

• Worked on biogeography of higher mammals: Mitochondrial and Microsatellite DNA extraction from fecal samples of higher mammals like Asian Elephants, Chital, etc; followed by PCR amplification to sequence and group the individuals into different haplotypes for genetic variation studies.

• Briefly worked on identification, fecal sample collection and behavioral interaction of Elephants in their natural habitat.

Research Intern

Dr. Reddy's Laboratories Ltd. Hyderabad, India October 2007 - March 2008

• Biologics Development Center.

• Transiently expressed three different genes in GLP conditions by Lipofection, Electroporation and Heat shock treatment. Performed clonal selection and expansion in yeast and bacterial cultures for in-house downstream analysis.

• Purified proteins using Ni-NTA agarose columns and analyzed expression of different drl genes in recombinant cell lines using SDS PAGE, Silver staining, Western Blot and ELISA.

• Performed mammalian cell culture (CHO cell line) in GLP conditions including cryopreservation/cell banking and assayed cytotoxicity by MTT assay. SKILLS SUMMARY

• Proteomic data interpretation and

collaboration with the nephrologists

• Zebrafish model exposure studies

• Mammalian cell culture

• Bacterial and Yeast culture

• In vitro Cytotoxicity assays

• DNA/RNA/Protein extraction, purification

• Recombinant DNA and Cloning

• Western blot, ChIP and ELISA

• RT-qPCR and NanoString

• Sanger and bisulfite Sequencing

• NGS library preparation and Illumina MiSeq

• Agilent BioAnalyzer and TapeStation systems

• Bioinformatic data analysis

• NGS data analysis using Bismark, Generous

and Sequencher

• Linux and R

PUBLICATIONS

Citation record at: https://scholar.google.com/citations?user=_tJHkPYAAAAJ&hl=en&oi=ao

• Ramya T. Kolli*, T.C. Glenn, R.B. Bringolf, B.S. Cummings and J.F. Kenneke, Changes in CpG- methylation of the Vitellogenin 1promoter in Adult Male Zebrafish after Exposure to 17α- Ethynylestradiol (EE2), Environmental Toxicology and Chemistry 2024, vol. 43 (7): 1547 - 1556

• Ramya T. Kolli*, Sameera C. Gunasekara, Matthew W. Foster, Sitaramaraju Adduri, Anna Strasma, Christina Wyatt, Nagarjun V. Konduru, Mangala C.S. De Silva and Nishad Jayasundara, The Urinary Proteome Infers Dysregulation of Mitochondrial, Lysosomal and Protein Reabsorption Processes in Chronic Kidney Disease of Unknown Etiology (CKDu), American Journal of Physiology Renal Physiology 2023, vol. 324(4): F387-F403

• S.W.A.M. Upamalika*, C.T. Wannige, S.M. Vidanagamachchi, S.C. Gunasekara, R.T. Kolli, P.M.C.S. De Silva, D. Kulasiri, N. Jayasundara, A Review of Molecular Mechanisms Linked to Potential Renal Injury Agents in Tropical Rural Farming Communities, Environmental Toxiclogy and Pharmacology 2022, vol. 92, 103850

• Ramya T. Kolli*, Zongli Xu, Vijayalakshmi Panduri, Jack A. Taylor, “Differential Gene Expression in Bladder Tumors from Workers Occupationally Exposed to Arylamines”, BioMed Research International 2021, vol. 2021, Article ID 2624433.

• T.C. Glenn*, T.W. Pierson, T.J. Kieran, N.J. Bayona-Vásquez, S.L. Hoffberg, J. Thomas, D.E. Lefever, J.W. Finger Jr., B. Gao, X. Bian, S. Louha, R.T. Kolli, K. Bentley, J. Rushmore, K. Wong, I. Shaw, M. Rothrock, A.M. McKee, T.L. Guo, R. Mauricio, M. Molina, B.S. Cummings, L.H. Lash, K. Lu and B.C. Faircloth, Adapterama II: Universal Amplicon Sequencing on Illumina Platforms (TaggiMatrix), Published online at PeerJ 2019, 7:e7786

• A.M. Moore*, Z. Xu, R.T. Kolli, A.J. White, D.P. Sandler and J.A. Taylor, Persistent Epigenetic Changes in Adult Daughters of Older Mothers, Epigenetics 2019, 14(5): 467–476

• R.T. Kolli*, T.C. Glenn, B.T. Brown, S.P. Kaur, L.M.Barnett, L.H. Lash and B.S. Cummings, Bromate- induced Changes in p21 DNA Methylation and Histone Acetylation in Renal Cells, Toxicological Sciences 2019, 168(2): 460-473

• N.E. Scholpa*, R.T. Kolli*, M. Moore, R.D. Arnold, T.C. Glenn, B.S. Cummings, Nephrotoxicity of epigenetic inhibitors used for the treatment of cancer, Chemico-biological Interactions 2016, 258: 21-29

• R.T. Kolli*, E. Kaivosoja and K. Levon, Choice of Reference Electrode is Critical for Potentiometric Whole Cell-based Sensor, Electroanalysis 2015, 27(7): 1636-1641

• K. Levon*, Q. Zhang, Y. Wang, A. Maathur and R.T. Kolli, Electrochemical Monitoring of the Well- being of Cells, Electrochemical Processes in Biological Systems 2015, Chapter 9: 213-230

• N.E. Scholpa*, X. Zhang, R.T. Kolli, B.S. Cummings, Epigenetic Changes in p21 Expression in Renal Cells after Exposure to Bromate, Toxicological Sciences 2014, 141 (2): 432-440 In draft:

• R.T. Kolli*, Z. Xu, V. Panduri, D. Shaughnessy and J.A. Taylor, Effect of Fried Meat and Putative Dietary Mutagen Inhibitors on DNA Methylation of Colon Epithelial Cells and Lymphocytes, Cancer Epidemiology, Biomarkers and Prevention (tentative).

• R.T. Kolli*, Z. Xu and J.A. Taylor, Hormone Replacement Therapy Use: Blood DNA Methylation and Epigenetic Age Acceleration, Cancer Epidemiology, Biomarkers and Prevention (tentative). SELECTED ACTIVITIES AND HONORS

• Platform presentation – on Environmental Exposures, Urinary Biomarkers and Children at the Environmental Exposures and Kidney Health consortium at Duke University (2023)

• Guest lecture – on Epigenetics and Toxicology in the Global Change Biology Spring 2022 course at the Nicholas School of the Environment at Duke University (2022)

• Poster presentation at the NC Global Health Conference (2022)

• Poster presentation at the SOT Annual (Virtual) Meeting (2020)

• Poster-pitch presentation at the NC SOT Annual (Virtual) Meeting (2020)

• Member of ESCBL Fellows Council at NIEHS (2018 - 2021)

• Teaching in College, 9-week course

• University of Georgia Emerging Leader (2016)

• Multiple graduate scholarships and travel awards for presenting at scientific meetings like Society of Toxicology (SOT), Gordon Research Conferences

• Second place in Renal Toxicology Fellowship Award Fund at SOT, New Orleans LA 2016

• First Place in poster award at the Southeastern Regional Chapter of SOT 2016

• Secretary of the Interdisciplinary Toxicology Program Student Organization at UGA (2014 - 2015).

• On-board Volunteer and Educator for water quality and awareness at the Hudson River Sloop Clearwater in New York (2012)

• Graduate school merit scholarship for Master of Science at NYU-Poly, NY (2009-2011)

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