Prospective PhD projects

Faculty in MRDG who would be interested in PhD students this year are as follows:

Arun Kumar 

The research interests of my laboratory, in a broad sense, lie in the area of Human Molecular Genetics and Cancer Biology. Currently, we are looking for motivated student(s) to work on any one of the following projects.

Project 1-Identification of TSC2-regulated protein coding and non-coding genes: Mutations in tumor suppressor TSC1 and TSC2 genes cause an autosomal dominant disorder, tuberous sclerosis complex (TSC). TSC1 and TSC2 proteins interact to form a complex, which negatively regulates mTORC1 in the PI3K-AKT-mTOR pathway, and in turn regulates cell proliferation. This is a well-known cytoplasmic function of these TSC genes. We and others have shown earlier that TSC1/hamartin localizes to the cytoplasm, whereas TSC2/tuberin shows nuclear as well as cytoplasmic localization. To elucidate the nuclear function of TSC2, we have used gene expression profiling of TSC2-overexpressing cells, luciferase reporter assay, siRNA knockdown, ChIP and EMSA techniques, and have shown for the first time that TSC2 also functions as a transcription factor and transcriptionally regulates Epiregulin, a ligand for EGFR. However, Epiregulin cannot be the only TSC2-regulated gene. Then, what are the other genes regulated by TSC2? The interested student(s) will thus explore and identify other (protein coding & non-coding) genes, which are transcriptionally regulated by TSC2, using a variety of molecular and cell biology approaches such as microRNA microarray analysis and RNASeq. The work will also involve the exploitation of TSC2-regulated gene(s) in oral cancer therapeutics.

Project 2-Molecular consequences of mutations in ATP7B, coding for a copper transporter: Wilson disease (WD) is an autosomal recessive disorder, characterized by excessive deposition of copper in various parts of the body, mainly in the liver and brain. It is caused by mutations in ATP7B, which codes for a trans-Golgi network residing copper transporter. We have recently performed the genetic analysis of 102 WD families from a south Indian population, and identified 36 different ATP7Bmutations, including 13 novel ones. However, the molecular consequences of these novel mutations in disease pathology are not known. Using a variety of molecular and cell biology approaches, the interested student(s) will explore and identify the role of these novel ATP7B mutations in disease pathology. The work will also involve the use of specific inhibitor(s) to restore the function of mutated ATP7B, with an aim to develop therapeutic treatment for WD.

Upendra Nongthomba and ► Arun Kumar 

Molecular genetic characterization of TRIM36 using zebrafish model system (Under the joint guidance of Prof. Upendra Nongthomba and Prof. Arun Kumar): E3 ubiquitin-protein ligases mediate ubiquitination and subsequent proteasomal degradation of target proteins and are involved in multiple cellular functions, including chromosome segregation, cell cycle regulation, apoptosis etc. TRIM36 is an E3 ubiquitin protein ligase and mutations in the TRIM36 gene have been shown to cause Colorectal cancer and Anencephaly (ANPH)- An extreme form of neural tube defect resulting in the absence of brain tissues. However, the detailed molecular mechanisms as to how TRIM36 mutations lead to these disorders/diseases are not clear. In this project, the prospective student is expected to generate human TRIM36 mutations in Zebrafish to study molecular and cellular mechanisms involved. Further literature: Singh et al. Human Molecular Genetics, Volume 26, Issue 6, 15 March 2017, Pages 1104-1114; Liang et al. Cell Death and Diseases, Volume 9, 2018, 155.

Sona Rajakumari

The research program in my laboratory focuses on key transcription factors and lipid molecules that regulate adipose tissue function and maintenance of pre-adipose stem cells. We employ several approaches including CRISPR-Cas9 mediated gene editing, transcriptomics, lipidomics and transgenic mouse models to understand the adipocyte lineage commitment and function.

Ramray Bhat

We are broadly interested in understanding how cancers invade and metastasize to different parts of the human body. Using experimental, bioinformatic and theoretical approaches, we focus on the cues from the stroma: cells, proteins and sugars that may be involved in this process in breast and ovarian cancer. The incoming student will be encouraged to frame her or his own research questions on this topic in relation to the aberrant metabolic regulation within invading cancer cells. Students interested in joining my group must get in touch with me by email.

Varsha Singh

Available projects

A. Regulation of longevity in C. elegans by GPCR signaling: We have recently discovered that an olfactory GPCR, STR-2, regulates life span of worms by regulating lipid metabolism (AGING CELL, 2020, also see Infec & Immun, 2020). Using a combination of proteomics, metabolomics and RNA sequencing approaches, we have found that a specific histone deacetylase is dysregulated in the short-lived mutant. This project involves study of the deacetylase as well as ligands of STR-2 to increase longevity and lipid homeostasis in C. elegans. It also involves analyses of mutants of other GPCRs to examine their effect on lipid metabolism and life span.

B. Molecular bases of Microbe Pattern recognition in Caenorhabditis elegans: We have found that sensing of specific bacterial volatiles (produced by Pseudomonas aeruginosa) by host sensory neurons drives calcium signaling in them and a flight or fight response in worms. We propose to extend this study by analyses of volatiles produced by other bacteria (Staphylococcus aureus, Klebsiella pneumoniae etc) and by studying the chemotaxis response of worms to them. This will be followed up with identification of C. elegans GPCRs responsible for sensing the bacterial signal and of signaling mechanisms underlying the flight or fight response.

C. Sensing of environmental signals drives swarming in bacteria: Collective behavior in prokaryotes allows them to engage in social traits like swarming and biofilm formation which provides antibiotic resistance and increases survival of the species. Swarming in P. aeruginosa entails rapid colonization of semi-solid surface such as soft agar (in lab) and believed to happen on the lumenal surfaces in host. However, the ecological motivations of swarming are poorly understood. We have found that as many as 44 genes encoding two component system (TCS) required for sensing environmental cues are necessary for swarming (iScience, 2019, see videos on the lab website). We find that TCS genes differentially regulate biofilm formation on endotracheal tube (J Med Microbiol, 2020). The swarm can sense and turn away from inert obstacles as well as antibiotics (Phy Rev E, 2020). We are in search for environmental cues for swarming under pathophysiological conditions (diabetic foot ulcer and cystic fibrosis) using genetics and interdisciplinary approaches.

For additional information, visit the lab page https://sites.google.com/view/varshalab/home and/or contact the PI.

Annapoorni Rangarajan

Cancer and stem cells: Akin to normal adult stem cells that are essential for the maintenance of the body, cancers contain within them a subpopulation of cancer stem cells that play a crucial role in cancer initiation, maintenance and recurrence. A long standing interest of my laboratory has been to understand the mechanisms of self-renewal in normal and cancerous stem cells. Recent work in the lab has identified a novel role for AMP-activated protein kinase (AMPK), a cellular energy sensor, in regulating stemness properties such as anchorage-independent growth, epithelial-to-mesenchymal-transition, and drug resistance. We aim to address the role of AMPK, and energy metabolism, in normal and cancer stem cells using murine mammary gland development and human breast cancer patient-derived tissue samples as model systems. In vivo studies in AMPK knockout animal models, ex-vivo mammary gland development in 3-dimension, and in vitro cell culture experiments involving cell biology, molecular biology, and signal transduction will be employed.

Deepak K Saini

The project/s available in the SAInI lab focusses on understanding the regulatory and evolutionary design of crosstalk between two-component signaling proteins in M. tuberculosis. We have previously identified crosstalk amongst various sensor kinase and response regulators proteins which has revealed a very intricate network in bacterial signaling pathways. We have also identified how these networks are tuned by post translational modifications such as acetylation and how protein-protein interactions modulate TCS signaling. The proposed project will dwell deeper into biophysical design logics which facilitate existence and operation of these networks and identify the physiological conditions where they are realizable. The projects will involve extensive use of various biochemical, biophysical, microbial genetics and pharmacological approaches.

Tanweer Hussain

The synthesis of proteins using genetic information is a fundamental process in all life forms. In higher organisms, the process is tightly controlled and much of this regulation occurs during the initial steps of translation. Translational control plays an important role in many key life processes including early embryonic development, learning and memory as well as in response to cellular stress. Although translation initiation is a fundamental and indispensable process, many of its aspects are poorly understood.  We employ biochemical, mutational and structural biology approaches to understand the molecular details of the initial steps of protein synthesis and to figure out how it is regulated. Understanding translation initiation and its regulation will be beneficial for many human disorders and cancers. Further, it may provide avenues to develop strategies for modulation of translation initiation and development of novel therapeutic strategies against bacterial, fungal and viral infection.

We have made some progress to understand eukaryotic translation initiation and its regulation in the lab. The incoming PhD student would build up on the ongoing project to understand the molecular details of processes involved, using molecular biology, biochemistry, and structural biology techniques. Cryo-electron microscopy (cryo-EM) will be used for determining the structures of biological complexes involved. Three-dimensional structures of individual domain / protein or smaller macromolecular complexes (not amenable to cryo-EM) will be determined using X-ray crystallography. Facilities for cryo-EM and X-ray crystallography are available in-house.

Srimonta Gayen

Epigenetics; X-chromosome inactivation; X-chromosome upregulation; Long non-coding RNAs; Chromatin modifiers; Pluripotent stem cells; Genomic imprinting; Random monoallelic gene expression.

Emerging evidence implicates that epigenetics plays a major role in developmental processes. However, often dysregulation of epigenetic processes leads to different human diseases such as cancer. Unlike irreversible mutations in DNA, epigenetic modifications are reversible. This inherent plasticity makes epigenetic changes associated with human diseases potentially amenable to manipulation via therapeutic intervention. Therefore, understanding of epigenetic regulation is crucial for our comprehension of the alterations that can lead to disease. However, much about the mechanistic aspects of epigenetic regulation remains to be understood. Our research strives to further the understanding of mechanism of epigenetic regulation through the study of X-chromosome inactivation/reactivation, X-chromosome upregulation, Genomic imprinting and Random monoallelic gene expression using mouse/human embryo and stem cells. We use regular molecular biology tools, single cell genomics, RNA-FISH and computational methods.

Incoming students can frame their future research in any of the following ongoing projects in the lab.

1. Dynamics of X-chromosome upregulation in mouse and human pluripotent stem cells.

2. Identification of factors responsible for maintenance of X-chromosome inactivation.

3. Role of X-chromosome inactivation escapees in sexual dimorphism.

4. Functional and molecular characterization of novel X-linked long non-coding RNAs transcribing from X-inactivation centre.

5. Association between transcriptional burst kinetics and random monoallelic gene expression.