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Mishra S, Manohar V, Chandel S, Manoj T, Bhattacharya S, Hegde N, Nath VR, Krishnan H, Wendling C, Di Mattia T, Martinet A, Chimata P, Alpy F, Raghu P. A genetic screen to uncover mechanisms underlying lipid transfer protein function at membrane contact sites. Life Sci Alliance 2024; 7:e202302525. [PMID: 38499328 PMCID: PMC10948934 DOI: 10.26508/lsa.202302525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/04/2024] [Accepted: 03/05/2024] [Indexed: 03/20/2024] Open
Abstract
Lipid transfer proteins mediate the transfer of lipids between organelle membranes, and the loss of function of these proteins has been linked to neurodegeneration. However, the mechanism by which loss of lipid transfer activity leads to neurodegeneration is not understood. In Drosophila photoreceptors, depletion of retinal degeneration B (RDGB), a phosphatidylinositol transfer protein, leads to defective phototransduction and retinal degeneration, but the mechanism by which loss of this activity leads to retinal degeneration is not understood. RDGB is localized to membrane contact sites through the interaction of its FFAT motif with the ER integral protein VAP. To identify regulators of RDGB function in vivo, we depleted more than 300 VAP-interacting proteins and identified a set of 52 suppressors of rdgB The molecular identity of these suppressors indicates a role of novel lipids in regulating RDGB function and of transcriptional and ubiquitination processes in mediating retinal degeneration in rdgB9 The human homologs of several of these molecules have been implicated in neurodevelopmental diseases underscoring the importance of VAP-mediated processes in these disorders.
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Affiliation(s)
- Shirish Mishra
- https://ror.org/03gf8rp76 National Centre for Biological Sciences-TIFR, GKVK Campus, Bangalore, India
| | - Vaishnavi Manohar
- https://ror.org/03gf8rp76 National Centre for Biological Sciences-TIFR, GKVK Campus, Bangalore, India
| | - Shabnam Chandel
- https://ror.org/03gf8rp76 National Centre for Biological Sciences-TIFR, GKVK Campus, Bangalore, India
| | - Tejaswini Manoj
- https://ror.org/03gf8rp76 National Centre for Biological Sciences-TIFR, GKVK Campus, Bangalore, India
| | - Subhodeep Bhattacharya
- https://ror.org/03gf8rp76 National Centre for Biological Sciences-TIFR, GKVK Campus, Bangalore, India
| | - Nidhi Hegde
- https://ror.org/03gf8rp76 National Centre for Biological Sciences-TIFR, GKVK Campus, Bangalore, India
| | - Vaisaly R Nath
- https://ror.org/03gf8rp76 National Centre for Biological Sciences-TIFR, GKVK Campus, Bangalore, India
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Harini Krishnan
- https://ror.org/03gf8rp76 National Centre for Biological Sciences-TIFR, GKVK Campus, Bangalore, India
| | - Corinne Wendling
- Université de Strasbourg, CNRS, Inserm, IGBMC UMR 7104- UMR-S 1258, Illkirch, France
| | - Thomas Di Mattia
- Université de Strasbourg, CNRS, Inserm, IGBMC UMR 7104- UMR-S 1258, Illkirch, France
| | - Arthur Martinet
- Université de Strasbourg, CNRS, Inserm, IGBMC UMR 7104- UMR-S 1258, Illkirch, France
| | - Prasanth Chimata
- https://ror.org/03gf8rp76 National Centre for Biological Sciences-TIFR, GKVK Campus, Bangalore, India
| | - Fabien Alpy
- Université de Strasbourg, CNRS, Inserm, IGBMC UMR 7104- UMR-S 1258, Illkirch, France
| | - Padinjat Raghu
- https://ror.org/03gf8rp76 National Centre for Biological Sciences-TIFR, GKVK Campus, Bangalore, India
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Usha Satheesan S, Chowdhury S, Kolthur-Seetharam U. Metabolic and circadian inputs encode anticipatory biogenesis of hepatic fed microRNAs. Life Sci Alliance 2024; 7:e202302180. [PMID: 38408795 PMCID: PMC10897495 DOI: 10.26508/lsa.202302180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 02/13/2024] [Accepted: 02/13/2024] [Indexed: 02/28/2024] Open
Abstract
Starvation and refeeding are mostly unanticipated in the wild in terms of duration, frequency, and nutritional value of the refed state. Notwithstanding this, organisms mount efficient and reproducible responses to restore metabolic homeostasis. Hence, it is intuitive to invoke expectant molecular mechanisms that build anticipatory responses to enable physiological toggling during fed-fast cycles. In this regard, we report anticipatory biogenesis of oscillatory hepatic microRNAs that peak during a fed state and inhibit starvation-responsive genes. Our results clearly demonstrate that the levels of primary and precursor microRNA transcripts increase during a fasting state, in anticipation of a fed response. We delineate the importance of both metabolic and circadian cues in orchestrating hepatic fed microRNA homeostasis in a physiological setting. Besides illustrating metabo-endocrine control, our findings provide a mechanistic basis for the overarching influence of starvation on anticipatory biogenesis. Importantly, by using pharmacological agents that are widely used in clinics, we point out the high potential of interventions to restore homeostasis of hepatic microRNAs, whose deregulated expression is otherwise well established to cause metabolic diseases.
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Affiliation(s)
- Sandra Usha Satheesan
- https://ror.org/03ht1xw27 Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Shreyam Chowdhury
- https://ror.org/03ht1xw27 Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Ullas Kolthur-Seetharam
- https://ror.org/03ht1xw27 Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
- https://ror.org/03ht1xw27 Tata Institute of Fundamental Research- Hyderabad (TIFR-H), Hyderabad, India
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Ghosh S, Patil V, Basu A, Kuldeep, Dutta A, Jangade DA, Kulkarni R, Thamizhavel A, Steiner JF, von Oppen F, Deshmukh MM. High-temperature Josephson diode. Nat Mater 2024; 23:612-618. [PMID: 38321240 DOI: 10.1038/s41563-024-01804-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 01/08/2024] [Indexed: 02/08/2024]
Abstract
Many superconducting systems with broken time-reversal and inversion symmetry show a superconducting diode effect, a non-reciprocal phenomenon analogous to semiconducting p-n-junction diodes. While the superconducting diode effect lays the foundation for realizing ultralow dissipative circuits, Josephson-phenomena-based diode effect (JDE) can enable the realization of protected qubits. The superconducting diode effect and JDE reported thus far are at low temperatures (~4 K), limiting their applications. Here we demonstrate JDE persisting up to 77 K using an artificial Josephson junction of twisted layers of Bi2Sr2CaCu2O8+δ. JDE manifests as an asymmetry in the magnitude and distributions of switching currents, attaining the maximum at 45° twist. The asymmetry is induced by and tunable with a very small magnetic field applied perpendicular to the junction and arises due to interaction between Josephson and Abrikosov vortices. We report a large asymmetry of 60% at 20 K. Our results provide a path towards realizing superconducting Josephson circuits at liquid-nitrogen temperature.
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Affiliation(s)
- Sanat Ghosh
- Department of Condensed Matter Physics and Materials Science, Tata Institute of Fundamental Research, Mumbai, India.
| | - Vilas Patil
- Department of Condensed Matter Physics and Materials Science, Tata Institute of Fundamental Research, Mumbai, India
| | - Amit Basu
- Department of Condensed Matter Physics and Materials Science, Tata Institute of Fundamental Research, Mumbai, India
| | - Kuldeep
- Department of Condensed Matter Physics and Materials Science, Tata Institute of Fundamental Research, Mumbai, India
| | - Achintya Dutta
- Department of Condensed Matter Physics and Materials Science, Tata Institute of Fundamental Research, Mumbai, India
| | - Digambar A Jangade
- Department of Condensed Matter Physics and Materials Science, Tata Institute of Fundamental Research, Mumbai, India
| | - Ruta Kulkarni
- Department of Condensed Matter Physics and Materials Science, Tata Institute of Fundamental Research, Mumbai, India
| | - A Thamizhavel
- Department of Condensed Matter Physics and Materials Science, Tata Institute of Fundamental Research, Mumbai, India
| | - Jacob F Steiner
- Dahlem Center for Complex Quantum Systems and Fachbereich Physik, Freie Universität Berlin, Berlin, Germany
| | - Felix von Oppen
- Dahlem Center for Complex Quantum Systems and Fachbereich Physik, Freie Universität Berlin, Berlin, Germany
| | - Mandar M Deshmukh
- Department of Condensed Matter Physics and Materials Science, Tata Institute of Fundamental Research, Mumbai, India.
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Patil SS, Sanghrajka K, Sriram M, Chakraborty A, Majumdar S, Bhaskar BR, Das D. Synaptobrevin2 monomers and dimers differentially engage to regulate the functional trans-SNARE assembly. Life Sci Alliance 2024; 7:e202402568. [PMID: 38238088 PMCID: PMC10796598 DOI: 10.26508/lsa.202402568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 01/12/2024] [Accepted: 01/12/2024] [Indexed: 01/22/2024] Open
Abstract
The precise cell-to-cell communication relies on SNARE-catalyzed membrane fusion. Among ∼70 copies of synaptobrevin2 (syb2) in synaptic vesicles, only ∼3 copies are sufficient to facilitate the fusion process at the presynaptic terminal. It is unclear what dictates the number of SNARE complexes that constitute the fusion pore assembly. The structure-function relation of these dynamic pores is also unknown. Here, we demonstrate that syb2 monomers and dimers differentially engage in regulating the trans-SNARE assembly during membrane fusion. The differential recruitment of two syb2 structures at the membrane fusion site has consequences in regulating individual nascent fusion pore properties. We have identified a few syb2 transmembrane domain residues that control monomer/dimer conversion. Overall, our study indicates that syb2 monomers and dimers are differentially recruited at the release sites for regulating membrane fusion events.
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Affiliation(s)
- Swapnali S Patil
- https://ror.org/03ht1xw27 Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Kinjal Sanghrajka
- https://ror.org/03ht1xw27 Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Malavika Sriram
- https://ror.org/03ht1xw27 Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Aritra Chakraborty
- https://ror.org/03ht1xw27 Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Sougata Majumdar
- https://ror.org/03ht1xw27 Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Bhavya R Bhaskar
- https://ror.org/03ht1xw27 Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Debasis Das
- https://ror.org/03ht1xw27 Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
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Varma A, Udupa S, Sengupta M, Ghosh PK, Thirumalai V. A machine-learning tool to identify bistable states from calcium imaging data. J Physiol 2024; 602:1243-1271. [PMID: 38482722 DOI: 10.1113/jp284373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 02/09/2024] [Indexed: 04/04/2024] Open
Abstract
Mapping neuronal activation using calcium imaging in vivo during behavioural tasks has advanced our understanding of nervous system function. In almost all of these studies, calcium imaging is used to infer spike probabilities because action potentials activate voltage-gated calcium channels and increase intracellular calcium levels. However, neurons not only fire action potentials, but also convey information via intrinsic dynamics such as by generating bistable membrane potential states. Although a number of tools for spike inference have been developed and are currently being used, no tool exists for converting calcium imaging signals to maps of cellular state in bistable neurons. Purkinje neurons in the larval zebrafish cerebellum exhibit membrane potential bistability, firing either tonically or in bursts. Several studies have implicated the role of a population code in cerebellar function, with bistability adding an extra layer of complexity to this code. In the present study, we develop a tool, CaMLSort, which uses convolutional recurrent neural networks to classify calcium imaging traces as arising from either tonic or bursting cells. We validate this classifier using a number of different methods and find that it performs well on simulated event rasters as well as real biological data that it had not previously seen. Moreover, we find that CaMLsort generalizes to other bistable neurons, such as dopaminergic neurons in the ventral tegmental area of mice. Thus, this tool offers a new way of analysing calcium imaging data from bistable neurons to understand how they participate in network computation and natural behaviours. KEY POINTS: Calcium imaging, compriising the gold standard of inferring neuronal activity, does not report cellular state in neurons that are bistable, such as Purkinje neurons in the cerebellum of larval zebrafish. We model the relationship between Purkinje neuron electrical activity and its corresponding calcium signal to compile a dataset of state-labelled simulated calcium signals. We apply machine-learning methods to this dataset to develop a tool that can classify the state of a Purkinje neuron using only its calcium signal, which works well on real data even though it was trained only on simulated data. CaMLsort (Calcium imaging and Machine Learning based tool to sort intracellular state) also generalizes well to bistable neurons in a different brain region (ventral tegmental area) in a different model organism (mouse). This tool can facilitate our understanding of how these neurons carry out their functions in a circuit.
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Affiliation(s)
- Aalok Varma
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Sathvik Udupa
- Department of Electrical Engineering, Indian Institute of Science, Bangalore, India
| | - Mohini Sengupta
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Prasanta Kumar Ghosh
- Department of Electrical Engineering, Indian Institute of Science, Bangalore, India
| | - Vatsala Thirumalai
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
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Das P, Chakrabarti O. ISGylation of DRP1 closely balances other post-translational modifications to mediate mitochondrial fission. Cell Death Dis 2024; 15:184. [PMID: 38431611 PMCID: PMC10908869 DOI: 10.1038/s41419-024-06543-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 03/05/2024]
Abstract
Dynamin related protein 1 (DRP1), a pivotal mitochondrial fission protein, is post-translationally modified by multiple mechanisms. Here we identify a new post-translational modification of DRP1 by the ubiquitin-like protein, interferon-stimulated gene 15 (ISG15). DRP1 ISGylation is mediated by ISG15 E3 ligase, HERC5; this promotes mitochondrial fission. DeISGylation of DRP1 however leads to hyperfusion. Heterologous expression of SARS-CoV2 PLpro, a deISGylating enzyme, results in similar mitochondrial filamentation, significant decrease in total DRP1 protein levels and efflux of mtDNA. We report that deISGylated DRP1 gets ubiquitylated and degraded by TRIM25, instead of PARKIN and MITOL. While the cytosolic pool of DRP1 is primarily ISGylated, both mitochondrial and cytosolic fractions may be ubiquitylated. It is known that phosphorylation of DRP1 at S616 residue regulates its mitochondrial localisation; we show that ISGylation of phospho-DRP1 (S616) renders fission competence at mitochondria. This is significant because DRP1 ISGylation affects its functionality and mitochondrial dynamics in Alzheimer's disease pathophysiology.
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Affiliation(s)
- Palamou Das
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
- Homi Bhabha National Institute, Mumbai, India
| | - Oishee Chakrabarti
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India.
- Homi Bhabha National Institute, Mumbai, India.
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7
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Sharma DK, Soni I, Misra HS, Rajpurohit YS. Natural transformation-specific DprA coordinate DNA double-strand break repair pathways in heavily irradiated D. radiodurans. Appl Environ Microbiol 2024; 90:e0194823. [PMID: 38193676 PMCID: PMC10880594 DOI: 10.1128/aem.01948-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/02/2023] [Indexed: 01/10/2024] Open
Abstract
Deinococcus radiodurans exhibits remarkable survival under extreme conditions, including ionizing radiation, desiccation, and various DNA-damaging agents. It employs unique repair mechanisms, such as single-strand annealing (SSA) and extended synthesis-dependent strand annealing (ESDSA), to efficiently restore damaged genome. In this study, we investigate the role of the natural transformation-specific protein DprA in DNA repair pathways following acute gamma radiation exposure. Our findings demonstrate that the absence of DprA leads to rapid repair of gamma radiation-induced DNA double-strand breaks primarily occur through SSA repair pathway. Additionally, our findings suggest that the DprA protein may hinder both the SSA and ESDSA repair pathways, albeit in distinct manners. Overall, our results highlight the crucial function of DprA in the selection between SSA and ESDSA pathways for DNA repair in heavily irradiated D. radiodurans.IMPORTANCEDeinococcus radiodurans exhibits an extraordinary ability to endure and thrive in extreme environments, including exposure to radiation, desiccation, and damaging chemicals, as well as intense UV radiation. The bacterium has evolved highly efficient repair mechanisms capable of rapidly mending hundreds of DNA fragments in its genome. Our research indicates that natural transformation (NT)-specific dprA genes play a pivotal role in regulating DNA repair in response to radiation. Remarkably, we found that DprA is instrumental in selecting DNA double-strand break repair pathways, a novel function that has not been reported before. This unique regulatory mechanism highlights the indispensable role of DprA beyond its native function in NT and underscores its ubiquitous presence across various bacterial species, regardless of their NT proficiency. These findings shed new light on the resilience and adaptability of Deinococcus radiodurans, opening avenues for further exploration into its exceptional survival strategies.
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Affiliation(s)
- Dhirendra Kumar Sharma
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute (DAE- Deemed University), Mumbai, India
| | - Ishu Soni
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute (DAE- Deemed University), Mumbai, India
| | - Hari S. Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Yogendra Singh Rajpurohit
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute (DAE- Deemed University), Mumbai, India
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8
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Sharma G, Verma R, Masuda S, Badawy KM, Singh N, Tsukuda T, Polshettiwar V. Pt-doped Ru nanoparticles loaded on 'black gold' plasmonic nanoreactors as air stable reduction catalysts. Nat Commun 2024; 15:713. [PMID: 38267414 PMCID: PMC10808126 DOI: 10.1038/s41467-024-44954-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 01/10/2024] [Indexed: 01/26/2024] Open
Abstract
This study introduces a plasmonic reduction catalyst, stable only in the presence of air, achieved by integrating Pt-doped Ru nanoparticles on black gold. This innovative black gold/RuPt catalyst showcases good efficiency in acetylene semi-hydrogenation, attaining over 90% selectivity with an ethene production rate of 320 mmol g-1 h-1. Its stability, evident in 100 h of operation with continuous air flow, is attributed to the synergy of co-existing metal oxide and metal phases. The catalyst's stability is further enhanced by plasmon-mediated concurrent reduction and oxidation of the active sites. Finite-difference time-domain simulations reveal a five-fold electric field intensification near the RuPt nanoparticles, crucial for activating acetylene and hydrogen. Kinetic isotope effect analysis indicates the contribution from the plasmonic non-thermal effects along with the photothermal. Spectroscopic and in-situ Fourier transform infrared studies, combined with quantum chemical calculations, elucidate the molecular reaction mechanism, emphasizing the cooperative interaction between Ru and Pt in optimizing ethene production and selectivity.
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Affiliation(s)
- Gunjan Sharma
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, 40005, India
| | - Rishi Verma
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, 40005, India
| | - Shinya Masuda
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | | | - Nirpendra Singh
- Department of Physics, Khalifa University, Abu Dhabi, 127788, United Arab Emirates
| | - Tatsuya Tsukuda
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.
| | - Vivek Polshettiwar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, 40005, India.
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9
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Raghuram GV, Tripathy BK, Avadhani K, Shabrish S, Khare NK, Lopes R, Pal K, Mittra I. Cell-free chromatin particles released from dying cells inflict mitochondrial damage and ROS production in living cells. Cell Death Discov 2024; 10:30. [PMID: 38225229 PMCID: PMC10789803 DOI: 10.1038/s41420-023-01728-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/06/2023] [Accepted: 11/16/2023] [Indexed: 01/17/2024] Open
Abstract
Mitochondrial damage and the resultant oxidative stress are associated with neurodegenerative diseases, ageing, and cancer. However, the triggers of mitochondrial damage remain unclear. We previously reported that cell-free chromatin particles (cfChPs) released from the billions of cells that die in the body every day can readily enter healthy cells and damage their DNA. Here, we show that cfChPs isolated from the sera of healthy individuals, when applied to NIH3T3 mouse fibroblast cells, cause physical damage to mitochondrial DNA (mtDNA). cfChPs also induce ultrastructural changes, increase mitochondrial mass, alter mitochondrial shape, upregulate mitochondrial outer membrane protein translocase of the outer membrane 20, and change mitochondrial membrane potential. Furthermore, a marked increase was observed in mitochondrial superoxide (ROS) production, as detected by MitoSOX Red, and intracellular superoxide dismutase-1 activation. ROS production was also activated when a conditioned medium containing cfChPs released from hypoxia-induced dying NIH3T3 cells was applied to healthy NIH3T3 cells. ROS activation was significantly reduced when the conditioned medium was pre-treated with three different cfChP-deactivating agents: anti-histone antibody-complexed nanoparticles, DNase I, and the novel pro-oxidant combination of the nutraceuticals resveratrol and copper. Given that 1 × 109-1 × 1012 cells die in the body every day, we hypothesise that cfChPs from dying cells are the major physiological triggers for mtDNA damage and ROS production. Deactivation of cfChPs may provide a novel therapeutic approach to retard ageing and associated degenerative conditions linked to oxidative stress.
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Affiliation(s)
- Gorantla V Raghuram
- Translational Research Laboratory Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Bhabesh Kumar Tripathy
- Translational Research Laboratory Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Kartikeya Avadhani
- Translational Research Laboratory Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Snehal Shabrish
- Translational Research Laboratory Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Naveen Kumar Khare
- Translational Research Laboratory Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Relestina Lopes
- Translational Research Laboratory Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Kavita Pal
- Translational Research Laboratory Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Indraneel Mittra
- Translational Research Laboratory Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India.
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India.
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10
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Ghosh A, Venugopal A, Shinde D, Sharma S, Krishnan M, Mathre S, Krishnan H, Saha S, Raghu P. PI3P-dependent regulation of cell size and autophagy by phosphatidylinositol 5-phosphate 4-kinase. Life Sci Alliance 2023; 6:e202301920. [PMID: 37316298 PMCID: PMC10267561 DOI: 10.26508/lsa.202301920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 06/02/2023] [Accepted: 06/02/2023] [Indexed: 06/16/2023] Open
Abstract
Phosphatidylinositol 3-phosphate (PI3P) and phosphatidylinositol 5-phosphate (PI5P) are low-abundance phosphoinositides crucial for key cellular events such as endosomal trafficking and autophagy. Phosphatidylinositol 5-phosphate 4-kinase (PIP4K) is an enzyme that regulates PI5P in vivo but can act on both PI5P and PI3P in vitro. In this study, we report a role for PIP4K in regulating PI3P levels in Drosophila Loss-of-function mutants of the only Drosophila PIP4K gene show reduced cell size in salivary glands. PI3P levels are elevated in dPIP4K 29 and reverting PI3P levels back towards WT, without changes in PI5P levels, can rescue the reduced cell size. dPIP4K 29 mutants also show up-regulation in autophagy and the reduced cell size can be reverted by depleting Atg8a that is required for autophagy. Lastly, increasing PI3P levels in WT can phenocopy the reduction in cell size and associated autophagy up-regulation seen in dPIP4K 29 Thus, our study reports a role for a PIP4K-regulated PI3P pool in the control of autophagy and cell size.
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Affiliation(s)
- Avishek Ghosh
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bangalore, India
| | | | - Dhananjay Shinde
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bangalore, India
| | - Sanjeev Sharma
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bangalore, India
| | - Meera Krishnan
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bangalore, India
| | - Swarna Mathre
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bangalore, India
| | - Harini Krishnan
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bangalore, India
| | - Sankhanil Saha
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bangalore, India
| | - Padinjat Raghu
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bangalore, India
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11
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Paul K, Mutneja A, Nandi SK, Karmakar S. Dynamical heterogeneity in active glasses is inherently different from its equilibrium behavior. Proc Natl Acad Sci U S A 2023; 120:e2217073120. [PMID: 37585467 PMCID: PMC10450852 DOI: 10.1073/pnas.2217073120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 07/12/2023] [Indexed: 08/18/2023] Open
Abstract
Activity-driven glassy dynamics, while ubiquitous in collective cell migration, intracellular transport, dynamics in bacterial and ant colonies, etc., also extends the scope and extent of the as-yet mysterious physics of glass transition. Active glasses are hitherto assumed to be qualitatively similar to their equilibrium counterparts at an effective temperature, [Formula: see text]. Here, we combine large-scale simulations and an analytical mode-coupling theory (MCT) for such systems and show that, in fact, an active glass is inherently different from an equilibrium glass. Although the relaxation dynamics can be equilibrium-like at a [Formula: see text], effects of activity on the dynamic heterogeneity (DH), which is a hallmark of glassy dynamics, are quite nontrivial and complex. With no preexisting data, we employ four distinct methods for reliable estimates of the DH length scales. Our work shows that active glasses exhibit dramatic growth of DH and systems with similar relaxation times, and thus, [Formula: see text] can have widely varying DH. To theoretically study DH, we extend active MCT and find good qualitative agreement between the theory and simulation results. Our results pave avenues for understanding the role of DH in glassy dynamics and can have fundamental significance even in equilibrium.
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Affiliation(s)
- Kallol Paul
- Tata Institute of Fundamental Research Center for Interdisciplinary Science, Hyderabad500046, Telangana, India
| | - Anoop Mutneja
- Tata Institute of Fundamental Research Center for Interdisciplinary Science, Hyderabad500046, Telangana, India
| | - Saroj Kumar Nandi
- Tata Institute of Fundamental Research Center for Interdisciplinary Science, Hyderabad500046, Telangana, India
| | - Smarajit Karmakar
- Tata Institute of Fundamental Research Center for Interdisciplinary Science, Hyderabad500046, Telangana, India
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12
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Nandavaram A, Nandakumar A, Kashif GM, Sagar AL, Shailaja G, Ramesh A, Siddavattam D. Unusual Relationship between Iron Deprivation and Organophosphate Hydrolase Expression. Appl Environ Microbiol 2023; 89:e0190322. [PMID: 37074175 PMCID: PMC10231211 DOI: 10.1128/aem.01903-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 03/08/2023] [Indexed: 04/20/2023] Open
Abstract
Organophosphate hydrolases (OPH), hitherto known to hydrolyze the third ester bond of organophosphate (OP) insecticides and nerve agents, have recently been shown to interact with outer membrane transport components, namely, TonB and ExbB/ExbD. In an OPH negative background, Sphingopyxis wildii cells failed to transport ferric enterobactin and showed retarded growth under iron-limiting conditions. We now show the OPH-encoding organophosphate degradation (opd) gene from Sphingobium fuliginis ATCC 27551 to be part of the iron regulon. A fur-box motif found to be overlapping with the transcription start site (TSS) of the opd gene coordinates with an iron responsive element (IRE) RNA motif identified in the 5' coding region of the opd mRNA to tightly regulate opd gene expression. The fur-box motif serves as a target for the Fur repressor in the presence of iron. A decrease in iron concentration leads to the derepression of opd. IRE RNA inhibits the translation of opd mRNA and serves as a target for apo-aconitase (IRP). The IRP recruited by the IRE RNA abrogates IRE-mediated translational inhibition. Our findings establish a novel, multilayered, iron-responsive regulation that is crucial for OPH function in the transport of siderophore-mediated iron uptake. IMPORTANCE Sphingobium fuliginis, a soil-dwelling microbe isolated from agricultural soils, was shown to degrade a variety of insecticides and pesticides. These synthetic chemicals function as potent neurotoxins, and they belong to a class of chemicals termed organophosphates. S. fuliginis codes for OPH, an enzyme that has been shown to be involved in the metabolism of several organophosphates and their derivatives. Interestingly, OPH has also been shown to facilitate siderophore-mediated iron uptake in S. fuliginis and in another Sphingomonad, namely, Sphingopyxis wildii, implying that this organophosphate-metabolizing protein has a role in iron homeostasis, as well. Our research dissects the underlying molecular mechanisms linking iron to the expression of OPH, prompting a reconsideration of the role of OPH in Sphingomonads and a reevaluation of the evolutionary origins of the OPH proteins from soil bacteria.
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Affiliation(s)
- Aparna Nandavaram
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Anirudh Nandakumar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bengaluru, India
- The University of Trans-Disciplinary Health Sciences & Technology (TDU), Bengaluru, Karnataka, India
| | - G. M. Kashif
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | | | - G. Shailaja
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Arati Ramesh
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bengaluru, India
| | - Dayananda Siddavattam
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
- Department of Biochemistry, School of Sciences, GITAM University, Visakhapatnam, India
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13
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Kumar A, Swain S, Prabhudesai VS. Inelastic electron scattering induced quantum coherence in molecular dynamics. Nat Commun 2023; 14:2769. [PMID: 37179339 PMCID: PMC10183011 DOI: 10.1038/s41467-023-38440-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
Quantum coherence is pivotal in various applications ranging from chemical control to quantum computing. An example of its manifestation in molecular dynamics is inversion symmetry breaking in the photodissociation of homonuclear diatomic molecules. On the other hand, the dissociative attachment of an incoherent electron also induces such coherent dynamics. However, these processes are resonant and occur for projectiles with a specific energy. Here we present the most general scenario of non-resonant inelastic electron scattering inducing such a quantum coherence in molecular dynamics. The ion-pair formation (H+ + H─) that proceeds after the electron impact excitation of H2 shows a forward-backward asymmetry about the incoming electron beam. Simultaneous transfer of multiple angular momentum quanta during the electron collision induces the underlying coherence in the system. The non-resonant nature of this process makes this effect generic and points to its possible prevalent role in particle collision processes, including electron-induced chemistry.
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Affiliation(s)
- Akshay Kumar
- Tata Institute of Fundamental Research, Colaba Mumbai, 400005, India
| | - Suvasis Swain
- Tata Institute of Fundamental Research, Colaba Mumbai, 400005, India
- Centre de Recherche sur les Ions, les Matériaux et la Photonique (CIMAP) - UMR 6252 - Normandie Université, ENSICAEN, UNICAEN, CEA, CNRS, 14000, Caen, France
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14
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Maity T, Malik P, Bawari S, Ghosh S, Mondal J, Haldar R. Chemically routed interpore molecular diffusion in metal-organic framework thin films. Nat Commun 2023; 14:2212. [PMID: 37072404 PMCID: PMC10113335 DOI: 10.1038/s41467-023-37739-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 03/27/2023] [Indexed: 04/20/2023] Open
Abstract
Transport diffusivity of molecules in a porous solid is constricted by the rate at which molecules move from one pore to the other, along the concentration gradient, i.e. by following Fickian diffusion. In heterogeneous porous materials, i.e. in the presence of pores of different sizes and chemical environments, diffusion rate and directionality remain tricky to estimate and adjust. In such a porous system, we have realized that molecular diffusion direction can be orthogonal to the concentration gradient. To experimentally determine this complex diffusion rate dependency and get insight of the microscopic diffusion pathway, we have designed a model nanoporous structure, metal-organic framework (MOF). In this model two chemically and geometrically distinct pore windows are spatially oriented by an epitaxial, layer-by-layer growth method. The specific design of the nanoporous channels and quantitative mass uptake rate measurements have indicated that the mass uptake is governed by the interpore diffusion along the direction orthogonal to the concentration gradient. This revelation allows chemically carving the nanopores, and accelerating the interpore diffusion and kinetic diffusion selectivity.
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Affiliation(s)
- Tanmoy Maity
- Tata Institute of Fundamental Research Hyderabad, Gopanpally, Hyderabad, 500046, Telangana, India
| | - Pratibha Malik
- Tata Institute of Fundamental Research Hyderabad, Gopanpally, Hyderabad, 500046, Telangana, India
| | - Sumit Bawari
- Tata Institute of Fundamental Research Hyderabad, Gopanpally, Hyderabad, 500046, Telangana, India
| | - Soumya Ghosh
- Tata Institute of Fundamental Research Hyderabad, Gopanpally, Hyderabad, 500046, Telangana, India
| | - Jagannath Mondal
- Tata Institute of Fundamental Research Hyderabad, Gopanpally, Hyderabad, 500046, Telangana, India
| | - Ritesh Haldar
- Tata Institute of Fundamental Research Hyderabad, Gopanpally, Hyderabad, 500046, Telangana, India.
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15
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Chaudhary R, Kota S, Misra HS. DivIVA Phosphorylation Affects Its Dynamics and Cell Cycle in Radioresistant Deinococcus radiodurans. Microbiol Spectr 2023; 11:e0314122. [PMID: 36744915 PMCID: PMC10100863 DOI: 10.1128/spectrum.03141-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 01/06/2023] [Indexed: 02/07/2023] Open
Abstract
DivIVA is a member of the Min family of proteins that spatially regulates septum formation at the midcell position and cell pole determination in Bacillus subtilis. Deinococcus radiodurans, a Gram-positive coccus-shaped bacterium, is characterized by its extreme resistance to DNA-damaging agents, including radiation. D. radiodurans cells exposed to gamma radiation undergo cell division arrest by as-yet-uncharacterized mechanisms. divIVA is shown to be an essential cell division gene in this bacterium, and DivIVA of D. radiodurans (drDivIVA) interacts with genome segregation proteins through its N-terminal region. Earlier, RqkA, a gamma radiation-responsive Ser/Thr quinoprotein kinase, was characterized for its role in radioresistance in D. radiodurans. Here, we showed that RqkA phosphorylates drDivIVA at the threonine 19 (T19) residue. The phospho-mimetic mutant with a mutation of T19 to E19 in DivIVA (DivIVAT19E) is found to be functionally different from the phospho-ablative mutant (DivIVAT19A) or the wild-type drDivIVA. A DivIVAT19E-red fluorescent protein (RFP) fusion expressed in the wild-type background showed the arrest in the typical dynamics of drDivIVA and the loss of its interaction with the genome segregation protein ParA2. The allelic replacement of divIVA with divIVAT19E-rfp was not tolerated unless drDivIVA was expressed episomally, while there was no phenotypic change when the wild-type allele was replaced with either divIVAT19A-rfp or divIVA-rfp. These results suggested that the phosphorylation of T19 in drDivIVA by RqkA affected its in vivo functions, which may contribute to the cell cycle arrest in this bacterium. IMPORTANCE Deinococcus radiodurans, a radioresistant bacterium, lacks LexA/RecA-mediated DNA damage response and cell cycle regulation as known in other bacteria. However, it adjusts its transcriptome and proteome upon DNA damage. In eukaryotes, the DNA damage response and cell cycle are regulated by Ser/Thr protein kinases. In D. radiodurans, we characterized a gamma radiation-responsive Ser/Thr quinoprotein kinase (RqkA) that phosphorylated DNA repair and cell division proteins in this bacterium. In previous work, the effect of S/T phosphorylation by RqkA on activity improvement of the DNA repair proteins has been demonstrated. This study reports that Ser phosphorylation by RqkA attenuates the function of a cell polarity and plane of cell division-determining protein, DivIVA, and its cellular dynamics in response to DNA damage, which might help to understand the mechanism of cell cycle regulation in this bacterium.
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Affiliation(s)
- Reema Chaudhary
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Life Sciences, Homi Bhabha National Institute, Mumbai, India
| | - Swathi Kota
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Life Sciences, Homi Bhabha National Institute, Mumbai, India
| | - Hari S. Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Life Sciences, Homi Bhabha National Institute, Mumbai, India
- School of Science, GITAM, Visakhapatnam, Andhra Pradesh, India
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16
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Clark CJ, Kerr M, Barr ED, Bhattacharyya B, Breton RP, Bruel P, Camilo F, Chen W, Cognard I, Cromartie HT, Deneva J, Dhillon VS, Guillemot L, Kennedy MR, Kramer M, Lyne AG, Sánchez DM, Nieder L, Phillips C, Ransom SM, Ray PS, Roberts MSE, Roy J, Smith DA, Spiewak R, Stappers BW, Tabassum S, Theureau G, Voisin G. Neutron star mass estimates from gamma-ray eclipses in spider millisecond pulsar binaries. Nat Astron 2023; 7:451-462. [PMID: 37096051 PMCID: PMC10119022 DOI: 10.1038/s41550-022-01874-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 12/01/2022] [Indexed: 05/03/2023]
Abstract
Reliable neutron star mass measurements are key to determining the equation of state of cold nuclear matter, but such measurements are rare. Black widows and redbacks are compact binaries consisting of millisecond pulsars and semi-degenerate companion stars. Spectroscopy of the optically bright companions can determine their radial velocities, providing inclination-dependent pulsar mass estimates. Although inclinations can be inferred from subtle features in optical light curves, such estimates may be systematically biased due to incomplete heating models and poorly understood variability. Using data from the Fermi Large Area Telescope, we have searched for gamma-ray eclipses from 49 spider systems, discovering significant eclipses in 7 systems, including the prototypical black widow PSR B1957+20. Gamma-ray eclipses require direct occultation of the pulsar by the companion, and so the detection, or significant exclusion, of a gamma-ray eclipse strictly limits the binary inclination angle, providing new robust, model-independent pulsar mass constraints. For PSR B1957+20, the eclipse implies a much lighter pulsar (1.81 ± 0.07 solar masses) than inferred from optical light curve modelling.
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Affiliation(s)
- C. J. Clark
- Max Planck Institute for Gravitational Physics (Albert Einstein Institute), Hannover, Germany
- Leibniz Universität Hannover, Hannover, Germany
- Jodrell Bank Centre for Astrophysics, Department of Physics and Astronomy, The University of Manchester, Manchester, UK
| | - M. Kerr
- Space Science Division, Naval Research Laboratory, Washington, DC USA
| | - E. D. Barr
- Max-Planck-Institut für Radioastronomie, Bonn, Germany
| | - B. Bhattacharyya
- National Centre for Radio Astrophysics, Tata Institute of Fundamental Research, Pune, India
| | - R. P. Breton
- Jodrell Bank Centre for Astrophysics, Department of Physics and Astronomy, The University of Manchester, Manchester, UK
| | - P. Bruel
- Laboratoire Leprince-Ringuet, École Polytechnique, CNRS/IN2P3, Palaiseau, France
| | - F. Camilo
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - W. Chen
- Max-Planck-Institut für Radioastronomie, Bonn, Germany
| | - I. Cognard
- Laboratoire de Physique et Chimie de l’Environnement et de l’Espace–Université d’Orléans, CNRS, Orléans, France
- Observatoire Radioastronomique de Nançay, Observatoire de Paris, Université PSL, Université d’Orléans, CNRS, Nançay, France
| | - H. T. Cromartie
- Cornell Center for Astrophysics and Planetary Science and Department of Astronomy, Cornell University, Ithaca, NY USA
| | - J. Deneva
- Space Science Division, Naval Research Laboratory, Washington, DC USA
- College of Science, George Mason University, Fairfax, VA USA
| | - V. S. Dhillon
- Department of Physics and Astronomy, University of Sheffield, Sheffield, UK
- Instituto de Astrofísica de Canarias, La Laguna, Spain
| | - L. Guillemot
- Laboratoire de Physique et Chimie de l’Environnement et de l’Espace–Université d’Orléans, CNRS, Orléans, France
- Observatoire Radioastronomique de Nançay, Observatoire de Paris, Université PSL, Université d’Orléans, CNRS, Nançay, France
| | - M. R. Kennedy
- Jodrell Bank Centre for Astrophysics, Department of Physics and Astronomy, The University of Manchester, Manchester, UK
- Department of Physics, University College Cork, Cork, Ireland
| | - M. Kramer
- Jodrell Bank Centre for Astrophysics, Department of Physics and Astronomy, The University of Manchester, Manchester, UK
- Max-Planck-Institut für Radioastronomie, Bonn, Germany
| | - A. G. Lyne
- Jodrell Bank Centre for Astrophysics, Department of Physics and Astronomy, The University of Manchester, Manchester, UK
| | - D. Mata Sánchez
- Jodrell Bank Centre for Astrophysics, Department of Physics and Astronomy, The University of Manchester, Manchester, UK
- Instituto de Astrofísica de Canarias, La Laguna, Spain
- Departamento de Astrofísica, Universidad de La Laguna, La Laguna, Spain
| | - L. Nieder
- Max Planck Institute for Gravitational Physics (Albert Einstein Institute), Hannover, Germany
- Leibniz Universität Hannover, Hannover, Germany
| | - C. Phillips
- University of Virginia, Charlottesville, VA USA
| | - S. M. Ransom
- National Radio Astronomy Observatory, Socorro, NM USA
| | - P. S. Ray
- Space Science Division, Naval Research Laboratory, Washington, DC USA
| | | | - J. Roy
- National Centre for Radio Astrophysics, Tata Institute of Fundamental Research, Pune, India
| | - D. A. Smith
- Laboratoire d’Astrophysique de Bordeaux, Université de Bordeaux, CNRS, Pessac, France
| | - R. Spiewak
- Jodrell Bank Centre for Astrophysics, Department of Physics and Astronomy, The University of Manchester, Manchester, UK
- ARC Centre of Excellence for Gravitational Wave Discovery (OzGrav), Centre for Astrophysics and Supercomputing, Swinburne University of Technology, Hawthorn, Victoria Australia
- Centre for Astrophysics and Supercomputing, Swinburne University of Technology, Hawthorn, Victoria Australia
| | - B. W. Stappers
- Jodrell Bank Centre for Astrophysics, Department of Physics and Astronomy, The University of Manchester, Manchester, UK
| | - S. Tabassum
- New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Department of Physics and Astronomy, West Virginia University, Morgantown, WV USA
| | - G. Theureau
- Laboratoire de Physique et Chimie de l’Environnement et de l’Espace–Université d’Orléans, CNRS, Orléans, France
- Observatoire Radioastronomique de Nançay, Observatoire de Paris, Université PSL, Université d’Orléans, CNRS, Nançay, France
- Laboratoire Univers et Théories, Observatoire de Paris, Université PSL, CNRS, Université de Paris, Meudon, France
| | - G. Voisin
- Jodrell Bank Centre for Astrophysics, Department of Physics and Astronomy, The University of Manchester, Manchester, UK
- Laboratoire Univers et Théories, Observatoire de Paris, Université PSL, CNRS, Université de Paris, Meudon, France
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17
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Sanjenbam P, Shivaprasad PV, Agashe D. Impact of Phyllosphere Methylobacterium on Host Rice Landraces. Microbiol Spectr 2022; 10:e0081022. [PMID: 35856668 PMCID: PMC9431194 DOI: 10.1128/spectrum.00810-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/24/2022] [Indexed: 11/20/2022] Open
Abstract
The genus Methylobacterium includes widespread plant-associated bacteria that are abundant in the plant phyllosphere (leaf surfaces), consume plant-secreted methanol, and can produce plant growth-promoting metabolites. However, despite the potential to increase agricultural productivity, their impact on host fitness in the natural environment is relatively poorly understood. Here, we conducted field experiments with three traditionally cultivated rice landraces from northeastern India. We inoculated seedlings with native versus nonnative phyllosphere Methylobacterium strains and found significant impacts on plant growth and grain yield. However, these effects were variable. Whereas some Methylobacterium isolates were beneficial for their host, others had no impact or were no more beneficial than the bacterial growth medium on its own. Host plant benefits were not consistently associated with Methylobacterium colonization and did not have altered phyllosphere microbiome composition, changes in the early expression of plant stress response pathways, or bacterial auxin production. We provide the first demonstration of the benefits of phyllosphere Methylobacterium for rice yield under field conditions and highlight the need for further analysis to understand the mechanisms underlying these benefits. Given that the host landrace-Methylobacterium relationship was not generalizable, future agricultural applications will require careful testing to identify coevolved host-bacterium pairs that may enhance the productivity of high-value rice varieties. IMPORTANCE Plants are associated with diverse microbes in nature. Do the microbes increase host plant health, and can they be used for agricultural applications? This is an important question that must be answered in the field rather than in the laboratory or greenhouse. We tested the effects of native, leaf-inhabiting bacteria (genus Methylobacterium) on traditionally cultivated rice varieties in a crop field. We found that inoculation with some bacteria increased rice grain production substantially while a nonnative bacterium reduced plant health. Overall, the effect of bacterial inoculation varied across pairs of rice varieties and their native bacteria. Thus, knowledge of evolved associations between specific bacteria hosted by specific rice varieties is necessary to develop ways to increase the yield of traditional rice landraces and preserve these important sources of cultural and genetic diversity.
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Affiliation(s)
- Pratibha Sanjenbam
- National Center for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - P. V. Shivaprasad
- National Center for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Deepa Agashe
- National Center for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
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18
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Mukherjee S, Adhikary S, Gadad SS, Mondal P, Sen S, Choudhari R, Singh V, Adhikari S, Mandal P, Chaudhuri S, Sengupta A, Lakshmanaswamy R, Chakrabarti P, Roy S, Das C. Suppression of poised oncogenes by ZMYND8 promotes chemo-sensitization. Cell Death Dis 2020; 11:1073. [PMID: 33323928 PMCID: PMC7738522 DOI: 10.1038/s41419-020-03129-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 02/06/2023]
Abstract
The major challenge in chemotherapy lies in the gain of therapeutic resistance properties of cancer cells. The relatively small fraction of chemo-resistant cancer cells outgrows and are responsible for tumor relapse, with acquired invasiveness and stemness. We demonstrate that zinc-finger MYND type-8 (ZMYND8), a putative chromatin reader, suppresses stemness, drug resistance, and tumor-promoting genes, which are hallmarks of cancer. Reinstating ZMYND8 suppresses chemotherapeutic drug doxorubicin-induced tumorigenic potential (at a sublethal dose) and drug resistance, thereby resetting the transcriptional program of cells to the epithelial state. The ability of ZMYND8 to chemo-sensitize doxorubicin-treated metastatic breast cancer cells by downregulating tumor-associated genes was further confirmed by transcriptome analysis. Interestingly, we observed that ZMYND8 overexpression in doxorubicin-treated cells stimulated those involved in a good prognosis in breast cancer. Consistently, sensitizing the cancer cells with ZMYND8 followed by doxorubicin treatment led to tumor regression in vivo and revert back the phenotypes associated with drug resistance and stemness. Intriguingly, ZMYND8 modulates the bivalent or poised oncogenes through its association with KDM5C and EZH2, thereby chemo-sensitizing the cells to chemotherapy for better disease-free survival. Collectively, our findings indicate that poised chromatin is instrumental for the acquisition of chemo-resistance by cancer cells and propose ZMYND8 as a suitable epigenetic tool that can re-sensitize the chemo-refractory breast carcinoma.
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MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- Breast Neoplasms/drug therapy
- Breast Neoplasms/genetics
- Breast Neoplasms/pathology
- Carcinogenesis/drug effects
- Carcinogenesis/genetics
- Carcinogenesis/pathology
- Cell Line, Tumor
- Cell Movement/drug effects
- Cell Movement/genetics
- Down-Regulation/drug effects
- Down-Regulation/genetics
- Doxorubicin/pharmacology
- Doxorubicin/therapeutic use
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Enhancer of Zeste Homolog 2 Protein/metabolism
- Epigenesis, Genetic/drug effects
- Epithelial-Mesenchymal Transition/drug effects
- Epithelial-Mesenchymal Transition/genetics
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic/drug effects
- Genome, Human
- Histone Demethylases/metabolism
- Humans
- Mice, Inbred BALB C
- Mice, Nude
- Neoplastic Stem Cells/metabolism
- Neoplastic Stem Cells/pathology
- Oncogenes
- Phenotype
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Treatment Outcome
- Triple Negative Breast Neoplasms/drug therapy
- Triple Negative Breast Neoplasms/genetics
- Triple Negative Breast Neoplasms/pathology
- Tumor Suppressor Proteins/metabolism
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Affiliation(s)
- Shravanti Mukherjee
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
| | - Santanu Adhikary
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata, 700032, India
| | - Shrikanth S Gadad
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, 79905, USA
- Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center El Paso, El Paso, TX, 79905, USA
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynaecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Payel Mondal
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
- Homi Bhaba National Institute, Mumbai, India
| | - Sabyasachi Sen
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
| | - Ramesh Choudhari
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, 79905, USA
- Shri B. M. Patil Medical College, Hospital and Research Centre, BLDE (Deemed to be University), Vijayapura, Karnataka, 586103, India
| | - Vipin Singh
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
- Homi Bhaba National Institute, Mumbai, India
| | - Swagata Adhikari
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
- Homi Bhaba National Institute, Mumbai, India
| | - Pratiti Mandal
- Cell Biology and Physiology Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata, 700032, India
| | - Soumi Chaudhuri
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
| | - Amrita Sengupta
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
| | - Rajkumar Lakshmanaswamy
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, 79905, USA
- Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center El Paso, El Paso, TX, 79905, USA
| | - Partha Chakrabarti
- Cell Biology and Physiology Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata, 700032, India
| | - Siddhartha Roy
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata, 700032, India
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India.
- Homi Bhaba National Institute, Mumbai, India.
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19
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Chakraborty P, Datta S, McEwen BS, Chattarji S. Corticosterone after acute stress prevents the delayed effects on the amygdala. Neuropsychopharmacology 2020; 45:2139-2146. [PMID: 32629457 PMCID: PMC7784883 DOI: 10.1038/s41386-020-0758-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/05/2020] [Accepted: 06/29/2020] [Indexed: 01/23/2023]
Abstract
Even a single 2-hour episode of immobilization stress is known to trigger anxiety-like behavior and increase spine-density in the basolateral amygdala (BLA) of rats 10 days later. This delayed build-up of morphological and behavioral effects offers a stress-free time window of intervention after acute stress, which we used to test a protective role for glucocorticoids against stress. We observed that post-stress corticosterone, given 1 day after acute stress in drinking water, reversed enhanced anxiety-like behavior 10 days later. Quantification of spine-density on Golgi-stained BLA principal neurons showed that the same intervention also prevented the increase in spine numbers in the amygdala, at the same delayed time-point. Further, stress elevated serum corticosterone levels in rats that received vehicle in the drinking water. However, when stress was followed 24 h later by corticosterone in the drinking water, the surge in corticosterone was prevented. Together, these observations suggest that corticosterone, delivered through drinking water even 24 h after acute stress, is capable of reversing the delayed enhancing effects on BLA synaptic connectivity and anxiety-like behavior. Strikingly, although the immobilization-induced surge in corticosterone by itself has delayed detrimental effects on amygdalar structure and function, there exists a window of opportunity even after stress to mitigate its impact with a second surge of exogenously administered corticosterone. This provides a framework in the amygdala for analyzing how the initial physiological and endocrine processes triggered by traumatic stress eventually give rise to debilitating emotional symptoms, as well as the protective effects of glucocorticoids against their development.
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Affiliation(s)
- Prabahan Chakraborty
- National Centre for Biological Sciences, Bangalore, 560065, India
- Institut de Genomique Fonctionnelle, Inserm U1191, CNRS UMR5203, University of Montpellier, Montpellier, 34090, France
| | - Siddhartha Datta
- Centre for Brain Development and Repair, Institute for Stem Cell Biology and Regenerative Medicine, Bangalore, 560065, India
| | - Bruce S McEwen
- Laboratory of Neuroendocrinology, The Rockefeller University, New York, NY, 10065, USA
| | - Sumantra Chattarji
- National Centre for Biological Sciences, Bangalore, 560065, India.
- Centre for Brain Development and Repair, Institute for Stem Cell Biology and Regenerative Medicine, Bangalore, 560065, India.
- Laboratory of Neuroendocrinology, The Rockefeller University, New York, NY, 10065, USA.
- Centre for Discovery Brain Sciences, Deanery of Biomedical Sciences, University of Edinburgh, Hugh Robson Building, 15 George Square, Edinburgh, EH89XD, UK.
- National Centre for Biological Sciences, GKVK Campus, Bellary Road, Bangalore, Karnataka, 560065, India.
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20
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Sinha S, Adak PC, Surya Kanthi RS, Chittari BL, Sangani LDV, Watanabe K, Taniguchi T, Jung J, Deshmukh MM. Bulk valley transport and Berry curvature spreading at the edge of flat bands. Nat Commun 2020; 11:5548. [PMID: 33144578 PMCID: PMC7641251 DOI: 10.1038/s41467-020-19284-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 09/25/2020] [Indexed: 11/24/2022] Open
Abstract
2D materials based superlattices have emerged as a promising platform to modulate band structure and its symmetries. In particular, moiré periodicity in twisted graphene systems produces flat Chern bands. The recent observation of anomalous Hall effect (AHE) and orbital magnetism in twisted bilayer graphene has been associated with spontaneous symmetry breaking of such Chern bands. However, the valley Hall state as a precursor of AHE state, when time-reversal symmetry is still protected, has not been observed. Our work probes this precursor state using the valley Hall effect. We show that broken inversion symmetry in twisted double bilayer graphene (TDBG) facilitates the generation of bulk valley current by reporting experimental evidence of nonlocal transport in a nearly flat band system. Despite the spread of Berry curvature hotspots and reduced quasiparticle velocities of the carriers in these flat bands, we observe large nonlocal voltage several micrometers away from the charge current path - this persists when the Fermi energy lies inside a gap with large Berry curvature. The high sensitivity of the nonlocal voltage to gate tunable carrier density and gap modulating perpendicular electric field makes TDBG an attractive platform for valley-twistronics based on flat bands.
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Affiliation(s)
- Subhajit Sinha
- Department of Condensed Matter Physics and Materials Science, Tata Institute of Fundamental Research, Mumbai, 400005, India
| | - Pratap Chandra Adak
- Department of Condensed Matter Physics and Materials Science, Tata Institute of Fundamental Research, Mumbai, 400005, India.
| | - R S Surya Kanthi
- Department of Condensed Matter Physics and Materials Science, Tata Institute of Fundamental Research, Mumbai, 400005, India
| | | | - L D Varma Sangani
- Department of Condensed Matter Physics and Materials Science, Tata Institute of Fundamental Research, Mumbai, 400005, India
| | - Kenji Watanabe
- National Institute for Materials Science, 1-1 Namiki, Tsukuba, 305-0044, Japan
| | - Takashi Taniguchi
- National Institute for Materials Science, 1-1 Namiki, Tsukuba, 305-0044, Japan
| | - Jeil Jung
- Department of Physics, University of Seoul, Seoul, 02504, Korea
| | - Mandar M Deshmukh
- Department of Condensed Matter Physics and Materials Science, Tata Institute of Fundamental Research, Mumbai, 400005, India.
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21
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Walavalkar K, Saravanan B, Singh AK, Jayani RS, Nair A, Farooq U, Islam Z, Soota D, Mann R, Shivaprasad PV, Freedman ML, Sabarinathan R, Haiman CA, Notani D. A rare variant of African ancestry activates 8q24 lncRNA hub by modulating cancer associated enhancer. Nat Commun 2020; 11:3598. [PMID: 32680982 PMCID: PMC7368061 DOI: 10.1038/s41467-020-17325-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 06/24/2020] [Indexed: 11/18/2022] Open
Abstract
Genetic variation at the 8q24 locus is linked with the greater susceptibility to prostate cancer in men of African ancestry. One such African ancestry specific rare variant, rs72725854 (A>G/T) (~6% allele frequency) has been associated with a ~2-fold increase in prostate cancer risk. However, the functional relevance of this variant is unknown. Here we show that the variant rs72725854 is present in a prostate cancer-specific enhancer at 8q24 locus. Chromatin-conformation capture and dCas9 mediated enhancer blocking establish a direct regulatory link between this enhancer and lncRNAs PCAT1, PRNCR1 and PVT1. The risk allele ('T') is associated with higher expression of PCAT1, PVT1 and c-myc in prostate tumors. Further, enhancer with the risk allele gains response to androgen stimulation by recruiting the transcription factor SPDEF whereas, non-risk alleles remain non-responsive. Elevated expression of these lncRNAs and c-myc in risk allele carriers may explain their greater susceptibility to prostate cancer.
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Affiliation(s)
- Kaivalya Walavalkar
- Genetics and Development, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, 560065, India
| | - Bharath Saravanan
- Genetics and Development, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, 560065, India
- Sastra Deemed University, Thanjavur, Tamil Nadu, 613401, India
| | - Anurag Kumar Singh
- Genetics and Development, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, 560065, India
| | - Ranveer Singh Jayani
- Howard Hughes Medical Institute, Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92037, USA
| | - Ashwin Nair
- Genetics and Development, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, 560065, India
- Sastra Deemed University, Thanjavur, Tamil Nadu, 613401, India
| | - Umer Farooq
- Genetics and Development, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, 560065, India
- Trans-Disciplinary University, IVRI road, Bangalore, Tamil Nadu, 560064, Karnataka, India
| | - Zubairul Islam
- Genetics and Development, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, 560065, India
- Sastra Deemed University, Thanjavur, Tamil Nadu, 613401, India
| | - Deepanshu Soota
- Genetics and Development, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, 560065, India
| | - Rajat Mann
- Genetics and Development, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, 560065, India
| | - Padubidri V Shivaprasad
- Genetics and Development, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, 560065, India
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142, USA
- Centre for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Radhakrishnan Sabarinathan
- Genetics and Development, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, 560065, India
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90007, USA
| | - Dimple Notani
- Genetics and Development, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, 560065, India.
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22
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Nilavar NM, Paranjape AM, Raghavan SC. Biochemical activity of RAGs is impeded by Dolutegravir, an HIV integrase inhibitor. Cell Death Discov 2020; 6:50. [PMID: 32566255 PMCID: PMC7293277 DOI: 10.1038/s41420-020-0281-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 03/26/2020] [Accepted: 04/22/2020] [Indexed: 02/03/2023] Open
Abstract
HIV is a retrovirus that infects CD4+ T lymphocytes in human beings and causes immunodeficiency. In the recent years, various therapies have been developed against HIV, including targeting the HIV specific protein, integrase, responsible for integration of HIV cDNA into host DNA. Although, integrase is specific to HIV, it has functional and structural similarity with RAG1, one of the partner proteins associated with V(D)J recombination, a process by which immune diversity is generated in humans. Currently, there are three HIV integrase inhibitors: Elvitegravir, Dolutegravir, and Raltegravir, in the market which have been approved by the FDA (USA). All three drugs are used in anti-retroviral therapy (ART). Previously, we showed that amongst the HIV inhibitors, Elvitegravir could significantly decrease B cell maturation in vivo and inhibit the physiological activities of RAGs in vitro, unlike Raltegravir. In the present study, we address the effect of second-generation integrase inhibitor, Dolutegravir on RAG activities. Binding and nicking studies showed that, Dolutegravir could decrease the binding efficiency of RAG1 domains and cleavage on DNA substrates, but not as considerably as Elvitegravir. Thus, we show that although the integrase inhibitors such as Elvitegravir show an affinity towards RAG1, the newer molecules may have lesser side-effects.
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Affiliation(s)
- Namrata M. Nilavar
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012 India
| | - Amita M. Paranjape
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012 India
| | - Sathees C. Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012 India
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23
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Kirolikar S, Prasannan P, Raghuram GV, Pancholi N, Saha T, Tidke P, Chaudhari P, Shaikh A, Rane B, Pandey R, Wani H, Khare NK, Siddiqui S, D'souza J, Prasad R, Shinde S, Parab S, Nair NK, Pal K, Mittra I. Prevention of radiation-induced bystander effects by agents that inactivate cell-free chromatin released from irradiated dying cells. Cell Death Dis 2018; 9:1142. [PMID: 30442925 PMCID: PMC6238009 DOI: 10.1038/s41419-018-1181-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 10/20/2018] [Accepted: 10/22/2018] [Indexed: 12/15/2022]
Abstract
Radiation-induced bystander effect (RIBE) is a poorly understood phenomenon wherein non-targeted cells exhibit effects of radiation. We have reported that cell-free chromatin (cfCh) particles that are released from dying cells can integrate into genomes of surrounding healthy cells to induce DNA damage and inflammation. This raised the possibility that RIBE might be induced by cfCh released from irradiated dying cells. When conditioned media from BrdU-labeled irradiated cells were passed through filters of pore size 0.22 µm and incubated with unexposed cells, BrdU-labeled cfCh particles could be seen to readily enter their nuclei to activate H2AX, active Caspase-3, NFκB, and IL-6. A direct relationship was observed with respect to activation of RIBE biomarkers and radiation dose in the range of 0.1-0 Gy. We confirmed by FISH and cytogenetic analysis that cfCh had stably integrated into chromosomes of bystander cells and had led to extensive chromosomal instability. The above RIBE effects could be abrogated when conditioned media were pre-treated with agents that inactivate cfCh, namely, anti-histone antibody complexed nanoparticles (CNPs), DNase I and a novel DNA degrading agent Resveratrol-copper (R-Cu). Lower hemi-body irradiation with γ-rays (0.1-50 Gy) led to activation of H2AX, active Caspase-3, NFκB, and IL-6 in brain cells in a dose-dependent manner. Activation of these RIBE biomarkers could be abrogated by concurrent treatment with CNPs, DNase I and R-Cu indicating that activation of RIBE was not due to radiation scatter to the brain. RIBE activation was seen even when mini-beam radiation was delivered to the umbilical region of mice wherein radiation scatter to brain was negligible and could be abrogated by cfCh inactivating agents. These results indicate that cfCh released from radiation-induced dying cells are activators of RIBE and that it can be prevented by treatment with appropriate cfCh inactivating agents.
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Affiliation(s)
- Saurabh Kirolikar
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Preeti Prasannan
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Gorantla V Raghuram
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Namrata Pancholi
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Tannishtha Saha
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Pritishkumar Tidke
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Pradip Chaudhari
- Comparative Oncology Program and Small Animal Imaging Facility, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Alfina Shaikh
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Bhagyeshri Rane
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Richa Pandey
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Harshada Wani
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Naveen K Khare
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Sophiya Siddiqui
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Jenevieve D'souza
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Ratnam Prasad
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Sushma Shinde
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Sailee Parab
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Naveen K Nair
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Kavita Pal
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Indraneel Mittra
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India.
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