Identification and characterization of novel histone modifications during cellular senescence

Cellular senescence is a stable cell cycle arrest and can be triggered by various signals including telomere shortening, oncogenic activation and other stress activators. Senescence is accompanied by changes in the cellular organization, gene expression and induction of the secretome. It is established and maintained by at least two major tumor suppressor pathways, the p53-p21 and p16-pRB pathways. Senescence is now recognized as a potent barrier to tumor progression and is directly and indirectly linked to a large array of age-related pathologies. However the precise molecular mechanisms of senescence, particularly how cells are driven into irreversible proliferation arrest, in not fully understood. It is well known that widespread changes in the chromatin structure of senescence contribute to the senescent phenotype. In line with this, the primary objective of this project is to understand how senescence is regulated by its chromatin structure. I have focussed on the identification and characterization of novel histone modifications that occur during senescence. Large-scale profiling of histone modifications was performed in replicatively senescent cells in comparison to proliferating cells. Candidate histone modifications were identified that alter during senescence from the screen. To our knowledge, this is the first study to have implied a novel role for these histone modifications during senescence. Also a third histone modification, H4K16ac, was chosen for study based on ChIP-seq observations made in the lab. The mark has also been extensively linked to cancer and aging. All together, work from this project imparts new knowledge on how certain novel histone modifications might regulate senescence via critical modulation of its chromatin structure and how they may impinge on senescence-associated effects such as ageing and cancer

Modeling the Closed and Open State Conformations of the GABA_A Ion Channel - Plausible Structural Insights for Channel Gating

Recent disclosure of high resolution crystal structures of <i>Gloeobacter violaceus</i> (GLIC) in open state and <i>Erwinia chrysanthemii</i> (ELIC) in closed state provides newer avenues to advance our knowledge and understanding of the physiologically and pharmacologically important ionotropic GABA_A ion channel. The present modeling study envisions understanding the complex molecular transitions involved in ionic conductance, which were not evident in earlier disclosed homology models. In particular, emphasis was put on understanding the structural basis of gating, gating transition from the closed to the open state on an atomic scale. Homology modeling of two different physiological states of GABA_A was carried out using their respective templates. The ability of induced fit docking in breaking the critical inter residue salt bridge (Glu155β₂ and Arg207β₂) upon endogenous GABA docking reflects the perceived side chain rearrangements that occur at the orthosteric site and consolidate the quality of the model. Biophysical calculations like electrostatic mapping, pore radius calculation, ion solvation profile, and normal-mode analysis (NMA) were undertaken to address pertinent questions like the following: How the change in state of the ion channel alters the electrostatic environment across the lumen; How accessible is the Cl^– ion in the open state and closed state; What structural changes regulate channel gating. A “Twist to Turn” global motion evinced at the quaternary level accompanied by tilting and rotation of the M2 helices along the membrane normal rationalizes the structural transition involved in gating. This perceived global motion hints toward a conserved gating mechanism among pLGIC. To paraphrase, this modeling study proves to be a reliable framework for understanding the structure function relationship of the hitherto unresolved GABA_A ion channel. The modeled structures presented herein not only reveal the structurally distinct conformational states of the GABA_A ion channel but also explain the biophysical difference between the respective states

Activation of the PIK3CA/AKT Pathway Suppresses Senescence Induced by an Activated RAS Oncogene to Promote Tumorigenesis

Mutations in both RAS and the PTEN/PIK3CA/AKT signaling module are found in the same human tumors. PIK3CA and AKT are downstream effectors of RAS, and the selective advantage conferred by mutation of two genes in the same pathway is unclear. Based on a comparative molecular analysis, we show that activated PIK3CA/AKT is a weaker inducer of senescence than is activated RAS. Moreover, concurrent activation of RAS and PIK3CA/AKT impairs RAS-induced senescence. In vivo, bypass of RAS-induced senescence by activated PIK3CA/AKT correlates with accelerated tumorigenesis. Thus, not all oncogenes are equally potent inducers of senescence, and, paradoxically, a weak inducer of senescence (PIK3CA/AKT) can be dominant over a strong inducer of senescence (RAS). For tumor growth, one selective advantage of concurrent mutation of RAS and PTEN/PIK3CA/AKT is suppression of RAS-induced senescence. Evidence is presented that this new understanding can be exploited in rational development and targeted application of prosenescence cancer therapies

Modeling the Closed and Open State Conformations of the GABAA Ion Channel - Plausible Structural Insights for Channel Gating

Recent disclosure of high resolution crystal structures of Gloeobacter violaceus (GLIC) in open state and Erwinia chrysanthemii (ELIC) in closed state provides newer avenues to advance our knowledge and understanding of the physiologically and pharmacologically important ionotropic GABAA ion channel. The present modeling study envisions understanding the complex molecular transitions involved in ionic conductance, which were not evident in earlier disclosed homology models. In particular, emphasis was put on understanding the structural basis of gating, gating transition from the closed to the open state on an atomic scale. Homology modeling of two different physiological states of GABAA was carried out using their respective templates. The ability of induced fit docking in breaking the critical inter residue salt bridge (Glu155β2 and Arg207β2) upon endogenous GABA docking reflects the perceived side chain rearrangements that occur at the orthosteric site and consolidate the quality of the model. Biophysical calculations like electrostatic mapping, pore radius calculation, ion solvation profile, and normal-mode analysis (NMA) were undertaken to address pertinent questions like the following: How the change in state of the ion channel alters the electrostatic environment across the lumen; How accessible is the Cl− ion in the open state and closed state; What structural changes regulate channel gating. A “Twist to Turn” global motion evinced at the quaternary level accompanied by tilting and rotation of the M2 helices along the membrane normal rationalizes the structural transition involved in gating. This perceived global motion hints toward a conserved gating mechanism among pLGIC. To paraphrase, this modeling study proves to be a reliable framework for understanding the structure function relationship of the hitherto unresolved GABAA ion channel. The modeled structures presented herein not only reveal the structurally distinct conformational states of the GABAA ion channel but also explain the biophysical difference between the respective state

Abstracts of National Conference on Research and Developments in Material Processing, Modelling and Characterization 2020

This book presents the abstracts of the papers presented to the Online National Conference on Research and Developments in Material Processing, Modelling and Characterization 2020 (RDMPMC-2020) held on 26th and 27th August 2020 organized by the Department of Metallurgical and Materials Science in Association with the Department of Production and Industrial Engineering, National Institute of Technology Jamshedpur, Jharkhand, India. Conference Title: National Conference on Research and Developments in Material Processing, Modelling and Characterization 2020Conference Acronym: RDMPMC-2020Conference Date: 26–27 August 2020Conference Location: Online (Virtual Mode)Conference Organizer: Department of Metallurgical and Materials Engineering, National Institute of Technology JamshedpurCo-organizer: Department of Production and Industrial Engineering, National Institute of Technology Jamshedpur, Jharkhand, IndiaConference Sponsor: TEQIP-