Summary
Overview
Work History
Education
Skills
Instruments Handled
Awards
Publications
Personal Information
Timeline
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Deepika Gautam

Rockville,MD

Summary

Accomplished Senior Research Associate at CSIR-IGIB with expertise in molecular biology techniques and project coordination. Demonstrated success in optimizing protein purification processes and conducting quantitative analyses, leading to significant insights in protein folding dynamics. Proven ability to collaborate cross-functionally and drive innovative research initiatives.

Overview

8
8
years of professional experience

Work History

Senior research associate

CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB)
New Delhi
04.2024 - 08.2024
  • Quantitative analysis of expression levels of various GFP mutants relative to the wild type protein was performed using flow cytometry (FACS) for in vivo cellular expression, and fluorescence spectroscopy for in vitro validation of fluorescence Intensity.
  • The fluorescence ratio of GFP to mCherry was measured in cells co-expressing both reporters, enabling normalization and quantitative assessment of protein expression levels.
  • Protein mutants exhibiting significant deviations in fluorescence intensity compared to wild-type were subjected to purification via Ni-NTA affinity chromatography, facilitating downstream biochemical and structural characterization of protein folding and stability properties.
  • Key Result Areas:

PhD scholar

CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB)
New Delhi
08.2017 - 04.2024
  • Project 2018-2019 “A clinical approach to quantify Mt-DAMPs in the Caerulein-induced a mice model of acute pancreatitis (AP)”
  • An acute pancreatitis model was established in Wistar mice through intravenous administration of cerulein, a known inhibitor of fatty acid synthase that induces pancreatic injury via disruption of lipid metabolism.
  • Experimental animals received cerulein, while control mice were administered physiological saline.
  • At defined time points (6h,8h,12h) post-injection, mice were euthanized, and a comprehensive tissue dissection was performed. Organs, including the pancreas, kidney, heart, and brain, were harvested for downstream analyses to assess the systemic and organ-specific effects of cerulein-induced pancreatic injury.
  • Quantification of damage-associated molecular patterns (DAMPs) such as mitochondrial DNA (mtDNA) and ATP was performed on serum samples from both control and disease model mice by qPCR.
  • Protein expression levels of cellular stress and apoptotic markers (Bax, Bad, caspases) were analyzed in tissues from both the disease model and control mice using Western blotting.
  • Studied the protein folding mechanism in the presence of different chaperones in vitro and in vivo.
  • Project 2017-2024“Understanding the protein folding capacity in the mammalian system”.
  • Different GFP mutants were generated for mammalian systems using site-directed mutagenesis (SDM) and cloned by Gibson assembly. Successful SDM mutants were cloned into viral vectors (pHIV-P2A-mCherry) by Gibson cloning and introduced into HEK cells via chemical transfection, and their folding process was observed using flow cytometry.
  • By utilizing the mitochondrial signal sequence construct, we tried to monitor the protein folding of the GFP mutants dependent on Hhsp60/10 found inside the mitochondria and visualization by Mito tracker dye.
  • Monitoring the impact of small molecules like Glutamate, succinate, etc., on protein folding inside mitochondria by suppressing the TCA cycle utilizing the rotenone and oligomycin.
  • Project 2017-2024: “Human Hsp60/10 interacts with dicarboxylic acids to mimic bacterial chaperone GroELES”.
  • The chaperonin system in prokaryotes is GroELES. We have investigated the characteristics responsible for its chaperone function.
  • Cloning of GFP and its mutants into a pet-SUMO vector for purification and transformation into E. coli strains like BL-21(DE3), Rosetta, Stbl 2.3 cells.
  • Chaperones (GroELES, Hhsp60/10, yHsp60/10, etc) were purified by using affinity chromatography (DEAE and ANX) and FPLC (AKTA pure and AKTA explorer)
  • GroELES makes it energetically favorable for a mutant GFP (K45E) to fold through a decrease in enthalpic barriers and reduces the entropic obstacles via a negatively charged environment within its cavity.
  • Human Hsp60/10 exhibits different negative charges in its cavities, which leads to different chaperone activities towards the same substrate. So, we investigated whether small negatively charged molecules could analyze the folding dynamics of model proteins.
  • Key Result Areas:

Research Associate

India Institute of Science (IISc)
Bangalore
08.2016 - 08.2017
  • Developed and optimized primary cultures of hippocampal neurons from postnatal pups to study neuronal growth and differentiation.
  • Investigated the effects of Cyclodextrin on neuronal development, assessing its impact on cell maturation and differentiation pathways.
  • Executed immunocytochemical analysis using Tau, β-III tubulin, and Map-2 antibodies to monitor neuronal differentiation and identify key maturation markers.
  • Conducted quantitative Sholl analysis using Neurolucida and Image-J software to evaluate dendritic complexity and neuronal connectivity in 2D and 3D models at various developmental stages.
  • Performed high-resolution imaging through Epifluorescence and confocal microscopy to capture dynamic neuronal development and structural changes in cultured neurons.
  • Key Result Areas:

Education

PhD - Biological Science

CSIR- Institute of Genomics and Integrative Biology
New Delhi, India
01.2024

M.Sc. - Biotechnology

BBAU (Central University)
Lucknow, India
01.2012

B.Sc. - Biotechnology

Chhatrapati Shahuji Maharaj University
Kanpur, India
01.2008

Skills

  • Requirement gathering and analysis
  • Research and development
  • Quality control and assurance
  • Method validation and transfer
  • Process optimization
  • Protocol development
  • Laboratory automation
  • Cross-functional collaboration
  • Project coordination
  • Team leadership
  • Molecular biology techniques
  • Protein analysis and purification
  • Cell and tissue culture
  • Microscopy and spectroscopy
  • Flow cytometry techniques
  • Quantitative analysis techniques
  • Animal handling and histology practices
  • Software proficiency

Instruments Handled

  • AKTA Explore and PURE
  • Flow cytometry (BD-LSR-II)
  • Fluorescence spectroscopy (Fluorolog-3, Horiba)
  • QPCR (Bio-Rad), PCR (Themo)
  • Microscope (confocal and Epifluorescence)
  • Cryostat (Leica)
  • Microtome (Leica)
  • MST (Microscale thermophoresis)

Awards

Senior Research Fellowship, 2019-01-01 to 2022-01-01, Joint CSIR-UGC NET-JRF Examination, Junior Research Fellowship, 2017-01-01 to 2019-01-01, Joint CSIR-UGC NET-JRF Examination, Graduate Aptitude Test in Engineering (GATE)

Publications

  • Dicarboxylic acids synergize with yeast and human Hsp60/10 systems to mimic GroEL/ES, BioRxiv, https://doi.org/10.1101/2024.05.15.594092
  • Conserved and divergent chaperoning effects of Hsp60/10 chaperonins on protein folding landscapes, https://doi.org/10.1073/pnas.2118465119
  • Poster Presentation: "Understanding the Underlying Problems in the Folding Landscape of Chaperone-Dependent Proteins," presented at the International Symposium on 'Mitochondria, Cell Death, and Human Diseases,' New Delhi, 2023-01-04.
  • FCSXIV - The 14th National Workshop on Fluorescence and Raman Spectroscopy, hosted by IISER Mohali and INST Mohali, 2023-12-15.
  • Poster Presentation: "Dicarboxylic Acids Synergize with Yeast and Human Hsp60/10 Systems to Mimic GroEL/ES," presented at EMBO India Conference on Post-Transcriptional Regulation in Aging and Age-Related Diseases, Noida, Uttar Pradesh, 2024-06-10.

Personal Information

Timeline

Senior research associate

CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB)
04.2024 - 08.2024

PhD scholar

CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB)
08.2017 - 04.2024

Research Associate

India Institute of Science (IISc)
08.2016 - 08.2017

PhD - Biological Science

CSIR- Institute of Genomics and Integrative Biology

M.Sc. - Biotechnology

BBAU (Central University)

B.Sc. - Biotechnology

Chhatrapati Shahuji Maharaj University

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