HARSHA NILAKANTAN

*** ********** *****, ***. ***,Detroit, MI 48226

Email: acdyxc@r.postjobfree.com Ph: 949-***-****

LinkedIn: www.linkedin.com/in/harshanilakantan

EDUCATION

Drexel University, School of Biomedical Engineering and Sciences, Philadelphia, PA.

Master of Science in Biomedical Sciences June 2012

Visvesvaraya Technological University, M. S. Ramaiah Institute of Technology, Bangalore, India.

Bachelor of Engineering in Biotechnology. June 2010

TECHNICAL & LABORATORY SKILLS

Laboratory Techniques: Immunohistochemistry (IHC), Immunofluorescence staining (IF), cryostat microtome

sectioning, frozen tissue and FFPE tissue handling and preparation for IHC and IF, DNA isolation, Colorimetric assays,

Protein Quantification, DNA extractions from blood, tissue and hair and bones, DNA preparation, buffer formulation,

ELISA, fluorescence in-situ hybridization (FISH), nucleic acid electrophoresis, PCR, qPCR/real-time PCR assays,

multiplex amplification assays, Amelogenin.

Analytical Instrumentation: UV-Visible Spectroscopy, Atomic Absorption Spectroscopy (AAS), basic Reverse Phase

- High Performance Liquid Chromatography (RP - HPLC) based purification of proteins, simple and fluorescence

microscopy, Confocal Laser Scanning Microscopy (Zeiss LSM 780), Laser Capture Microsdissection (LCM).

Microbial Techniques: Bacterial culture techniques, Sterilization and Aseptic techniques.

Computer: MATLAB, SPSS, eCognition, ImageJ, MS Office, Endnote, MS Project, MeV, Zeiss Zen

2011, CellProfiler.

Regulatory & Safety: 21CFR 50, 54, 56; 45 CFR Parts A-D (IRB), GLPs, GMPs, GCPs, proposal &

protocol preparation.

RELEVANT COURSEWORK

Theoretical Coursework: Medical Imaging Systems, Anatomy & Physiology, Genetic Engineering,

Biochemistry, Biostatistics and Experimental Design, Biomedical Ethics & Law, Principles of

Pharmacology.

Hands-on Coursework: Forensic DNA Analysis, Chemical Instrumentation, Biological Systems

Analysis & Mathematical Modeling, Microbiology, Molecular Biology.

RESEARCH EXPERIENCE

• Liver Histopathology in the Rat Model of Alcoholic Steatosis, Thomas Jefferson

Nov '12 - Present

Utilized the Rat model of alcoholic steatosis to identify localization of transcription factors

using Immunofluorescence (IF) and Immunohistochemistry (IHC).

Worked with cryosections of Rat Liver tissue. Developed an optimized staining protocol for

specific transcription factors. Following staining, tissue was imaged using Epifluorescence

and Laser Scanning Confocal Microscopy (Zeiss LSM 780).

Utilized CellProfiler to develop an image segmentation pipeline. Images were run through the

pipeline to derive intensity-based data on localization of transcription factors in the Liver.

Data analysis was carried out in programming Language R. Additional Work is currently

ongoing to better understand the localization per cell and cell type, and around specific areas

such as the portal and central veins.

LABORATORY & INSTRUMENTATION PROJECTS

• Forensic DNA Analysis for Match Profiling, Drexel

Jan '12 - Apr '12

Extracted DNA by chelex, organic and inorganic methods from blood, bone, saliva, hair and

mammalian cells. Led a team of three graduate students, was responsible for DNA extractions,

quantifications and electrophoresis.

Utilized fluorometric and qPCR quantifications of DNA.

Analyzed amplicons by Agarose Gel Electrophoresis and matched the unidentified against

reference profiles.

• Biosynthesis and characterization of Silver nanoparticles, VTU

Jan '10 - Jun '10

Silver nanoparticles were synthesized by “green” method using Neem (Azhadiracta indica)

extract and Silver Nitrate solution. Among a group of three, main tasks included microbial

cultures and analysis using UV-Vis Spectroscopy. Silver nanoparticles were impregnated on

PU foam cubes and discs.

Anti-microbial properties were studied on solutions and plate cultures using UV-Vis

Spectroscopy.

• Testing of Heavy Metal Contamination in Fish (Atomic Absorption Spect.), Drexel

Feb '11 - Mar '11

Fish samples obtained from local commercial sources were desiccated and then digested in a

concentrated acid mixture to present to atomizer flame.

The Graphite furnace was used to determine the Lead and Mercury contamination levels in

the fish samples using Atomic Absorption Spectroscopy.

DATA ANALYSIS PROJECTS

• Studying the Effects of Chronic Alcohol Consumption on Gene Expression in Adiponectin

Knockout Mice and Wild-Type Controls, Thomas Jefferson

Apr '13 - Present

The statistical programming language R was used to organize and perform statistical analyses

of gene expression data obtained from high-throughput qPCR (Fluidigm Biomark).

Analysis of the high-dimensional gene expression data included using R and MeV for:

identification of housekeeping genes, normalization of expression levels across animals and

conditions, statistical testing (including t-test and ANOVA) to identify genes with altered

expression patterns across treatments and genotypes, statistical and functional clustering, and

principal component analysis (PCA).

Data was visualized using plotting functions in R as well as using the data analysis software

MeV. Bioinformatics tools (PAINT, IPA) were used to identify potential upstream regulators

of differentially expressed genes which could contribute to the altered regulation caused by

genotype and alcohol.

• Biostatistical Data Analysis, Drexel

Oct '11 - Dec '11

Undertook statistical analysis of externally obtained Cardioverter-Defibrillator (ICD) and

Pacemaker data. This analysis was done post-hoc. Statistical program, SPSS, was used to

implement the analyses.

Research questions/hypotheses were evaluated with a problem solving approach using

specifically designed statistical tests for data analysis and inference. Part of a 4 member team,

specific responsibilities included determining if age affected implantation time and if age and

race affected remaining battery voltage using appropriate statistical tests.

• Microarray Data Analysis, Drexel

Oct '11 - Dec '11

Led a team of two graduate students to perform the analysis to provide the highest intensity of

protein ubiquitination to find potential new substrates for Ubiquitin. Specific duties included

implementing the data analysis algorithm and design of GUI on MATLAB.

GUI was designed to accept input data as well as the input number of proteins of highest

intensity to be displayed.

Output provided a heat map of the microarray active and control intensities, input number of

highest fluorescing proteins as well as a scatter plot of active against control intensities.

Each of the signal duplicates were averaged, corrected for background absorbance and

compared to their respective threshold intensities to ascertain the highest fluorescents.

TECHNICAL PRESENTATIONS

• “Immobilized Enzyme Reactors” (VTU, 2010).

Discussed assembly, advantages and uses of Immobilized enzyme reactors.

• “Atomic Fluorescence Microscopy” (Drexel, 2010).

Key points highlighted - working principle, modes, merits and applications Atomic

Fluorescence Microscopy.

• “Super Resolution-Structured Illumination Microscopy (SR-SIM)” (Drexel, 2011).

Key aspects covered - principle, merits and state-of-the-art of SR-SIM.

TEACHING EXPERIENCE

• Graduate Teaching Assistant, Department of Physics, Drexel University

Mar '11 - Jun '12

Responsible for teaching theory recitation classes as well as laboratory instruction.

Assisted in designing and grading of quizzes, assignments and examinations.

Cemented effective communication skills and leadership abilities.

OTHER ACTIVITIES

• A member of the organizing committee for the “National Conference on Medical

Biotechnology and Clinical Research”, 2009.

• A member of Student coordinating team for the “Conference on Nanobiotechnology”, 2008.

• Participated in a robotics workshop held in April 2007 at MSRIT, in association with IEEE, on the

construction, programming and operation of a semi-autonomous robot.

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