Please note there will be two rounds of interviews. Round 1 will be from 13th May – 15th May 2024 (Mon-Wed), Round 2 from 16th – 17th May 2024 (Thu-Fri). You will receive date and time for Round 1 interviews from Admission Section of IISc.
*** At the end of each day of Round 1 interviews (13th – 15th May 2024), a list of shortlisted candidates for Round 2 interviews will be announced on the DBG website and on the department’s notice boards.
Please make it convenient to appear for Round 2 interviews (16th – 17th May 2024) if shortlisted.
Please bring the following documents for the interviews:
1. IISc issued interview letter.
2. Government-issued ID card.
3. Mark sheets for 10th, 12th, Graduate and Post-Graduate courses (if applicable).
4. National entrance test certificate/score card.
Molecular mechanisms of cancer stemness and drug resistance
Cancer stem cells (CSCs) are a rare sub-population of cancer cells identified within several cancers that possess properties of normal stem cells such as self-renewal and the ability to give rise to diverse cell types. These properties of CSCs also contribute to cancer heterogeneity and disease complexity resulting in metastasis, drug resistance, and disease relapse. Therefore, understanding the mechanisms of cancer stemness and drug resistance is of utmost importance to improve treatment outcomes.
Epithelial to mesenchymal transition (EMT) is a developmental programme hijacked by cancer cells and is considered to be a pre-requisite for cancer spread by metastasis. Prior work in AR lab has identified the energy sensor kinase AMPK as a central player contributing to EMT, stemness and drug resistance phenotypes, thereby aiding metastasis. This study will aim to understand the role of AMPK in EMT during normal embryonic development and cancer metastasis using Drosophila, mouse models, and human cancer cell lines.
References-
• Saha M, Kumar S, Bukhari S, Balaji SA, Kumar P, Hindupur SK, Rangarajan A. AMPK-AKT double negative feedback loop in breast cancer cells regulates their adaptation to matrix deprivation. Cancer Res. 2018 Mar 15;78(6):1497-1510. doi: 10.1158/0008-5472.CAN-17-2090.
• Saxena M, Balaji SA, Deshpande N, Ranganathan S, Pillai DM, Hindupur SK, Rangarajan A. (2018). AMP-activated protein kinase promotes epithelial-mesenchymal transition in cancer cells through Twist1 upregulation. J Cell Sci. 2018 Jul 26;131(14). pii: jcs208314.
• Andugulapati SB, Sundararaman A, Lahiry M, Rangarajan A. AMP-activated protein kinase promotes breast cancer stemness and drug resistance. Disease Models & Mechanisms. 2022 Jun 1;15(6):dmm049203.
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Position open to study signaling in aging and implications of its metabolic remodeling
Two-Component Systems (TCS) are essential Mycobacterial signaling systems that aid in sensing and adapting the bacteria to their ever-changing environment. Mycobacteria have 12 pairs of TCSs, and several studies have been carried out to characterize each pair extensively. Towards understanding the network among these systems, we previously identified the presence of unsual and extensive crosstalk, which leads to the formation of various networks and generates hierarchy in these signaling systems.
Given that these systems also regulate critical cellular adaptive processes, the present opening allows the candidate to characterize the implications of cross talk on regulating specified cellular mechanisms such as virulence, cell wall integrity, growth, and adaptation to environmental changes using biochemical and biophysical approaches. In vivo analysis of crosstalk between and across different TCSs using knock-out strains and identification of regulons impinge on crosstalk and their role in virulence and infection will be examined. The long-term question is to understand the evolutionary design of crosstalk or its absence.
Please check faculty home page for more details.
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Parasite Epigenetics Lab
Lab website: www.meetaliLab.com
Twitter: @meetalichauhan
meetalisingh@iisc.ac.in
RNA interference (RNAi) is a conserved pathway across all eukaryotic species, with a notable exception of some parasitic protozoa, including Plasmodium falciparum. On the other hand, protozoan parasites like Toxoplasma, Trichomonas, and Trypanosoma, among others, retained RNAi, however, with minimal components and RNAi factors with atypical domains. Our understanding of RNAi (small RNA) pathways in most of these organisms is very limited. In this proposed study, we will investigate the functions of this minimal RNAi pathway using Toxoplasma gondii as a model system. Toxoplasma gondii can infect any nucleated cell in warm-blooded animals, where it reproduces asexually, with the sexual cycle taking place in the definitive hosts of the cat family. Despite a minimal RNAi pathway, deep sequencing has identified small RNAs in Toxoplasma gondii. Yet, their function in the life cycle and pathogenesis of the parasite is entirely unknown.
To address the big question of how this atypical small RNA pathway mediates epigenetic regulation of pathogenesis and host-parasite interaction, we will implement the following projects using state-of-the-art methods, including Next-Gen sequencing methods (Illumina and nanopore platform), proteomics (Mass-spec), molecular biology, biochemistry, and computational data analysis.:
If you would like to explore the world of small RNAs with us, visit our lab (GB-01) during the interviews while you are in Bangalore.
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Developmental epigenetic regulation through the lens of X-chromosome inactivation and reactivation.
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 and reactivation during transition of pluripotent sub states using mouse embryo and stem cells.
Please check faculty home page for more details.
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The research program in our laboratory focuses on key transcription factors and lipid molecules that regulate adipose tissue development, function, and maintenance of pre-adipose stem cells under various metabolic conditions, including diet-induced obesity, aging, type 2 diabetes etc. To address our research hypothesis, we employ several cutting-edge approaches, including CRISPR-Cas9 mediated gene editing, transcriptomics, lipidomics, and tissue-specific or transgenic mouse models.
References:
1. Divakaran SJ, Srivastava S, Jahagirdar A, Rajendran R, Sukhdeo SV, Rajakumari S. (2020) Sesaminol induces brown and beige adipocyte formation through suppression of myogenic program. FASEB J.
34(5):6854-6870.
2. Shapira SN, Lim HW, Rajakumari S, Sakers AP, Ishibashi J, Harms MJ, Won KJ, Seale P. (2017). EBF2 transcriptionally regulates brown adipogenesis via the histone reader DPF3 and the BAF chromatin remodeling complex.
Genes Dev. 31(7):660-673.
3. Rajakumari S, Wu J, Ishibashi J, Lim HW, Giang AH, Won KJ, Reed RR, and Seale P. (2013) EBF2 Determines and Maintains Brown Adipocyte Identity.
Cell Metab. 17(4):562-574.
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The synthesis of proteins using genetic information and its regulation is a fundamental process in all life forms. These processes play 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. This is essential for developing novel therapeutic strategies for many human disorders/ cancers and against bacterial, fungal and viral infection.
We have made good progress in understanding eukaryotic translation initiation and its regulation (see recent publications). 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 and X-ray crystallography). Facilities for cryo-EM and X-ray crystallography are available in IISc.
For further details of the project, contact Prof. Tanweer Hussain (Lab: GB-04; Email: hussain@iisc.ac.in)
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The main focus of my group is to understand the molecular and cellular basis of myopathies and neurodegenerative disorders. We use two genetically tractable model organisms, Drosophila melanogaster (fruit fly) and Danio rerio (zebrafish), to trace the aetiology of these diseases and dissect the associated mechanisms. Experimental approaches include genetic, molecular, biochemical and biophysical assays, electron and confocal microscopy and behavioural tests. We are doing drug screening for many myopathies, neurological disorders, and nutraceutical implementation. Particularly, we are interested in increase strengthening of the muscle, isoform switching and the retaining of specific muscle patterning.
Please check faculty home page for more details.
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Epigenetic mechanisms have emerged as key players in the regulation of cancer cell-states such as matrix-attached vs detached, stem vs non-stem, EMT vs MET that contribute to cancer heterogeneity and therapy failure. In this study we will explore epigenetic mechanisms such as histone modification, DNA methylation, and X-chromosome re-activation (XCR) in the regulation of cancer cell plasticity by employing ChIP sequencing and transcriptomics approaches. This study will be undertaken jointly with Dr. Srimonta Gayen.
• Mandal, S., Chandel, D., Kaur, H., Majumdar, S., Arava, M. and Gayen, S., 2020. Single-cell analysis reveals partial reactivation of X chromosome instead of chromosome-wide dampening in naive human pluripotent stem cells. Stem Cell Reports, 14(5), pp.745-754.
• Naik, H.C., Hari, K., Chandel, D., Jolly, M.K. and Gayen, S., Single-cell analysis reveals X upregulation is not global in pre-gastrulation embryos. Iscience,25(6), p.104465.
• Naik, H.C., Hari, K., Chandel, D., Mandal, S., Jolly, M.K. and Gayen, S., Semicoordinated allelic-bursting shape dynamic random monoallelic expression in pregastrulation embryos. Iscience,24(9), p.102954.
Title: Metabolism as a modulator of cancer metastasis
Blurb: As cancer cells migrate out of their primary focus and travel to different parts of the body, they show distinct and sometimes seemingly contradictory phenotypes, such as fast amoeboid migration, unbridled proliferation or dormant (asleep) behavior. It is reasonable to surmise that such behaviors are driven by differences in bioenergetics, redox status and biomaterial synthesis-degradation: all these processes are intimately associated with the metabolic infrastructure of the cells, and its alterations in cancer. We will investigate the causes and effects of such changes in breast and ovarian cancer metastasis using a multidisciplinary approach.
Tools: organoids, organ-on-chips, classical cell and molecular biology, various modes of fluorescence microscopy, NMR spectroscopy, omics, time lapse imaging, (Optional, depending on aptitude: genome scale metabolic modeling, agent-based computer modeling)
Primer: For an introduction to our group’s approach to research please see the following primer https://www.youtube.com/watch?v=EMxqx684yWk
References:
Contact: Please visit our site https://morphogenesisiisc.wixsite.com/home for more details and get in touch with me at ramray@iisc.ac.in to set up an in person meeting.
Dear Candidates,
We welcome you to the Interview at the Department of Development Biology and Genetics (DBG) at IISc.
The interview will be conducted offline, in person at DBG.
Please carry a Govt approved ID card (eg, Passport, Driver’s Licence, Pan Card, AADHAAR Card) to verify your identity.
You will be interviewed for approximately 10-15 minutes
INSTRUCTIONS TO CANDIDATES
Please look for signboards and instructions in the main lobby of the Biological Sciences Building.
You should reach the DBG seminar hall and sign in the attendance sheet on the date of your Interview. The seminar hall is located on the First Floor of the New Biological Sciences Building.
You will be assigned to Committees (1/ 2/ 3) for interview. Committee Rooms are located in the ‘D Wing, First Floor.
Names of the candidates who have been shortlisted for second interview will be displayed on the DBG Website and DBG Notice Board at the end of the same day.
All candidates shortlisted for second interview must report at 9 am (on the prescribed day), to DBG Seminar Hall for instructions on the venue and time of the second interview.
Candidates who are short-listed for second interview must collect the “Faculty Preference Form” from the DBG Office and submit the same to the DBG office before noon on the day of the second interview.
Should you need any further information, kindly contact the DBG office (office.dbg@iisc.ac.in) or Interview Coordinators (admissions.dbg@iisc.ac.in)
For further information, please also visit faculty home pages.
All the best,
Chair, DBG. IISC
Admission to the department for Ph.D degree is through a departmental selection process for which student are considered through a number of channels.
Admission to the department for this degree is through a division wide selection process which involves qualifying a written test followed by a interview process.