User:Samata Chaudhuri

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Samata Chaudhuri (an artistic interpretation)

<html><b>Samata Chaudhuri</b></html> <html><br>Email:<a href=""></a></html> <html><br>Email:<a href=""></a><br></html> <html> I am presently a predoctoral student in <a href=""> Diez group </a> at Max Planck Institute for Cell, Molecular Biology and Genetics, Dresden. </html>


<html> <ul> <li><b>Integrated (5 years) Masters in Chemistry, <a href="">IIT Kharagpur</a> (2014)</b><br> CGPA- 8.39/10 <br> <b>Minor in Biotechnology and Biochemical Engineering, <a href="">IIT Kharagpur </a> (2014)</b></li> CGPA-8.43/10<br> <li><b>All India Senior School Certificate Examination (2008)</b><br> School: Bharatiya Vidya Bhawan, Kolkata </li> Graduated with 95.0% <br> <li><b>Indian Certificate of Secondary Examination (2006)</b><br> School: Julien Day School, Kolkata<br> Graduated with 94.5% </li> </ul> </html>

Research Experience

Masters Thesis Project

<html> <ul> <li><b> Protein nanoparticles and their characterization<br> Guide:</b> <a href:""> Dr. Swagata Dasgupta </a>, Biophysical chemistry group, Department of Chemistry, Indian Institute of Technology, Kharagpur, India. [August, 2013-present] </ul> </li> </html>


<html> <ul> <li><b>Understanding the role of Lnp1 in endoplasmic network formation using <i>Schizosaccharomyces pombe</i> as a model organism</b><br> <b> Undergraduate Training Program, 2013</b><br> <b>Guide:</b> <a href:""> Dr. Snehazana Oliferenko</a>, Cell Biology Group, Temasek Life Sciences Laboratory, Singapore<br> [May-July,2013]<br> <p><b>Abstract:</b> Endoplasmic Reticulum(ER) is a highly dynamic organelle, continuously undergoing rearrangements throughout the entire cell volume. Analysis of mutants defective in ER morphogenesis demonstrates that maintenance of ER morphology is required for vital intracellular events. Therefore, it is imperative to undertake morphological studies of ER for better understanding of correlation between ER morphology and dynamics and its multifunctional role. This is particularly relevant in medicine as several studies indicate that defect in ER morphology is particularly significant in many neurological disorders. lnp1, a member of the conserved Lunapark protein family, is a protein that resides in three-way ER tubule junctions in both yeast and mammalian cells. It has been found to be required for ER network formation and also to interact with other proteins that are involved in generation and stabilization of ER network. <br> The aim of the study was to understand the role of lnp1 in fission yeast, ''Schizosaccharomyces pombe'' by obtaining strains lacking the gene lnp1 as well as generating wild type strains containing lnp1 by tagging with fluorescent markers (GFP, mCherry). The lnp1Δ strains, as well as the strains containing labelled lnp1-GFP/lnp-mCherry, were crossed with strains containing ER specific proteins tagged with fluorescent markers that localize in different regions of the ER. The strains thus generated were visualized by live cell imaging using confocal microscopy. Also, the doubling time was monitored in both lnp1Δ cells and wild type cells to find out if the deletion has an impact on the growth rate in the mutant.</p>

<p><b>Major Techniques:</b> Yeast cell culture and genetics, Dissection Microscopy, Confocal Microscopy(spinning disc,scanning confocal) </li> </p> </ul> </html>

<html> <ul> <li><b>To study and modulate photophysical and chemical dynamics properties of Curcumin in zwitterionic micellar system to obtain stable aggregate encapsulating the drug molecule</b><br> <b>Guide:</b> <a href:""> Dr. Nilmoni Sarkar</a>, Photophysics and Chemical Dynamics Group, Department of Chemistry, Indian Institute of Technology, Kharagpur, India <br> [December,2012 - January,2013]<br> <p><b>Abstract:</b> This project involved studies on the photophysical properties of anticancer drug, curcumin in a zwitterionic (N-hexadecyl-N,N-dimethylammonio-1-propanesulfonate (SB-16)) micellar aggregates, with addition of anionic surfactant SDS,by using steady state fluorescence spectroscopic technique. The absorbance and emission spectra, partition coefficient, steady state anisotropy were determined at different temperatures in an effort to understand the microheterogeneous environments of zwitterionic micellar system by monitoring the modified photophysics of the external probe, curcumin upon interaction with SB-16 micelle.</p>

<p><b>Major Techniques:</b> UV-VIS Spectroscopy, Fluorescence Spectroscopy (Steady state, time-resolved) </li> </p> </ul> </html>

<html> <ul> <li><b>Characterization of differentiated macrophages using M1/M2 gene profiling and studying the expression of RhoC in Inflammatory Breast Cancer (IBC) cells stimulated with macrophage conditioned media </b><br> <b><a href:"">Khorana Scholar</a>, 2012 </b><br> <b>Guide:</b> <a href:""> Dr. Sofia Merajver </a>, Department of Internal Medicine, University of Michigan, Ann Arbor, USA<br> [May-July, 2012]<br> <p><b>Abstract:</b> Inflammatory breast cancer (IBC) is a rare and very aggressive type of breast cancer accounting for 1-5% of all breast cancers diagnosed in United States. Typically IBCs are invasive ductal carcinomas, i.e. they develop from cells that line the milk ducts of the breasts and spread beyond the ducts, usually progressing rapidly in a matter of weeks or few months. Smoldering inflammation is a component of the tumor microenvironment and represents the 7th hallmark of cancer. Tumor associated macrophages (TAMs) serve as one paradigm for cancer promoting inflammation. Circulating blood monocytes differentiate into M1 or M2 polarised macrophages when exposed to different cytokines and stimulating factors. Stimuli such as bacterial products (lipopolysaccharide) or interferon-gamma polarise them to M1 type cells with high microbicidal activity, immune-stimulatory functions, and tumor cytotoxicity; therefore typically conferring them with a tumor suppressive role. Whereas, factors like interleukin-4 and interleukin-13 stimulate polarisation to M2 type cells associated with pro-tumoral functions, such as promoting angiogenesis, enhancing tumor cell invasion and migration, suppressing antitumor immune responses, and even enhancing metastasis. Differentiating monocytes in the tumor microenvironment encounter factors that more frequently polarise them toward the M2-type pro-tumor macrophages. It is also evident that TAMs and tumor cells communicate to one another via secreted signals in order to serve these pro-tumor functions. <br>

In this scheme of work, we characterized differentiated monocytes based on their M1/M2 gene profile. We also studied the RhoC protein expression in IBC-derived cells with macrophage conditioned media. RhoC, a small GTPase, is a recognized oncogene for IBC and is overexpressed in over 90% of IBC tumor samples. Studying the expression of RhoC in correlation with TAMs would help in understanding if polarized TAMs contribute to stimulating the RhoC oncogene, which in turn enhances the invasive and metastatic properties of IBC.</p>

<p><b>Major Techniques:</b> Mammalian cell culture, RT-qPCR, Western blotting </li> </p> </ul> </html>

<html> <ul> <li><b>Steady state and time resolved photophysical studies on interaction between Acridine and Tryptophan in homogeneous and heterogeneous solvents</b><br> <b>Guide:</b><a href=""> Dr. Samita Basu </a>, Chemical Sciences Division, Saha Institute of Nuclear Physics, Kolkata, India<br> [December, 2011]<br> <p><b>Abstract:</b> Interaction between Acridine and Tryptophan was investigated by monitoring the UV-Vis absorbance spectra, fluroscence spectra and time resolved fluorescence (TCSPC) studies in different solvent systems: homogeneous aprotic solvents (Tetrahydrofuran and Acetonitrile), homogeneous protic solvents (Ethanol and water) and heterogeneous solvent systems(SDS and AOT).</p>

<p><b>Major Techniques:</b> UV-VIS Spectroscopy, Fluorescence Spectroscopy (Steady state, time-resolved)<br> </li> </p> </ul> </html>

<html> <ul> <li><b>Cloning, expression, purification and biochemical studies of C-terminal deleted Mom protein of bacteriophage Mu</b><br> <b><a href:"">Indian Academy of Science</a>-Summer Research Fellowship, 2011</b><br> <b>Guide:</b><a href=""> Dr. Valakunja Nagaraja </a> ,Department of Microbiology and Cell Biology, Indian Institute of Sciences, Bangalore, India <br> [May-July 2011]<br> <p><b>Abstract:</b> Mu is a temperate bacteriophage that infects ''E.coli'' and a wide range of other Gram negative enteric bacteria. possessing a novel host-range expansion mechanism involving post-replicative DNA modification function, encoded by the phage mom gene. This mom-specific modification(called “momification”)ensures bacteriophage Mu of an expanded range of hosts by providing protection against a wide range of bacterial restriction endonucleases. Besides this, momification seems to be indispensible for viral growth or lysogeny. This special advantage, however, comes at a cost as untimely expression of mom is fatal to the phage. Mom protein is toxic to the bacterial host and causes its death by indiscriminate momification of the host DNA, thereby rendering the phage unable to exploit the resources offered by the host cell.<br>

Although the regulation of the mom expression has been studied and established, the biochemical characterization of the protein is yet to be done. The major hindrance to isolate Mom protein was its expression in host without killing the latter due to toxicity of the expressed protein. When attempts were made to clone an intact mom gene located 3’ end to a constitutive vector, no viable transformants were obtained, indicating that Mom protein is indeed toxic to the host.

To overcome this difficulty, a novel regulatory circuit utilizing T7-expression system was used. This system allowed expression of restriction endonucleases in the absence of their cognate methyl transferases. It contained a combination of two plasmids that ensures that there is no leaky expression in the absence of inducer while in presence of inducer, there is over-expression of the protein. Extending this concept, I cloned the mom gene and expressed it in bacterial cells by inducing at different temperatures and concentrations of IPTG. Addition of hexa-histidine tag allowed the protein to be purified using Ni-NTA column. Mass spectroscopy of the protein and DNA-binding studies were performed for both the intact as well as the C-terminal deleted protein.</p>

<p><b>Major Techniques:</b> Bacterial cell culture, Affinity chromatography, Western Blotting, Electrophoretic Mobility Shift Assay (EMSA) </li> </p> </ul> </html>

Term Projects

<html> <ul> <li><b>Computational Chemistry: Developed a Full molecular dynamics(MD) code for a model system : Argon<br> Guide:</b> <a href=""> Dr. Sanjoy Bandyopadhyay </a>, Department of Chemistry, Indian Institute of Technology, Kharagpur, India <br> [August-November, 2012]

<li><b>Organometallic Chemistry: Synthesis of macrocyclic molecules using dipyrrolylmethanes with potential application in anion binding<br> Guide:</b> <a href=""> Dr. Ganeshan Mani </a>, Department of Chemistry, Indian Institute of Technology, Kharagpur, India <br> [January, 2011] </li> </ul> </html>


<html> <ul> <li><b> <a href:"">East India Pharmaceutical Works Limited</a>, Kolkata, India </b><br> [July,2011]<br> Rotations at Research and Development, Liquid and Oral Drug Formulation, and Quality Management Sections of the organisation to gain an understanding of the nature of research work undertaken and functioning of a Pharmaceutical Industry. <br>

<li><b> <a href:"">Indian Institute of Science, Education and Research, Mohali, </a> India </b><br> [May,2010]<br> Attended a summer camp which involved series of popular lectures by eminent scientists,rotations at different research laboratories at the institute and close interaction with the Principal Investigator and researchers of different research groups.<br> </li> </ul> </html>

Awards and Honors

<html> <ul> <li><b> <a href:"">Kishore Vaigyanik Protsahan Yojana (KVPY) Scholarship</a></b>, 2010-present</br> National Scholarship for students interested in pursuing a career in science. Around 60 undergraduate students were selected from over 60,000 candidates based on written test and personal interview

<li><b> <a href:"">Khorana Scholar,</a></b> 2012 <br> Selected as one of the 30 students selected from over 1100 applicants from undergraduate and post-graduate level as Exchange Scholars to pursue summer internship in different US university laboratories under the auspices of The Department of Biotechnology (DBT), Government of India, the University of Wisconsin-Madison (UW) and the Indo-US Science and Technology Forum (IUSSTF)

<li><b> Indian Academy of Sciences Summer Research Fellowship,</b> 2011</br>

<li><b> <a href:"">Innovation In Science Pursuits for Inspired Research (INSPIRE)-Scholarship for Higer Education (SHE)</a>, </b>2009<br>

<li> Awards from several organisations for being the <b>topper among girl candidates (overall rank-16 out of about 40,000 candidates) in West Bengal Joint Entrance Examination-Medical</b><br>

<li> Secured <b>24th position</b> in <b>National Science Olympiad,</b> 2007<br>

<li><b> Best outgoing student</b> in school, 2006 <br>

<li><b> Certificate of Merit,</b> 2006<br> Awarded by State Government for securing third position in the state in Secondary Examination </ul> </html>


  • Spectroscopy: UV-VIS, Fluorescence, LC-MS, FT-IR, NMR, CD
  • Chromatography: HPLC, Affinity Chromatography, Ion Exchange Chromatography
  • Microscopy: Confocal, TEM
  • Biological: cell culture, bioassays, EMSA, Western blotting, PCR
  • Softwares: ChemDraw, PyMol, Origin, MS Office, Adobe Photoshop
  • Programming Languages: C, Python, R (Intermediate)

Courses Undertaken

  • Physical Chemistry-I,II
  • Colloids and Surface Chemistry
  • Intorduction to Quantum Chemistry & Spectroscopy
  • Molecular Thermodynamics & Kinetics
  • Group Theory for Chemists
  • Molecular Spectroscopy & Molecular Structure
  • Spectroscopic Methods of structure determination
  • Biophysical Chemistry
  • Computational Chemistry
  • Inorganic Chemistry-I,II,III
  • Organic Chemistry-I,II,III
  • Strategies & Methods in Organic Synthesis
  • Principles of Organic Synthesis
  • Analytical & Environmental Chemistry
  • Inorganic Chemistry: Structure, Principle, & Reactivity
  • Solid State Chemistry
  • Principles of Organometallic & Bio-inorganic Chemistry
  • Drug Design and Development
  • Science of Living Systems
  • Microbiology
  • Biochemistry
  • Environmental Science
  • Structure & function of biomolecules
  • Cell & Molecular Biology
  • Biochemical Reaction Engineering & Bioenergetics
  • Bioreactor Analysis & Design
  • Downstream Processing
  • Protein Engineering
  • Differential & Integral Calculus
  • Numerical Solution to Ordinary & Partial Differential Equations
  • Programming & Data Structure
  • Electrical Technology
  • Basic Electronics
  • Physics-I,II
  • Mechanics
  • Visual Communication
  • Organisational Psychology
  • Rural Development
  • Introduction to Financial Management

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