Resume

Clinical Research Data

Location:

Bridgewater, NJ

Posted:

March 21, 2017

Contact this candidate

Resume:

Vijayalakshmi (Viji) Nagaraj

** ******* ***** **

NJ 07920, USA

Basking Ridge

Cell: 908-***-****

Email: acze0i@r.postjobfree.com

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CAREER SUMMARY:

Experimental Biology and Computer Skills:

Helped in setting up a quantitative systems biology lab after transitioning from conventional microbiology/molecular biology/biochemistry to systems biology. Collaborated with groups of bioinformaticians and with mathematical model builders. Obtained and analyzed large data sets from medium/large-scale gene expression assays and from microscopic imaging. Protein Purification: use of E. coli, Yeast and Neurospora use of conventional columns and FPLC for protein purification, glycerol density gradients, sucrose density gradients and size exclusion for separating native complexes SDS-PAGE Western Blots, Immunoassays, Synthetic Biology, In vitro transcription translation (TX-TL) system Use of BioTeK Synergy H1 and Tecan Infinite M 200 PRO plate readers using 384 well plates for assaying RNA and Protein expression dynamics EMSA (Gelshift) SELEX-SAGE Procedure Chromatin Immunoprecipitation Microbiology: Isolation and identification of bacteria from various sources and classifying them using morphology, Gram staining, endospore staining, and other methods. Good sterile techniques and ability to grow large-scale bacterial and yeast cultures. Molecular Biology Techniques: Cloning, techniques like Gibson assembly, conventional cloning, PCR, RT PCR, Multiplex PCR, Sequencing, high-throughput SELEX_SAGE sequence for transcription factor binding sites, DNA and RNA extraction purification of mRNA and setting up translation assays using the purified transcript, Translation inhibition assays using Cycloheximide, Hygromycin, Paramomycin, Use of HDAC inhibitors to analyze yeast silencing (ADE 2 and 5 FOA colony assays and microscopy were used for monitoring ). Microscopy: Use of Nikon TE 2000 S inverted microscope for live cell microscopy and fluorescence microscopy using GFP, YFP and CFP tagged proteins to monitor epigenetic switching of single cells Fluorescent in-Situ hybridization Data analysis and Image Processing 2

Computer Skills: Regular use of Word, PowerPoint and Excel; Image generation by Canvas, Adobe Photoshop and Xara; Use of Image J and Image Pro Premier along with custom-made MATLAB Image Processing code for segmentation and annotation of microscopic images. Adapted existing MATLAB code for specific data files from multi-well plate-reader. Dealt with different data-file formats. Have passing familiarity with VBA, Python (notebooks) and R. Worked in Windows and in Mac OS X environments, comfortable with Unix command line. Biosafety Experience:

Followed personal and General Laboratory Safety, Chemical Safety, Standard Operating Procedures

(SOP) and Good Laboratory Practice (GLP) for the past 21 years at Rutgers University as per NIH guidelines. Oversaw and implemented daily operational aspects of Lab safety. Wrote research protocols and got it approved by IRB.

Performed administrative tasks including maintaining budget for the lab, creating purchase orders, ordering Lab supplies. Obtained bids for the lab equipment by negotiating with multiple vendors. Maintained and calibrated various instruments like freezers, centrifuges, PCR machines, plate reader and microscopy.

Clinical Research Training Certificates:

Completed Biomedical/Clinical Research Investigators course (11/03/2016) from CITI

(https://www.citiprogram.org/verify/?bf54feb9-72a8-4a27-84ed-2f006559edb2). HIPPA Training (08/12/2016)

Online Biosafety/Blood borne Pathogens Refresher (06/16/2016), Online Laboratory Safety Refresher course (06/16/2016) Previously had done Radiation Refresher Safety training. Part of Onsemble/OnCore community and went through basic navigation tutorials and attending few webinars to know more about it.

Experience in scientific speaking, writing and mentoring: Help in reparation and editing of scientific grants and manuscripts. Presenting the research findings. Interacting with graduate and undergraduate students and postdocs. CURRENT POSITION

2002- Research Associate, BioMaPS Institute/Center for Quantitative Biology. Semi-independent position: Collaborated on diverse topics in quantitative biology with several groups at Rutgers University and at Robert Wood Johnson Medical School.

Recent work:

In-Vitro Transcription_Translation System For Studying Synthetic Genetic Networks:

Set up the Transcription Translation System at CQB entirely by reading the relevant literature and adapting the system to work to perfection. Involved growing large scale cultures of E. coli and making extracts, Using plasmids containing GFP and RNA tags to monitor both RNA and protein production dynamics. To understand the resource limitation on gene expression, experiments are done in 384 well plates using Bio TeK Synergy H1 plate reader by titrating with various levels of NTP and other factors. To further understand the role of resources on Transcription and Translation, we either use DNA or purified RNA as the starting material. This large-scale data is exported using Excel and analyzed in MATLAB using the pre existing programs with slight modifications.Using Gibson assembly to construct vectors. Trying to further expand this approach to adapt to eukaryotic expression systems such as Neurospora crassa.

Observation of hysteresis in 5-FOA survival rates

Hysteresis experiments with 5-FOA survival: Freshly grown YPD culture yeast strain with an URA3 gene located at telomere 11L, was diluted in two separate batches: one in regular YPD media and the other with YPD media containing 60 μM splitomycin and grown for 24 hours after which, the cells grown in absence of the drug, or grown in the presence of the splitomycin were allowed to grow for another 24 hours in the intermediate drug concentrations. Then, these cells were spun, washed with sterile water and s serial dilutions were made and plated on to YPD plates and 5-FOA plates. Colonies were counted after 2–4 days of growth at 30 C. The serial dilutions were adjusted so that one can get reliable counts of the colonies. Errors in estimating the survival fractions were calculated based on expected variance of colony counts, separately for YPD and 5-FOA plates. Studying The Approach To Bifurcation By Pigmentation In ADE2 Silencing: Yeast strain UCC7366 was used to study ADE2 variegation near telomere. The strain was streaked out on YPD media. From YPD plate single colony was streaked out on to YC medium and further inoculated into 4 ml of YC liquid medium. Overnight grown culture was diluted one to 100 into fresh 2 ml YC medium, containing no splitomycin. Cultures were grown for 24 hours. The cells were pelleted, washed with sterile water and finally re-suspended in 200 μl of water. From here, 10 2, 10 4 and 10 6 dilutions were made and 10 μl from 10 4 and 10 6 were plated onto 60 15 mm Petri dishes containing solidified 10 ml YC medium with various concentrations of splitomycin (spread on to the plates prior to use). After 3–4 days of growth, plates were kept over night in cold room and images were acquired using a 3rd generation iPad 5 Megapixel iSight camera. The segmentation of the images to extract individual colonies was done using Image-Pro Premier v9.0 Image Analysis Demo software from Media Cybergenetics. The mean intensities for the three channels (RGB) for each colony were exported using the same software. Further analysis of the channel intensities was done using Python and NumPy.

Combined Analysis Of Expression Data and Transcription Factor Binding Sites In The Yeast Genome :

Chromatin immunoprecipitation (ChIP) were carried out to identify a 1-α 2 binding sites predicted from the computational approach by combining the microarray data with the binding site preference data. The immunoprecipitated samples was subjected to multiplex PCR amplification with primers specific for the STE6 promoter as a positive control for the immunoprecipitation of α 2 and the YDL223C ORF as a negative control for nonspecific immunoprecipitation, along with the specific primers for candidate α 2-a 1 target sites.

One of the targets identified contained a1-alpha2 binding site downstream of the IME4 open reading frame (ORF). This site plays an indirect role in controlling the expression of IME4 through the regulation of an antisense ncRNA. ChIP assays were done for experimental verification of this site. Other relevant work: Please see the publication list. 4

PREVIOUS WORK EXPERIENCE:

2001-2002 Research Associate, CABM, Rutgers University, Piscataway, NJ, USA, in Prof. Steven Brill’s lab. Purification and characterization of DNA repair proteins using various assays** 2000-2001 Research Associate, Waksman Institute, Rutgers University, Piscataway, NJ, USA, in Prof. Andrew Vershon’s lab.

Role of Sfp1p in ribosome biogenesis** translation drug sensitivity assays using cyclohexamide, hygromycin and paromomycin in yeast**

1995-2000 Post-doctoral fellow, Waksman Institute, Rutgers University, Piscataway, NJ, USA in Prof. David Norris’s lab.

Purification and characterization of recombination proteins in yeast using radioactive D-Loop (Joint molecule) assay ** suppressor screens for SFP1 gene** localization of various proteins in WT and SFP1 knockout strains using microscopy**

1993-1995 Post-doctoral trainee, ICGEB, Trieste, Italy, in Prof. Carlo Bruschi’s lab Purification and characterization of a ferulate decarboxylase from Bacillus licheniformis** EDUCATION

1989-1993 Ph.D. in Microbiology, Indian Agricultural Research Institution, New Delhi, India. Characterization of lignocellulose biodegradation using various fungi** Identification of metabolites** calculation of C/N ratio during degradation** 1986-1989 M.Sc. in Microbiology, University of Agricultural Sciences, Bangalore, India Effect of pesticide carbofuran on beneficial microorganisms** Testing the volatile loss of carbofuran through plants** identification of metabolites using TLC** 1983-1986 B.Sc. in Microbiology, University of Agricultural Sciences, Bangalore, India Enrichment and isolation of keratin-degrading bacteria from various sources** classification of microorganisms**

RESEARCH EXPERIENCE

SYNTHETIC BIOLOGY

2015- Eukaryotic Cell-free Expression System

Worked on optimizing a eukaryotic transcription-translation (TX-TL) system using Neurospora crassa extract that could be used to study interesting gene expression dynamics. 2014- Resource-dependence of Cell-free Expression System 5

Investigated the multidimensional space of control variables like abundances of Mg2+, K+ and NTP’s for the TX-TL system. Our experiments reveal a complex landscape of dependence of gene expression, especially of translation rate, on these control variables. The results raise interesting questions about how the cell maintains homeostasis of concentrations of these key resources. SYSTEMS BIOLOGY OF EPIGENETIC SILENCING

2009-2013 Experimental Study of Bifurcations in Epigenetic Silencing Using HDAC Inhibitors 2010- Hysteresis in Epigenetic Chromatin Silencing under HDAC Inhibitors TRANSCRIPTIONAL REGULATION

2008-2009 Role of Non-coding RNA in Yeast Transcriptional Regulation 2008-2009 NF- κ B Target Discovery

2002-2005 SELEX-SAGE and EMSA (Electrophoretic Mobility Shift Assay) for characterizing the binding motif of transcription factors with variable binding sites 2003-2005 ChIP and Gel-shift Validations for Analysis of Yeast Mating Type Regulation 1998-2001 Transcriptional Regulation by Sfp1

RECOMBINATION

1995-2002 Identification of Components in Yeast Recombination PUBLICATIONS

Journal articles

2014 Breaking an epigenetic chromatin switch: curious features of hysteresis in Saccharomyces cerevisiae telomeric silencing, Nagaraj VH, Mukhopadhyay S, Dayarian A and Sengupta AM, Plos One, 10.1371/journal.pone.0113516(2014)

2011 Regulated Antisense Transcription Controls Expression of Cell-type- specific Genes in Yeast, Gelfand B, Mead J, Bruning A, Apostolopoulos N, Tadigotla V, Nagaraj VH, Sengupta AM and Vershon AK, M0l Cell Biol. 31:1701-1709(2011)

2010 Locus Dependence in Epigenetic Chromatin Silencing, Mukhopadhyay S, Nagaraj VH and Sengupta AM, Biosystems, 102, 49-54 (2010)

2009 OHMM: a Hidden Markov Model Accurately Predicting the Occupancy of a Transcription Factor with a Self-overlapping Binding Motif, Drawid A, Gupta N, Nagaraj VH, Gelinas C and Sengupta AM, BMC Bioinformatics 10:208(2009)

2008 Better Estimation of Protein-DNA Interaction Parameters Improve Prediction of Functional Sites, BMC Biotechnology, Nagaraj VH, O’Flanagan RA and Sengupta AM, BMC Biotechnology, 8, 94.

(2008)

2004 Combined Analysis of Expression Data and Transcription Binding Sites in the Yeast Genome, Nagaraj VH, O’Flanagan RA, Bruning AR, Mathias JR, Vershon AK and Sengupta AM, BMC Genomics, 5:59(2004)

2003 Sfp1 Plays a Key Role in Yeast Ribosome Biogenesis, Fingerman I, Nagaraj VH, Norris D, and Vershon AK, Eukaryot. Cell, 2, 1061-8. (2003)

2000 Yeast Cell-Free System that Catalyzes Joint-molecule Formation in a Rad51p-and Rad52p- dependent Fashion, Nagaraj VH and Norris, Biochem. J. 347, 363-368(2000) Manuscript under revision:

Drawid A, Nagaraj VH and Sengupta AM, PHYLOQPMEME: Integrating Evolutionary Conservation into a One-Class SVM for Identifying Transcription Factor Binding Sites. Book chapter:

Nagaraj VH and Sengupta AM, Dissecting Transcriptional Networks, pp 106-123, in Introduction to Systems Biology, ed S. Choi, Humana Press, 2007.