10 research outputs found
Lysosome-mediated processing of chromatin in senescence
Cellular senescence is a stable proliferation arrest, a potent tumor suppressor mechanism, and a likely contributor to tissue aging. Cellular senescence involves extensive cellular remodeling, including of chromatin structure. Autophagy and lysosomes are important for recycling of cellular constituents and cell remodeling. Here we show that an autophagy/lysosomal pathway processes chromatin in senescent cells. In senescent cells, lamin A/C–negative, but strongly γ-H2AX–positive and H3K27me3-positive, cytoplasmic chromatin fragments (CCFs) budded off nuclei, and this was associated with lamin B1 down-regulation and the loss of nuclear envelope integrity. In the cytoplasm, CCFs were targeted by the autophagy machinery. Senescent cells exhibited markers of lysosomal-mediated proteolytic processing of histones and were progressively depleted of total histone content in a lysosome-dependent manner. In vivo, depletion of histones correlated with nevus maturation, an established histopathologic parameter associated with proliferation arrest and clinical benignancy. We conclude that senescent cells process their chromatin via an autophagy/lysosomal pathway and that this might contribute to stability of senescence and tumor suppression
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<sub>A</sub> 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<sub>A</sub> 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<sub>A</sub> was carried
out using their respective templates. The ability of induced fit docking
in breaking the critical inter residue salt bridge (Glu155β<sub>2</sub> and Arg207β<sub>2</sub>) 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<sup>–</sup> 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<sub>A</sub> ion channel. The modeled
structures presented herein not only reveal the structurally distinct
conformational states of the GABA<sub>A</sub> ion channel but also
explain the biophysical difference between the respective states
Modeling the Closed and Open State Conformations of the GABA<sub>A</sub> 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<sub>A</sub> 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<sub>A</sub> was carried
out using their respective templates. The ability of induced fit docking
in breaking the critical inter residue salt bridge (Glu155β<sub>2</sub> and Arg207β<sub>2</sub>) 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<sup>–</sup> 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<sub>A</sub> ion channel. The modeled
structures presented herein not only reveal the structurally distinct
conformational states of the GABA<sub>A</sub> ion channel but also
explain the biophysical difference between the respective states
Modeling the Closed and Open State Conformations of the GABA<sub>A</sub> 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<sub>A</sub> 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<sub>A</sub> was carried
out using their respective templates. The ability of induced fit docking
in breaking the critical inter residue salt bridge (Glu155β<sub>2</sub> and Arg207β<sub>2</sub>) 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<sup>–</sup> 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<sub>A</sub> ion channel. The modeled
structures presented herein not only reveal the structurally distinct
conformational states of the GABA<sub>A</sub> 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-