Podcasts about narlikar

In this episode of the Epigenetics Podcast, we talked with Geeta Narlikar from UCSF about her work on chromatin remodeling, Heterochromatin Protein 1, and the molecular mechanisms that influence the genome. The conversation starts with a pivotal paper from the early days of Dr. Narlikars research career, titled "Distinct Strategies to Make Nucleosomal DNA Accessible," focused on two ATP-dependent remodelers, BRG1 and SNF2H. Here, she notes that while both enzymes operate similarly, they generate different outputs and play distinct biological roles within the cell. The research revealed that BRG1 is more aggressive in altering nucleosome configuration, aligning with its role in transcription activation, while SNF2H showed a more refined approach in the formation of heterochromatin. Transitioning to her work at UCSF, she emphasized the importance of collaboration and mentoring within a research group. Her focus then shifted towards the ACF ATP-dependent chromatin assembly factor, hypothesizing how ACF measures nucleosome distance—an inquiry that led to exciting insights regarding dynamic enzyme behavior. This includes findings that ACF operates not through a static ruler mechanism but rather through a kinetic mechanism, thus continuously adjusting nucleosome positioning based on DNA length during chromatin assembly. Dr. Narlikar also delved into her studies on heterochromatin protein 1 (HP1), highlighting how HP1 recognizes methylation marks and assembles on chromatin to facilitate gene silencing. This segment of the discussion underscored her shift to studying phase separation and its implications in the organization of chromatin. Notably, her lab made significant advancements in understanding how HP1 forms phase-separated droplets, a finding that was independently corroborated by other laboratories, demonstrating the utility of collaborative scientific inquiry. In discussing the nuances of chromatin dynamics, Dr. Narlikar also introduced her investigations into the INO80 complex, detailing its distinct mechanism for nucleosome movement compared to other remodelers. Each remodeling complex, as she elucidated, has unique catalytic capabilities while still utilizing similar biochemical foundations, highlighting the diverse regulatory roles these proteins play within cells.   References Racki LR, Yang JG, Naber N, Partensky PD, Acevedo A, Purcell TJ, Cooke R, Cheng Y, Narlikar GJ. The chromatin remodeller ACF acts as a dimeric motor to space nucleosomes. Nature. 2009 Dec 24;462(7276):1016-21. doi: 10.1038/nature08621. PMID: 20033039; PMCID: PMC2869534. Canzio D, Liao M, Naber N, Pate E, Larson A, Wu S, Marina DB, Garcia JF, Madhani HD, Cooke R, Schuck P, Cheng Y, Narlikar GJ. A conformational switch in HP1 releases auto-inhibition to drive heterochromatin assembly. Nature. 2013 Apr 18;496(7445):377-81. doi: 10.1038/nature12032. Epub 2013 Mar 13. PMID: 23485968; PMCID: PMC3907283. Sinha KK, Gross JD, Narlikar GJ. Distortion of histone octamer core promotes nucleosome mobilization by a chromatin remodeler. Science. 2017 Jan 20;355(6322):eaaa3761. doi: 10.1126/science.aaa3761. PMID: 28104838; PMCID: PMC5656449. Larson AG, Elnatan D, Keenen MM, Trnka MJ, Johnston JB, Burlingame AL, Agard DA, Redding S, Narlikar GJ. Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin. Nature. 2017 Jul 13;547(7662):236-240. doi: 10.1038/nature22822. Epub 2017 Jun 21. PMID: 28636604; PMCID: PMC5606208. Sanulli S, Trnka MJ, Dharmarajan V, Tibble RW, Pascal BD, Burlingame AL, Griffin PR, Gross JD, Narlikar GJ. HP1 reshapes nucleosome core to promote phase separation of heterochromatin. Nature. 2019 Nov;575(7782):390-394. doi: 10.1038/s41586-019-1669-2. Epub 2019 Oct 16. PMID: 31618757; PMCID: PMC7039410.   Related Episodes Enhancers and Chromatin Remodeling in Mammary Gland Development (Camila dos Santos) Heterochromatin Protein 1 and its Influence on the Structure of Chromatin (Serena Sanulli) Heterochromatin and Phase Separation (Gary Karpen)   Contact Epigenetics Podcast on Mastodon Epigenetics Podcast on Bluesky Dr. Stefan Dillinger on LinkedIn Active Motif on LinkedIn Active Motif on Bluesky Email: podcast@activemotif.com

Amrita Narlikar is President of the German Institute for Global and Area Studies and Professor of International Relations at the University of Hamburg. She is currently also serving as a co-chair of the T20's Task Force 3, which forms a part of the G20 process under India's Presidency.In this episode, she talks about why the West should engage and cooperate with India a lot more than it's doing now, about the new character of globalised trade, and the unique perspective India brings to its current G20 presidency.STATE OF ASIA brings you engaging conversations with leading minds on the issues that shape Asia and affect us all. New episodes are released every other Tuesday.Stay up-to-date on all our activities: subscribe to the newsletter and support our work by becoming a member.-STATE OF ASIA is a podcast from Asia Society Switzerland.  Season 4, episode 5 - Published: June 20, 2023Host: Serena Jung, Program and Communications Director, Asia Society SwitzerlandEditor/Producer: Remko Tanis, Programs and Editorial Manager, Asia Society Switzerland

In this episode of the Epigenetics Podcast, we caught up with Karim-Jean Armache from New York University - Grossman School of Medicine to talk about his work on the structural analysis of Polycomb Complex Proteins. Karim-Jean Armache started his research career with the structural characterization of the 12-subunit RNA Polymerase II. After starting his own lab he used this knowledge in x-ray crystallography and electron microscopy to study how gene silencing complexes like the PRC complex act on chromatin and influence transcription. Further work in the Armache Lab focused on Dot, a  histone H3K79 methyltransferase, and how it acts on chromatin, as well as how it is regulated by Histone-Histone crosstalk. References Armache, K. J., Garlick, J. D., Canzio, D., Narlikar, G. J., & Kingston, R. E. (2011). Structural basis of silencing: Sir3 BAH domain in complex with a nucleosome at 3.0 Å resolution. Science (New York, N.Y.), 334(6058), 977–982. https://doi.org/10.1126/science.1210915 Lee, C. H., Holder, M., Grau, D., Saldaña-Meyer, R., Yu, J. R., Ganai, R. A., Zhang, J., Wang, M., LeRoy, G., Dobenecker, M. W., Reinberg, D., & Armache, K. J. (2018). Distinct Stimulatory Mechanisms Regulate the Catalytic Activity of Polycomb Repressive Complex 2. Molecular cell, 70(3), 435–448.e5. https://doi.org/10.1016/j.molcel.2018.03.019 De Ioannes, P., Leon, V. A., Kuang, Z., Wang, M., Boeke, J. D., Hochwagen, A., & Armache, K. J. (2019). Structure and function of the Orc1 BAH-nucleosome complex. Nature communications, 10(1), 2894. https://doi.org/10.1038/s41467-019-10609-y Valencia-Sánchez, M. I., De Ioannes, P., Wang, M., Truong, D. M., Lee, R., Armache, J. P., Boeke, J. D., & Armache, K. J. (2021). Regulation of the Dot1 histone H3K79 methyltransferase by histone H4K16 acetylation. Science (New York, N.Y.), 371(6527), eabc6663. https://doi.org/10.1126/science.abc6663   Related Episodes Transcription and Polycomb in Inheritance and Disease (Danny Reinberg) From Nucleosome Structure to Function (Karolin Luger) Oncohistones as Drivers of Pediatric Brain Tumors (Nada Jabado)   Contact Epigenetics Podcast on Twitter Epigenetics Podcast on Instagram Epigenetics Podcast on Mastodon Active Motif on Twitter Active Motif on LinkedIn eMail: podcast@activemotif.com

In this episode of the Epigenetics Podcast, we caught up with Serena Sanulli from Stanford University to talk about her work on Heterochromatin Protein 1 (HP1), the structure of chromatin on the atomic-scale and the meso-scale, and phase separation. The Laboratory of Serena Sanulli is interested in finding connections between changes that happen on the nucleosomal level and the resulting impact on chromatin conformation on the meso-scale. They combine methods like NMR and Hydrogen-Deuterium Exchange-MS with Cell Biology and Genetics. This enables them to dissect how cells use the diverse biophysical properties of chromatin to regulate gene expression across length and time scales. A second focus of the lab is HP1, which interacts with the nucleosome and changes its conformation, enabling the compaction of the genome into heterochromatin, effectively silencing genes in that region. A high concentration of HP1 leads to the phenomenon of phase separation in the nucleus, which the Sanulli lab is now investigating.   References Sanulli, S., Justin, N., Teissandier, A., Ancelin, K., Portoso, M., Caron, M., Michaud, A., Lombard, B., da Rocha, S. T., Offer, J., Loew, D., Servant, N., Wassef, M., Burlina, F., Gamblin, S. J., Heard, E., & Margueron, R. (2015). Jarid2 Methylation via the PRC2 Complex Regulates H3K27me3 Deposition during Cell Differentiation. Molecular Cell, 57(5), 769–783. https://doi.org/10.1016/j.molcel.2014.12.020 Sanulli, S., Trnka, M. J., Dharmarajan, V., Tibble, R. W., Pascal, B. D., Burlingame, A. L., Griffin, P. R., Gross, J. D., & Narlikar, G. J. (2019). HP1 reshapes nucleosome core to promote phase separation of heterochromatin. Nature, 575(7782), 390–394. https://doi.org/10.1038/s41586-019-1669-2 Sanulli, S., & Narlikar, G. J. (2021). Generation and Biochemical Characterization of Phase‐Separated Droplets Formed by Nucleic Acid Binding Proteins: Using HP1 as a Model System. Current Protocols, 1(5). https://doi.org/10.1002/cpz1.109   Related Episodes Transcription and Polycomb in Inheritance and Disease (Danny Reinberg) Heterochromatin and Phase Separation (Gary Karpen)   Contact Active Motif on Twitter Epigenetics Podcast on Twitter Active Motif on LinkedIn Active Motif on Facebook Email: podcast@activemotif.com

Mahabharat Lessons For Sportsmen And Fans:Aruna Narlikar:The Speaking Tree

Besides scientific papers and books and popular science literature, Narlikar has written science fiction, novels, and short stories in English, Hindi, and Marathi: Facts and Speculations in Cosmology, with G. Burbidge, Current Issues in Cosmology, 2006 A Different Approach to Cosmology: From a Static Universe through the Big Bang towards Reality, 2005 Fred Hoyle's Universe, 2003 Scientific Edge: The Indian Scientist from Vedic to Modern Times, 2003 An Introduction to Cosmology, 2002 A Different Approach to Cosmology, with G. Burbidge and Fred Hoyle Quasars and Active Galactic Nuclei: An Introduction, 1999 From Black Clouds to Black Holes, 1996 From Black Clouds to Black Holes (Third Edition), 2012 Seven Wonders of the Cosmos, 1995 Philosophy of Science: Perspectives from Natural and Social Sciences, 1992 The extragalactic universe: an alternative view, with Fred Hoyle and Chandra Wickramasinghe, Nature 346:807–812, 30 August 1990 Support the podcast: https://www.patreon.com/drbriankeating And please join my mailing list to get resources and enter giveaways to win a FREE copy of my book (and more) http://briankeating.com/mailing_list.php

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.17.387662v1?rss=1 Authors: Johnson, S. L., Narlikar, G. Abstract: ATP-dependent chromatin remodelers are essential enzymes that restructure eukaryotic genomes to enable all DNA-based processes. The diversity and complexity of these processes are matched by the complexity of the enzymes that carry them out, making remodelers a challenging class of molecular motors to study by conventional methods. Here we use a single molecule biophysical assay to overcome some of these challenges, enabling a detailed mechanistic dissection of a paradigmatic remodeler reaction, that of sliding a nucleosome towards the longer DNA linker. We focus on how two motors of a dimeric remodeler coordinate to accomplish such directional sliding. We find that ATP hydrolysis by both motors promotes coordination, suggesting a role for ATP in resolving the competition for directional commitment. Furthermore, we show an artificially constitutive dimer is no more or less coordinated, but is more processive, suggesting a cell could modulate a remodeler's oligomeric state to modulate local chromatin dynamics. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.10.30.362772v1?rss=1 Authors: Keenen, M. M., Brown, D., Brennan, L. D., Renger, R., Khoo, H., Carlson, C. R., Huang, B., Grill, S. W., Narlikar, G. J., Redding, S. Abstract: In mammals HP1-mediated heterochromatin forms positionally and mechanically stable genomic domains even though the component HP1 paralogs, HP1, HP1{beta}, and HP1{gamma}, display rapid on-off dynamics. Here we investigate whether phase-separation by HP1 proteins can explain these biological observations. Using bulk and single-molecule methods, we show that, within phase-separated HP1-DNA condensates, HP1 acts as a dynamic liquid, while compacted DNA molecules are constrained in local territories. These condensates are resistant to large forces yet can be readily dissolved by HP1{beta}. Finally, we find that differences in each HP1 paralog's DNA compaction and phase-separation properties arise from their respective disordered regions. Our findings suggest a generalizable model for genome organization in which a pool of weakly bound proteins collectively capitalize on the polymer properties of DNA to produce self-organizing domains that are simultaneously resistant to large forces at the mesoscale and susceptible to competition at the molecular scale. Copy rights belong to original authors. Visit the link for more info

This story is written by Jayant Narlikar and shows us how Gangadharpant aka Professor Gaitonde, time travels. It begins with the professor wondering about the fate of India if the Marathas had not allowed a concession to the East India Company to stay in Mumbai.

Narlikar

Author Amrita Narlikar discusses Doha, the WTO, and her recent article "The Power of the Powerless," with Foreign Affairs Deputy Web Editor Rebecca Chao.

SynTalk thinks about the unidirectional nature of time and wonders if time is a separate ‘category’ at all. We dip into cosmology, computer science, neuroscience, quantum physics, & philosophy. We wonder whether time is essentially a (background) variable. Is time nature’s way of preventing everything from happening at the same time (a la Wheeler)? The concepts are derived off / from Newton, Fred Hoyle, Maxwell, Dirac, Planck, Godel, Bohr, Einstein, H G Wells, Wheeler, Feynman, Prigogine, Landauer, Roy Kerr, Everett, Novikov, & Zeldovich, among others. How has the notion of time changed with digital watches? What is ‘logical time’, & the importance of multiple systems synchronizing with each other? What would happen if we hit an electron with a hammer? Do we get ‘it from bit’, and what is the possible link of time with (quantized) information? Can neurons be thought of as being probabilistically synchronized oscillators? We also discuss the concept of Planck’s time as the fundamental unit, & the resultant notion of whether time is discrete or continuous. What is the link between causality and time? We discuss the fascinating links of time with thermodynamics, entropy, ‘action at a distance’, & closed / open systems. What would happen, surprisingly, if a hot star were to be connected with a cold star via a conducting wire? The nature of neurological time, and its links with octopuses, crabs, speeding cars, a ‘cache of situations’, & reflex actions. How do (memory) space & time tradeoffs impact computer algorithms? Can time be lost? How ‘branching time’ creates possible worlds that are not known a priori? Is time travel possible (via a worm holes), and does it need a conception different from ‘state-based’ time? Do animals ‘have’ time? The SynTalkrs are: Prof. Jayant V. Narlikar (astrophysics, IUCAA, Pune), Prof. Krithi Ramamritham (computer science, IITB, Mumbai), & Prof. Sisir Roy (theoretical physics, NIAS, IISc, Bangalore).

Amrita Narlikar of the University of Cambridge talks with EconTalk host Russ Roberts about fair trade and policy issues related to trade. Narlikar argues--based on a recent article with Dan Kim--that the Fair Trade movement hurts workers outside of the fair trade umbrella and does little for those it is trying to help. She advocates free trade, particularly the elimination of agricultural subsidies in the developed world and the best way to help workers in poor nations. Drawing on a recent article with Jagdish Bhagwati, she criticizes the international response to recent deaths in Bangladesh factories. In the last part of the conversation, she defends the World Trade Organization.

Amrita Narlikar of the University of Cambridge talks with EconTalk host Russ Roberts about fair trade and policy issues related to trade. Narlikar argues--based on a recent article with Dan Kim--that the Fair Trade movement hurts workers outside of the fair trade umbrella and does little for those it is trying to help. She advocates free trade, particularly the elimination of agricultural subsidies in the developed world and the best way to help workers in poor nations. Drawing on a recent article with Jagdish Bhagwati, she criticizes the international response to recent deaths in Bangladesh factories. In the last part of the conversation, she defends the World Trade Organization.

Amrita Narlikar of the University of Cambridge talks with EconTalk host Russ Roberts about fair trade and policy issues related to trade. Narlikar argues--based on a recent article with Dan Kim--that the Fair Trade movement hurts workers outside of the fair trade umbrella and does little for those it is trying to help. She advocates free trade, particularly the elimination of agricultural subsidies in the developed world and the best way to help workers in poor nations. Drawing on a recent article with Jagdish Bhagwati, she criticizes the international response to recent deaths in Bangladesh factories. In the last part of the conversation, she defends the World Trade Organization.

Rising Powers in the International System: Harnessing Opportunities, Managing Challenges Rising Powers in the International System Chair and Discussant: Professor Andrew Gamble The Rise of the BRICs – Dr Jim O’Neill (Goldman Sachs) The Historic Struggle for Mastery – Professor Brendan Simms (POLIS, Cambridge; Member, Steering Committee, CRP) Negotiating with and as New Powers – Dr Amrita Narlikar (POLIS, Cambridge; Director, CRP)