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526 results on '"Tata Institute of Fundamental Research [Bangalore]"'

1. Rigid N3O2-Pentadentate Ligand-Assisted Octacoordinate Mononuclear Ln(III) Complexes: Syntheses, Characterization, and Slow Magnetization Relaxation

Author

Vaibhav Singh, Dhiraj Das, Srinivas Anga, Jean-Pascal Sutter, Vadapalli Chandrasekhar, Arun Kumar Bar, Indian Institute of Science Education and Research (IISER) Tirupati (IISER Tirupati), Tata Institute of Fundamental Research [Bangalore], Laboratoire de chimie de coordination (LCC), Institut de Chimie de Toulouse (ICT), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and Ministry of Education, Government of India, Scheme for Transformational and Advanced Research in Sciences (STARS, MoE/STARS-1/Apr2019/333)

Subjects
Ions, Mathematical methods, General Chemical Engineering, Magnetic properties, [CHIM.COOR]Chemical Sciences/Coordination chemistry, General Chemistry, Group theory, Ligands
Abstract

International audience; A series of air-stable mononuclear octacoordinate Ln(III) complexes, [(L)Ln(TPPO)3]OTf (Ln = Y (1·Y); Gd (1·Gd); Tb (1·Tb); Dy (1·Dy); Ho (1·Ho); and Er (1·Er)) and [(L)Ln(TPPO)(NO3)] (Ln = Y (2·Y) and Dy (2·Dy)), are synthesized employing a rigid N3O2-pentadentate chelating ligand as the basis ligand and meridional ancillary ligands (where H2L = 2,6-diacetylpyridine bis-benzoylhydrazone, TPPO = triphenylphosphine oxide, and OTf– = trifluoromethanesulfonate). All the complexes are synthesized under aerobic conditions and characterized comprehensively by spectroscopic and X-ray crystallographic techniques. Magnetic property investigation on the polycrystalline solid samples of 1·Ln (Ln = Gd, Tb, Dy, Ho, and Er) and 2·Dy are reported. A field-induced single-molecule magnet behavior was observed for the Dy derivatives. 1·Dy exhibits the highest effective energy barrier of magnetization reversal, Ueff/kB = 47 K under Hdc = 1 kOe among the complexes presented herein.

Published
2022

2. Uniqueness and regularity of weak solutions of a fluid-rigid body interaction system under the Prodi-Serrin condition

Author

Maity, Debayan, Takahashi, Takéo, Centre for Applicable Mathematics, Tata Institute of Fundamental Research, Bangalore, Systems with physical heterogeneities : inverse problems, numerical simulation, control and stabilization (SPHINX), Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Institut Élie Cartan de Lorraine (IECL), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), and ANR-20-CE40-0009,TRECOS,Nouvelles directions en contrôle et stabilisation: Contraintes et termes non-locaux(2020)

Subjects
Navier-Stokes system, fluid-structure interaction, [MATH.MATH-AP]Mathematics [math]/Analysis of PDEs [math.AP], weak solution
Abstract

In this article, we study the weak uniqueness and the regularity of the weak solutions of a fluid-structure interaction system. More precisely, we consider the motion of a rigid ball in a viscous incompressible fluid and we assume that the fluid-rigid body system fills the entire space $\mathbb{R}^3$. We prove that the corresponding weak solutions that additionally satisfy a classical Prodi-Serrin condition, including a critical one, are unique. We also show that the weak solutions are regular under the Prodi-Serrin conditions, with a smallness condition in the critical case.

Published
2023

3. Magnetocaloric effect and slow magnetic relaxation in peroxide-assisted tetranuclear lanthanide assemblies

Author

Pawan Kumar, Jessica Flores Gonzalez, Prem Prakash Sahu, Naushad Ahmed, Joydev Acharya, Vierandra Kumar, Olivier Cador, Fabrice Pointillart, Saurabh Kumar Singh, Vadapalli Chandrasekhar, Indian Institute of Technology Kanpur (IIT Kanpur), Institut des Sciences Chimiques de Rennes (ISCR), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Indian Institute of Technology [Hyderabad] (IIT Hyderabad), Department of Chemistry [Kanpur] (IIT Kanpur), and Tata Institute of Fundamental Research [Bangalore]

Subjects
Inorganic Chemistry, expert elicitation, Chemical risk assessment chemical risk matrix expert elicitation real work situation, real work situation, Chemical risk assessment, chemical risk matrix, [CHIM]Chemical Sciences, [CHIM.INOR]Chemical Sciences/Inorganic chemistry
Abstract

International audience; The synthesis, structure and magnetism of tetranuclear complexes, [Ln4(LH2)2(η1-Piv)2(η2-Piv)2(μ3-O2)2(H2O)2]·2MeOH (1, Ln = GdIII; 2,Ln = TbIII; 3, Ln = DyIII; and 4, Ln = ErIII) (LH4 = 6-((bis(2-hydroxyethyl)amino)-N′-(2-hydroxybenzylidene)picolinohydrazide) (piv = pivalate ion) are reported. Interestingly, the formation of these tetranuclear assemblies is assisted by two side-on coordinating peroxide ligands which bind in a μ3-η2:η2:η2 fashion. DC magnetic behaviour revealed the existence of a dominating but weak intramolecular antiferromagnetic interaction in the cases of 1, 2, and 4, while a small structural change in complex 3 turns this into a ferromagnetic interaction. We have investigated the magnetothermal behaviour of 1 which shows a magnetocaloric effect with the value of maximum entropy change of −ΔSm = 33.60 J K−1 kg−1 at 4 K (ΔH = 13–0 T). This is close to the calculated value of 36.45 J K−1 kg−1. The ac magnetic susceptibility study confirms zero-field out-of-phase magnetic susceptibility signals only for 3 which get well resolved on the application of a 1 kOe dc magnetic field. The energy barrier for the Orbach process of spin reversal was found to be 23 K (τ0 = 9 × 10−7 s). We also report detailed theoretical studies to rationalize and understand the observed magnetic behaviour.

Published
2022

4. A comprehensive phylogeny and revised taxonomy illuminate the origin and diversification of the global radiation of Papilio (Lepidoptera: Papilionidae)

Author

Condamine, Fabien, Allio, Rémi, Reboud, Eliette, Dupuis, Julian, Toussaint, Emmanuel, Mazet, Nathan, Hu, Shao-Ji, Lewis, Delano, Kunte, Krushnamegh, Cotton, Adam, Sperling, Felix, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), University of Kentucky (UK), Museum d'Histoire Naturelle [Genève] (MHN), Yunnan Agricultural University, Burman University, Tata Institute of Fundamental Research [Bangalore], National Centre for Biological Sciences [TIFR] (NCBS), Tata Institute for Fundamental Research (TIFR), Chercheur indépendant, University of Alberta, This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (project GAIA, agreement no. 851188), and an ‘Investissement d’Avenir’ grant from the Agence Nationale de la Recherche (project CASMA, CEBA, ref. ANR-10-LABX-0025) to F.L.C., a Ramanujan Fellowship from the Dept. of Science and Technology, Govt. of India, to K.K., and support of the Dept. of Atomic Energy, Govt. of India, under project nos. 12-RandD-TFR-5.04-0800 and 12-RandD-TFR-5.04-0900 to TIFR/NCBS, a Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grant to F.A.H.S. Sequencing of most Indian Papilio was done at NCBS under research and voucher specimen collection permits issued to K.K. by the state forest departments in Kerala (permit no. WL 10-3781/2012 dated 18/12/2012, and GO (RT) No. 376/2012/FandWLD dated 26/07/2012) and Nagaland (permit no. CWL/GEN/240/522-39 dated 14 August 2012). Alberto Fracasso (Italy) and Laurie Wills (New Zealand) are thanked for providing samples of some hard to obtain taxa., ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), and European Project: 851188,GAIA

Subjects
[SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Systematics, Genetics, Macroevolution, Paleotropics, Butterflies, Molecular Biology, Historical biogeography, Ecology, Evolution, Behavior and Systematics, Taxonomy
Abstract

International audience; Highlights:• A dense and robust phylogeny of Papilio is reconstructed with seven DNA markers.• A taxonomic working list is proposed, including 235 extant species• Papilio originated in the Oligocene in a northern region centered on the Bering Land Bridge• The role of Paleotropics is revealed within the radiation of Old World Papilio• Synchronous southward dispersals explained the current tropical distribution of PapilioAbstract:The swallowtail genus Papilio (Lepidoptera: Papilionidae) is species rich, distributed worldwide, and has broad morphological habits and ecological niches. Because of its elevated species richness, it has been historically difficult to reconstruct a densely sampled phylogeny for this clade. Here we provide a taxonomic working list for the genus, resulting in 235 Papilio species, and assemble a molecular dataset of seven gene fragments representing ca. 80% of the currently described diversity. Phylogenetic analyses reconstructed a robust tree with highly supported relationships within subgenera, although a few nodes in the early history of the Old World Papilio remain unresolved. Contrasting with previous results, we found that Papilio alexanor is sister to all Old World Papilio and that the subgenus Eleppone is no longer monotypic. The latter includes the recently described Fijian Papilio natewa with the Australian Papilio anactus and is sister to subgenus Araminta (formerly included in subgenus Menelaides) occurring in Southeast Asia. Our phylogeny also includes rarely studied (P. antimachus, P. benguetana) or endangered species (P. buddha, P. chikae). Taxonomic changes resulting from this study are elucidated. Molecular dating and biogeographic analyses indicate that Papilio originated ca. 30 million years ago (Oligocene), in a northern region centered on Beringia. A rapid early Miocene radiation in the Paleotropics is revealed within Old World Papilio, potentially explaining their low early branch support. Most subgenera originated in the early to middle Miocene followed by synchronous southward biogeographic dispersals and repeated local extirpations in northern latitudes. This study provides a comprehensive phylogenetic framework for Papilio with clarification of subgeneric systematics and species taxonomic changes enumerated, which will facilitate further studies to address questions on their ecology and evolutionary biology using this model clade.

Published
2023

5. Alternating Tree Automata with Qualitative Semantics

Author

Sasha Rubin, Emmanuel Filiot, Aniello Murano, Sophie Pinchinat, Olivier Serre, Shibashis Guha, Bastien Maubert, Nathanaël Fijalkow, Laureline Pinault, Raphaël Berthon, Université libre de Bruxelles (ULB), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Département d'Informatique [Bruxelles] (ULB), Faculté des Sciences [Bruxelles] (ULB), Université libre de Bruxelles (ULB)-Université libre de Bruxelles (ULB), Tata Institute of Fundamental Research [Bangalore], University of Naples Federico II = Università degli studi di Napoli Federico II, Université de Lyon, Université de Rennes (UR), Logic and applications (LOGICA), LANGAGE ET GÉNIE LOGICIEL (IRISA-D4), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), The University of Sydney, Institut de Recherche en Informatique Fondamentale (IRIF (UMR_8243)), Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), University of Naples Federico II, Università degli studi di Napoli Federico II, Preuves et Langages (PLUME), Laboratoire de l'Informatique du Parallélisme (LIP), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES), Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Berthon, R., Fijalkow, N., Filiot, E., Guha, S., Maubert, B., Murano, A., Pinault, L., Pinchinat, S., Rubin, S., Serre, O., École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL)

Subjects
FOS: Computer and information sciences, Computer Science - Logic in Computer Science, TheoryofComputation_COMPUTATIONBYABSTRACTDEVICES, General Computer Science, Formal Languages and Automata Theory (cs.FL), Logic, Computer science, Semantics (computer science), Computer Science - Formal Languages and Automata Theory, ω-regular conditions, 0102 computer and information sciences, 02 engineering and technology, 01 natural sciences, Tree automata, Theoretical Computer Science, Computer Science::Logic in Computer Science, 0202 electrical engineering, electronic engineering, information engineering, [INFO]Computer Science [cs], Alternation (linguistics), Discrete mathematics, Binary tree, [INFO.INFO-LO]Computer Science [cs]/Logic in Computer Science [cs.LO], almost-sure semantic, Logic in Computer Science (cs.LO), Automaton, Decidability, Computational Mathematics, TheoryofComputation_MATHEMATICALLOGICANDFORMALLANGUAGES, Quantifier (logic), 010201 computation theory & mathematics, TheoryofComputation_LOGICSANDMEANINGSOFPROGRAMS, Emptiness, 020201 artificial intelligence & image processing, Tree (set theory), Computer Science::Formal Languages and Automata Theory
Abstract

We study alternating automata with qualitative semantics over infinite binary trees: Alternation means that two opposing players construct a decoration of the input tree called a run, and the qualitative semantics says that a run of the automaton is accepting if almost all branches of the run are accepting. In this article, we prove a positive and a negative result for the emptiness problem of alternating automata with qualitative semantics. The positive result is the decidability of the emptiness problem for the case of Büchi acceptance condition. An interesting aspect of our approach is that we do not extend the classical solution for solving the emptiness problem of alternating automata, which first constructs an equivalent non-deterministic automaton. Instead, we directly construct an emptiness game making use of imperfect information. The negative result is the undecidability of the emptiness problem for the case of co-Büchi acceptance condition. This result has two direct consequences: the undecidability of monadic second-order logic extended with the qualitative path-measure quantifier and the undecidability of the emptiness problem for alternating tree automata with non-zero semantics, a recently introduced probabilistic model of alternating tree automata.

Published
2020

6. High Order Asymptotic Preserving and Classical Semi-implicit RK Schemes for the Euler-Poisson System in the Quasineutral Limit

Author

Arun, K.R., Crouseilles, Nicolas, Samataray, Saurav, Department of Science & Technology [New Delhi], Science and Engineering Research Board [New Delhi], Université de Rennes (UR), Multi-scale numerical geometric schemes (MINGUS), École normale supérieure - Rennes (ENS Rennes)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut de Recherche Mathématique de Rennes (IRMAR), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut Agro Rennes Angers, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut Agro Rennes Angers, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Tata Institute of Fundamental Research [Bangalore]

Subjects
Incompressible Euler system, Finite volume method, Primary 35L45, 35L60, 35L65, 35L67, Secondary 65M06, 65M08, Asymptotic preserving, Numerical Analysis (math.NA), 35L60, 65M08 Compressible Euler-Poisson system, [PHYS.PHYS.PHYS-COMP-PH]Physics [physics]/Physics [physics]/Computational Physics [physics.comp-ph], Secondary 65M06, September 21, 35L67, 35L65, Quasineutral limit, FOS: Mathematics, 2022. 2010 Mathematics Subject Classification. Primary 35L45, SI-IMEX-RK schemes, Mathematics - Numerical Analysis, [MATH.MATH-NA]Mathematics [math]/Numerical Analysis [math.NA]
Abstract

In this paper, the design and analysis of high order accurate IMEX finite volume schemes for the compressible Euler-Poisson (EP) equations in the quasineutral limit is presented. As the quasineutral limit is singular for the governing equations, the time discretisation is tantamount to achieving an accurate numerical method. To this end, the EP system is viewed as a differential algebraic equation system (DAEs) via the method of lines. As a consequence of this vantage point, high order linearly semi-implicit (SI) time discretisation are realised by employing a novel combination of the direct approach used for implicit discretisation of DAEs and, two different classes of IMEX-RK schemes: the additive and the multiplicative. For both the time discretisation strategies, in order to account for rapid plasma oscillations in quasineutral regimes, the nonlinear Euler fluxes are split into two different combinations of stiff and non-stiff components. The high order scheme resulting from the additive approach is designated as a classical scheme while the one generated by the multiplicative approach possesses the asymptotic preserving (AP) property. Time discretisations for the classical and the AP schemes are performed by standard IMEX-RK and SI-IMEX-RK methods, respectively so that the stiff terms are treated implicitly and the non-stiff ones explicitly. In order to discretise in space a Rusanov-type central flux is used for the non-stiff part, and simple central differencing for the stiff part. AP property is also established for the space-time fully-discrete scheme obtained using the multiplicative approach. Results of numerical experiments are presented, which confirm that the high order schemes based on the SI-IMEX-RK time discretisation achieve uniform second order convergence with respect to the Debye length and are AP in the quasineutral limit.

Published
2022
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7. Mere end lugtesans - COVID-19 er associeret med svær påvirkning af lugtesansen, smagssansen og mundfølelsen

Author

Parma, Valentina, Ohla, Kathrin, Veldhuizen, Maria G, Niv, Masha Y, Kelly, Christine E, Bakke, Alyssa J, Cooper, Keiland W, Bouysset, Cédric, Pirastu, Nicola, Dibattista, Michele, Kaur, Rishemjit, Liuzza, Marco Tullio, Pepino, Marta Y, Schöpf, Veronika, Pereda-Loth, Veronica, Olsson, Shannon B, Gerkin, Richard C, Rohlfs Domínguez, Paloma, Albayay, Javier, Farruggia, Michael C, Bhutani, Surabhi, Fjaeldstad, Alexander W, Kumar, Ritesh, Menini, Anna, Bensafi, Moustafa, Sandell, Mari, Konstantinidis, Iordanis, Di Pizio, Antonella, Genovese, Federica, Öztürk, Lina, Thomas-Danguin, Thierry, Frasnelli, Johannes, Boesveldt, Sanne, Saatci, Özlem, Saraiva, Luis R, Lin, Cailu, Golebiowski, Jérôme, Hwang, Liang-Dar, Ozdener, Mehmet Hakan, Guàrdia, Maria Dolors, Laudamiel, Christophe, Ritchie, Marina, Havlícek, Jan, Pierron, Denis, Roura, Eugeni, Navarro, Marta, Nolden, Alissa A, Lim, Juyun, Whitcroft, Katherine L, Colquitt, Lauren R, Ferdenzi, Camille, Brindha, Evelyn V, Altundag, Aytug, Macchi, Alberto, Nunez-Parra, Alexia, Patel, Zara M, Fiorucci, Sébastien, Philpott, Carl M, Smith, Barry C, Lundström, Johan N, Mucignat, Carla, Parker, Jane K, van den Brink, Mirjam, Schmuker, Michael, Fischmeister, Florian Ph S, Heinbockel, Thomas, Shields, Vonnie D C, Faraji, Farhoud, Santamaría, Enrique, Fredborg, William E A, Morini, Gabriella, Olofsson, Jonas K, Jalessi, Maryam, Karni, Noam, D’Errico, Anna, Alizadeh, Rafieh, Pellegrino, Robert, Meyer, Pablo, Huart, Caroline, Chen, Ben, Soler, Graciela M, Alwashahi, Mohammed K, Welge-Lüssen, Antje, Freiherr, Jessica, de Groot, Jasper H B, Klein, Hadar, Okamoto, Masako, Singh, Preet Bano, Hsieh, Julien W, Abdulrahman, Olagunju, Dalton, Pamela, Yan, Carol H, Voznessenskaya, Vera V, Chen, Jingguo, Sell, Elizabeth A, Walsh-Messinger, Julie, Archer, Nicholas S, Koyama, Sachiko, Deary, Vincent, Roberts, S Craig, Yanık, Hüseyin, Albayrak, Samet, Nováková, Lenka Martinec, Croijmans, Ilja, Mazal, Patricia Portillo, Moein, Shima T, Margulis, Eitan, Mignot, Coralie, Mariño, Sajidxa, Georgiev, Dejan, Kaushik, Pavan K, Malnic, Bettina, Wang, Hong, Seyed-Allaei, Shima, Yoluk, Nur, Razzaghi-Asl, Sara, Justice, Jeb M, Restrepo, Diego, Reed, Danielle R, Hummel, Thomas, Munger, Steven D, Hayes, John E, Indústries Alimentàries, Qualitat i Tecnologia Alimentària, Tecnologia Alimentària, Temple University [Philadelphia], Pennsylvania Commonwealth System of Higher Education (PCSHE), Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association, Mersin University, The Hebrew University of Jerusalem (HUJ), AbScent, Pennsylvania State University (Penn State), Penn State System, University of California [Irvine] (UC Irvine), University of California (UC), Université Côte d'Azur (UCA), University of Edinburgh, Università degli studi di Bari Aldo Moro = University of Bari Aldo Moro (UNIBA), Central Scientific Instruments Organisation (CSIR), Università degli Studi 'Magna Graecia' di Catanzaro = University of Catanzaro (UMG), University of Illinois at Urbana-Champaign [Urbana], University of Illinois System, Medizinische Universität Wien = Medical University of Vienna, Groupement scientifique de Biologie et de Medecine Spatiale (GSBMS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National d'Études Spatiales [Toulouse] (CNES), Tata Institute for Fundamental Research (TIFR), Arizona State University [Tempe] (ASU), Universidad de Extremadura - University of Extremadura (UEX), Università degli Studi di Padova = University of Padua (Unipd), Yale School of Medicine [New Haven, Connecticut] (YSM), San Diego State University (SDSU), Aarhus University [Aarhus], University of Hertfordshire [Hatfield] (UH), Scuola Internazionale Superiore di Studi Avanzati / International School for Advanced Studies (SISSA / ISAS), Neurosciences Sensorielles Comportement Cognition, Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, University of Turku, Aristotle University of Thessaloniki, Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Monell Chemical Senses Center, Centre des Sciences du Goût et de l'Alimentation [Dijon] (CSGA), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Bourgogne Franche-Comté [COMUE] (UBFC), Université de Montréal (UdeM), Wageningen University and Research Centre (WUR), Medical Science University, Sidra Medicine [Doha, Qatar], Institut de Chimie de Nice (ICN), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), University of Southern Queensland (USQ), Institut de Recerca i Tecnologia Agroalimentàries = Institute of Agrifood Research and Technology (IRTA), DreamAir Llc, Charles University [Prague] (CU), Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), University of Massachusetts System (UMASS), Oregon State University (OSU), Ear Institute, UCL, Lyon Neuroscience Research center, Karunya University, Biruni University, Assi Sette Llaghi Varese, Stanford School of Medicine [Stanford], Stanford Medicine, Stanford University-Stanford University, University of East Anglia [Norwich] (UEA), California Department of Food and Agriculture (CDFA), Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Maastricht University [Maastricht], Institute for Biology - Neurobiology, Freie Universität Berlin, Karl-Franzens-Universität Graz, Howard University College of Medicine, Towson University, University of California [San Diego] (UC San Diego), Proteomics, Center for Applied Medical Research (CIMA), Stockholm University, University of Gastronomic Sciences, Iran University of Medical Sciences, Goethe Universität Frankfurt, University of Tennessee, IBM T.J. Watson Research Center, Université libre de Bruxelles (ULB), Guangzhou Medical University, Buenos Aires University and GEOG (Grupo de Estudio de Olfato y Gusto), Sultan Qaboos University (SQU), Federal University of Technology of Akure (FUTA), A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences [Moscow] (RAS), Hospital of Xi'an Jiaotong University, University of Pennsylvania, University of Dayton, CSIRO Agriculture and Food (CSIRO), Indiana University [Bloomington], Indiana University System, University of Northumbria at Newcastle [United Kingdom], University of Stirling, Middle East Technical University [Ankara] (METU), Utrecht University [Utrecht], Instituto Universitario del Hospital Italiano [Buenos Aires, Argentina], Institute for Research in Fundamental Sciences [Tehran] (IPM), Hebrew University of Jerusalem, Technische Universität Dresden = Dresden University of Technology (TU Dresden), Terrazas del Club Hipico, University Medical Centre Ljubljana [Ljubljana, Slovenia] (UMCL), Tata Institute of Fundamental Research [Bangalore], Universidade de São Paulo = University of São Paulo (USP), University of Florida [Gainesville] (UF), University of Colorado Anschutz [Aurora], Center for Smell and Taste, Department of Food Science, Pennsylvania State University., Julien, Sabine, Tıp Fakültesi, UCL - SSS/IONS/NEUR - Clinical Neuroscience, UCL - (SLuc) Service d'oto-rhino-laryngologie, Department of Food and Nutrition, Senses and Food, Research Center Jülich, University of California [Irvine] (UCI), University of California, Università degli studi di Bari Aldo Moro (UNIBA), Università degli Studi 'Magna Graecia' di Catanzaro [Catanzaro, Italie] (UMG), University of Extremadura, University of Padova, Yale University School of Medicine, Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, University of Helsinki, Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Institute of Agrifood Research and Technology (IRTA), Universita degli Studi di Padova, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Karl-Franzens-Universität [Graz, Autriche], University of California San Diego Health, University of Brussels, University of Pennsylvania [Philadelphia], Tata Institute of Fundamental Research, University of São Paulo (USP), UCL - SSS/IONS - Institute of NeuroScience, FSE Campus Venlo, and RS: FSE UCV

Subjects
Male, Taste, Physiology, Smagstab, Audiology, AcademicSubjects/SCI01180, Settore BIO/09 - Fisiologia, Behavioral Neuroscience, chemistry.chemical_compound, Olfaction Disorders, Taste Disorders, 0302 clinical medicine, RATINGS, Hyposmia, Surveys and Questionnaires, CHEMOSENSITIVITY, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Viral, PALADAR, 030223 otorhinolaryngology, Sensory Science and Eating Behaviour, media_common, TASTE, US NATIONAL-HEALTH, [SDV.IDA] Life Sciences [q-bio]/Food engineering, Middle Aged, Biological Sciences, 16. Peace & justice, Sensory Systems, 3. Good health, Smell, GCCR Group Author, ddc:540, Smell loss, Female, Original Article, medicine.symptom, Corrigendum, Coronavirus Infections, olfaction, Adult, somatosensation, medicine.medical_specialty, 663/664, Coronavirus disease 2019 (COVID-19), OLFACTORY DISORDERS, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), media_common.quotation_subject, Pneumonia, Viral, head and neck surgery, Aged, Betacoronavirus, COVID-19, Humans, Pandemics, SARS-CoV-2, Self Report, Somatosensory Disorders, Young Adult, Anosmia, Sensory system, Olfaction, 03 medical and health sciences, Chemesthesis, Physiology (medical), Perception, medicine, Neurology & Neurosurgery, Behaviour Change and Well-being, business.industry, R-PACKAGE, 3112 Neurosciences, Pneumonia, Parosmia, COMPONENT, Smagssans, [SDV.AEN] Life Sciences [q-bio]/Food and Nutrition, Sensoriek en eetgedrag, chemistry, Lugtetab, business, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, 030217 neurology & neurosurgery, Lugtesans
Abstract

Correction: Chemical Senses, Volume 46, 2021, bjab050, https://doi.org/10.1093/chemse/bjab050 Published: 08 December 2021 Recent anecdotal and scientific reports have provided evidence of a link between COVID-19 and chemosensory impairments, such as anosmia. However, these reports have downplayed or failed to distinguish potential effects on taste, ignored chemesthesis, and generally lacked quantitative measurements. Here, we report the development, implementation, and initial results of a multilingual, international questionnaire to assess self-reported quantity and quality of perception in 3 distinct chemosensory modalities (smell, taste, and chemesthesis) before and during COVID-19. In the first 11 days after questionnaire launch, 4039 participants (2913 women, 1118 men, and 8 others, aged 19-79) reported a COVID-19 diagnosis either via laboratory tests or clinical assessment. Importantly, smell, taste, and chemesthetic function were each significantly reduced compared to their status before the disease. Difference scores (maximum possible change +/- 100) revealed a mean reduction of smell (-79.7 +/- 28.7, mean +/- standard deviation), taste (-69.0 +/- 32.6), and chemesthetic (-37.3 +/- 36.2) function during COVID-19. Qualitative changes in olfactory ability (parosmia and phantosmia) were relatively rare and correlated with smell loss. Importantly, perceived nasal obstruction did not account for smell loss. Furthermore, chemosensory impairments were similar between participants in the laboratory test and clinical assessment groups. These results show that COVID-19-associated chemosensory impairment is not limited to smell but also affects taste and chemesthesis.The multimodal impact of COVID-19 and the lack of perceived nasal obstruction suggest that severe acute respiratory syndrome coronavirus strain 2 (SARS-CoV-2) infection may disrupt sensory-neural mechanisms.

Published
2020

8. Distinct actin-dependent nanoscale assemblies underlie the dynamic and hierarchical organization of E-cadherin

Author

Girish R Kale, Rumamol Chandran, Thomas Lecuit, Satyajit Mayor, Jean-Marc Philippe, Tata Institute of Fundamental Research [Bangalore], Manipal academy of Higher Education, Institut de Biologie du Développement de Marseille (IBDM), Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Centre National de la Recherche Scientifique (CNRS), Collège de France - Chaire Dynamiques du vivant, Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Centre National de la Recherche Scientifique (CNRS), and ANR-11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011)

Subjects
0301 basic medicine, [SDV]Life Sciences [q-bio], Morphogenesis, Biology, General Biochemistry, Genetics and Molecular Biology, Article, Nanoclusters, Adherens junction, 03 medical and health sciences, 0302 clinical medicine, Cell Adhesion, Animals, Cell adhesion, Actin, 030304 developmental biology, 0303 health sciences, Cadherin, Chemistry, Actomyosin, Adhesion, Cadherins, Transmembrane protein, Actins, 030104 developmental biology, Ectodomain, Biophysics, Drosophila, Ectopic expression, General Agricultural and Biological Sciences, 030217 neurology & neurosurgery
Abstract

SUMMARYIntercellular adhesion mediated by E-cadherin is pivotal in maintaining epithelial tissue integrity and for tissue morphogenesis. Adhesion requires homophilic interactions between extracellular domains of E-cadherin molecules from neighboring cells. The interaction of its cytoplasmic domains with the cortical acto-myosin network, appears to strengthen adhesion, although, it is unclear how cortical actin affects the organization and function of E-cadherin dynamically. Here we use the ectopic expression ofDrosophilaE-cadherin (E-cad) in larval hemocytes, which lack endogenous E-cad, to recapitulate functional cell-cell junctions in a convenient model system. We used fluorescence emission anisotropy-based microscopy and Fluorescence Correlation Spectroscopy (FCS) to probe the nanoscale organization of E-cad. We find that E-cad at cell-cell junctions in hemocytes exhibits a clusteredtrans-paired organization, similar to that reported for the adherens junction in the developing embryonic epithelial tissue. Further, we find that extra-junctional E-cad is also organized as relatively immobile nanoclusters as well as diffusive and more loosely packed oligomers and monomers. These oligomers are promoted bycis-interactions of the ectodomain and, strikingly, their growth is constantly counteracted by cortical actomyosin. Oligomers in turn assist in generating nanoclusters that are stabilized by cortical acto-myosin. Thus, actin remodels oligomers and stabilizes nanoclusters, revealing a requirement for actin in the dynamic organization of E-cad at the nanoscale. This dynamic organization is also present at cell-cell contacts (junction), and its disruption affects junctional integrity in the hemocyte system, as well as in the embryo. Our observations uncover a hierarchical mechanism for the nanoscale organization of E-cad, which is necessary for dynamic adhesion and maintaining junctional integrity in the face of extensive remodeling.

Published
2021

9. A Bit of Nondeterminism Makes Pushdown Automata Expressive and Succinct

Author

Guha, Shibashis, Jecker, Ismaël, Lehtinen, Karoliina, Zimmermann, Martin, Aix Marseille Université (AMU), Université de Toulon (UTLN), Centre National de la Recherche Scientifique (CNRS), Tata Institute of Fundamental Research [Bangalore], Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria), Laboratoire d'Informatique et Systèmes (LIS), Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Modélisation et Vérification (MOVE), Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), University of Liverpool, Filippo Bonchi, and Simon J. Puglisi

Subjects
FOS: Computer and information sciences, Synthesis, Computer Science - Logic in Computer Science, Formal Languages and Automata Theory (cs.FL), Theory of computation → Formal languages and automata theory, [INFO]Computer Science [cs], Computer Science - Formal Languages and Automata Theory, Pushdown Automata, Succintness, Good-for-games, Logic in Computer Science (cs.LO)
Abstract

We study the expressiveness and succinctness of good-for-games pushdown automata (GFG-PDA) over finite words, that is, pushdown automata whose nondeterminism can be resolved based on the run constructed so far, but independently of the remainder of the input word. We prove that GFG-PDA recognise more languages than deterministic PDA (DPDA) but not all context-free languages (CFL). This class is orthogonal to unambiguous CFL. We further show that GFG-PDA can be exponentially more succinct than DPDA, while PDA can be double-exponentially more succinct than GFG-PDA. We also study GFGness in visibly pushdown automata (VPA), which enjoy better closure properties than PDA, and for which we show GFGness to be ExpTime-complete. GFG-VPA can be exponentially more succinct than deterministic VPA, while VPA can be exponentially more succinct than GFG-VPA. Both of these lower bounds are tight. Finally, we study the complexity of resolving nondeterminism in GFG-PDA. Every GFG-PDA has a positional resolver, a function that resolves nondeterminism and that is only dependant on the current configuration. Pushdown transducers are sufficient to implement the resolvers of GFG-VPA, but not those of GFG-PDA. GFG-PDA with finite-state resolvers are determinisable., LIPIcs, Vol. 202, 46th International Symposium on Mathematical Foundations of Computer Science (MFCS 2021), pages 53:1-53:20

Published
2021

10. Editorial: The Second Intercontinental NMR Conference ICONS2021

Author

Daniel Abergel, Konstantin L. Ivanov, Gerd Buntkowsky, Perunthiruthy K. Madhu, Laboratoire des biomolécules (LBM UMR 7203), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Chimie Moléculaire de Paris Centre (FR 2769), Institut de Chimie du CNRS (INC)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Technical University Darmstadt (TU), Tata Institute of Fundamental Research, Gestionnaire, Hal Sorbonne Université, Chimie Moléculaire de Paris Centre (FR 2769), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Technische Universität Darmstadt - Technical University of Darmstadt (TU Darmstadt), and Tata Institute of Fundamental Research [Bangalore]

Subjects
Engineering, business.industry, [SDV]Life Sciences [q-bio], 010402 general chemistry, 01 natural sciences, Data science, Atomic and Molecular Physics, and Optics, 030218 nuclear medicine & medical imaging, 0104 chemical sciences, [SDV] Life Sciences [q-bio], 03 medical and health sciences, 0302 clinical medicine, Editorial, business, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2021

11. A Test of the Cosmological Principle with Quasars

Author

Sebastian von Hausegger, M. Rameez, Roya Mohayaee, Subir Sarkar, Nathan J. Secrest, Jacques Colin, U.S. Naval Observatory, Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique (Inria), Institut d'Astrophysique de Paris (IAP), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Rudolf Peierls Center for Theoretical Physics, University of Oxford [Oxford], Department of High Energy Physics, Tata Institute of Fundamental Research, Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Structurer des formes géométriques (PIXEL), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Department of Algorithms, Computation, Image and Geometry (LORIA - ALGO), Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), and Tata Institute of Fundamental Research [Bangalore]

Subjects
cosmological model, Active galactic nucleus, Cosmology and Nongalactic Astrophysics (astro-ph.CO), 010504 meteorology & atmospheric sciences, statistical analysis: confidence limit, Cosmic microwave background, FOS: Physical sciences, Astrophysics, General Relativity and Quantum Cosmology (gr-qc), Astrophysics::Cosmology and Extragalactic Astrophysics, cosmic background radiation, anisotropy, 01 natural sciences, Cosmology, General Relativity and Quantum Cosmology, High Energy Physics - Phenomenology (hep-ph), Observational cosmology, 0103 physical sciences, quasar, angular distribution, AGN, 010303 astronomy & astrophysics, Astrophysics::Galaxy Astrophysics, 0105 earth and related environmental sciences, Physics, Infrared astronomy, Cosmological principle, Computer Science::Information Retrieval, Astrophysics::Instrumentation and Methods for Astrophysics, Astronomy and Astrophysics, Quasar, flux, Dipole, High Energy Physics - Phenomenology, Space and Planetary Science, kinematics, cryogenics, infrared, galaxy, [PHYS.ASTR]Physics [physics]/Astrophysics [astro-ph], dipole, Astrophysics - Cosmology and Nongalactic Astrophysics, experimental results
Abstract

We study the large-scale anisotropy of the Universe by measuring the dipole in the angular distribution of a flux-limited, all-sky sample of 1.36 million quasars observed by the Wide-field Infrared Survey Explorer (WISE). This sample is derived from the new CatWISE2020 catalog, which contains deep photometric measurements at 3.4 and 4.6 $\mu$m from the cryogenic, post-cryogenic, and reactivation phases of the WISE mission. While the direction of the dipole in the quasar sky is similar to that of the cosmic microwave background (CMB), its amplitude is over twice as large as expected, rejecting the canonical, exclusively kinematic interpretation of the CMB dipole with a p-value of $5\times10^{-7}$ ($4.9\sigma$ for a normal distribution, one-sided), the highest significance achieved to date in such studies. Our results are in conflict with the cosmological principle, a foundational assumption of the concordance $\Lambda$CDM model., Comment: 8 pages, 4 figures, accepted for publication in ApJ Letters. Code and data available at https://doi.org/10.5281/zenodo.4431089

Published
2021

12. Intact in situ Preparation of the Drosophila melanogaster Lymph Gland for a Comprehensive Analysis of Larval Hematopoiesis

Author

Diana Rodrigues, Lucas Waltzer, K. VijayRaghavan, Maneesha S. Inamdar, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Tata Institute of Fundamental Research [Bangalore], Génétique, Reproduction et Développement (GReD), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), and Waltzer, Lucas

Subjects
Strategy and Management, Spleen, Biology, [SDV.IMM.II]Life Sciences [q-bio]/Immunology/Innate immunity, Industrial and Manufacturing Engineering, Blood progenitor, Posterior lobes, [SDV.BDD] Life Sciences [q-bio]/Development Biology, medicine, Progenitor cell, [SDV.BDD]Life Sciences [q-bio]/Development Biology, [SDV.IMM.II] Life Sciences [q-bio]/Immunology/Innate immunity, Progenitor, Drosophila hematopoiesis, Tertiary lobes, Mechanical Engineering, Dissection, fungi, Metals and Alloys, biology.organism_classification, Phenotype, Cell biology, Haematopoiesis, medicine.anatomical_structure, Complete larval lymph gland, Bone marrow, Secondary lobes, Drosophila melanogaster, Developmental biology
Abstract

International audience; Blood cells have a limited lifespan and are replenished by a small number of hematopoietic stem and progenitor cells (HSPCs). Adult vertebrate hematopoiesis occurs in the bone marrow, liver, and spleen, rendering a comprehensive analysis of the entire HSPC pool nearly impossible. The Drosophila blood system is well studied and has developmental, molecular, and functional parallels with that of vertebrates. Unlike vertebrates, post-embryonic hematopoiesis in Drosophila is essentially restricted to the larval lymph gland (LG), a multi-lobed organ that flanks the dorsal vessel. Because the anterior-most or primary lobes of the LG are easy to dissect out, their cellular and molecular characteristics have been studied in considerable detail. The 2-3 pairs of posterior lobes are more delicate and fragile and have largely been ignored. However, posterior lobes harbor a significant blood progenitor pool, and several hematopoietic mutants show differences in phenotype between the anterior and posterior lobes. Hence, a comprehensive analysis of the LG is important for a thorough understanding of Drosophila hematopoiesis. Most studies focus on isolating the primary lobes by methods that generally dislodge and damage other lobes. To obtain preparations of the whole LG, including intact posterior lobes, here we provide a detailed protocol for larval fillet dissection. This allows accessing and analyzing complete LG lobes, along with dorsal vessel and pericardial cells. We demonstrate that tissue architecture and integrity is maintained and provide methods for quantitative analysis. This protocol can be used to quickly and effectively isolate complete LGs from first instar larval to pupal stages and can be implemented with ease.

Published
2021

13. Azide-Coordination in Homometallic Dinuclear Lanthanide(III) Complexes Containing Nonequivalent Lanthanide Metal Ions: Zero-Field SMM Behavior in the Dysprosium Analogue

Author

Sourav Biswas, Pankaj Kalita, Olivier Cador, Abinash Swain, Pawan Kumar, Vierandra Kumar, Gopalan Rajaraman, Jessica Flores Gonzalez, Vadapalli Chandrasekhar, Joydev Acharya, Fabrice Pointillart, Indian Institute of Technology Kanpur (IIT Kanpur), Indian Institute of Technology Bombay (IIT Bombay), Tata Institute of Fundamental Research, Institut des Sciences Chimiques de Rennes (ISCR), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), We thank the Department of Science and Technology (DST), India, the CNRS, Université de Rennes 1, the European Commission through the ERC-CoG 725184 MULTIPROSMM (Project No. 725184) for financial support, and also support for the Single Crystal CCD X-ray Diffractometer facility at IIT-Kanpur. V.C. is grateful to the DST for a J. C. Bose fellowship. P.K. and A.S. thank the University Grants Commission (UGC), India for Senior Research Fellowships. G.R. acknowledges DST/SERB for funding (Nos. CRG/2018/000430, DST/SJF/CSA-03/2018-10, SB/SJF/2019-20/12). We sincerely thank Mr. Prakash Nayak, NISER, Bhubanswar, Odisha, India, for the PXRD measurements., European Project: 725184,H2020-EU.1.1. - EXCELLENT SCIENCE - European Research Council (ERC),MULTIPROSMM(2017), Tata Institute of Fundamental Research [Bangalore], Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Ions, Lanthanide, Azides, Schiff base, 010405 organic chemistry, Chemistry, Ligand, Metal ions in aqueous solution, Ab initio, [CHIM.INOR]Chemical Sciences/Inorganic chemistry, Ligands, 010402 general chemistry, 01 natural sciences, 0104 chemical sciences, Inorganic Chemistry, chemistry.chemical_compound, Crystallography, Deprotonation, Magnetic properties, Lanthanides, [CHIM]Chemical Sciences, Density functional theory, Azide, Physical and Theoretical Chemistry
Abstract

International audience; A series of homometallic dinuclear lanthanide complexes containing nonequivalent lanthanide metal centers [Ln(2)(LH(2))(LH)(CH(3)OH)(N(3))]·xMeOH·yH(2)O [1, Ln = Dy(III), x = 0, y = 2; 2, Ln = Tb(III), x = 1, y = 1] have been synthesized [LH(4) = 6-((bis(2-hydroxyethyl)amino)-N’-(2-hydroxybenzylidene)picolinohydrazide] and characterized. The dinuclear assembly contains two different types of nine-coordinated lanthanide centers, because the nonequivalent binding of the azide co-ligand as well as the varying coordination of the deprotonated Schiff base ligand. Detailed magnetic studies have been performed on the complexes 1 and 2. Complex 1 and its diluted analogue (1(5%)) are zero-field SMMs with effective energy barriers (U(eff)) of magnetization reversal equal to 59(3) K and 66(3) K and relaxation times of τ(0) = 10(4) × 10(-6) s and 10(4) × 10(-8) s, respectively. On the other hand, complex 2 shows a field-induced SMM behavior. Combined ab initio and density functional theory calculations were performed to explain the experimental findings and to unravel the nature of the magnetic anisotropy, exchange-coupled spectra, and magnetic exchange interactions between the two lanthanide centers.

Published
2021
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14. The best COVID-19 predictor is recent smell loss: a cross-sectional study

Author

Gerkin, Richard, Ohla, Kathrin, Veldhuizen, Maria Geraldine, Joseph, Paule, Kelly, Christine, Bakke, Alyssa, Steele, Kimberley, Pellegrino, Robert, Pepino, Marta, Bouysset, Cédric, Soler, Graciela, Pereda-Loth, Veronica, Dibattista, Michele, Cooper, Keiland, Croijmans, Ilja, Di Pizio, Antonella, Ozdener, M. Hakan, D'Errico, Anna, Fischmeister, Florian Ph.S, Bock, María Adelaida, Domínguez, Paloma Paloma, Yanık, Hüseyin, Boesveldt, Sanne, de Groot, Jasper, Dinnella, Caterina, Freiherr, Jessica, Laktionova, Tatiana, Mariño, Sajidxa, Monteleone, Erminio, Nunez-Parra, Alexia, Abdulrahman, Olagunju, Ritchie, Marina, Thomas-Danguin, Thierry, Walsh-Messinger, Julie, Al Abri, Rashid, Alizadeh, Rafieh, Bignon, Emmanuelle, Cantone, Elena, Cecchini, Maria Paola, Chen, Jingguo, Guàrdia, Maria Dolors, Hoover, Kara, Karni, Noam, Navarro, Marta, Nolden, Alissa, Mazal, Patricia Portillo, Rowan, Nicholas, Sarabi-Jamab, Atiye, Archer, Nicholas, Chen, Ben, Di Valerio, Elizabeth, Feeney, Emma, Frasnelli, Johannes, Hannum, Mackenzie, Hopkins, Claire, Klein, Hadar, Mignot, Coralie, Mucignat, Carla, Ning, Yuping, Ozturk, Elif, Peng, Mei, Saatci, Ozlem, Sell, Elizabeth, Yan, Carol, Alfaro, Raul, Cecchetto, Cinzia, Coureaud, Gérard, Herriman, Riley, Justice, Jeb, Kaushik, Pavan Kumar, Koyama, Sachiko, Overdevest, Jonathan, Pirastu, Nicola, Ramirez, Vicente, Roberts, S. Craig, Smith, Barry, Cao, Hongyuan, Wang, Hong, Balungwe, Patrick, Baguma, Marius, Veldhuizen, Maria, Farruggia, Michael, Pizio, Antonella, Hakan Ozdener, M, Fjaeldstad, Alexander, Lin, Cailu, Sandell, Mari, Singh, Preet, Brindha, V. Evelyn, Olsson, Shannon, Saraiva, Luis, Ahuja, Gaurav, Alwashahi, Mohammed, Bhutani, Surabhi, Fornazieri, Marco, Golebiowski, Jérôme, Hwang, Liang-Dar, Öztürk, Lina, Roura, Eugeni, Spinelli, Sara, Whitcroft, Katherine, Faraji, Farhoud, Fischmeister, Florian, Heinbockel, Thomas, Hsieh, Julien, Huart, Caroline, Konstantinidis, Iordanis, Menini, Anna, Morini, Gabriella, Olofsson, Jonas, Philpott, Carl, Pierron, Denis, Shields, Vonnie, Voznessenskaya, Vera, Albayay, Javier, Altundag, Aytug, Bensafi, Moustafa, Bock, María, Calcinoni, Orietta, Fredborg, William, Laudamiel, Christophe, Lim, Juyun, Lundström, Johan, Macchi, Alberto, Meyer, Pablo, Moein, Shima, Santamaría, Enrique, Sengupta, Debarka, Rohlfs Dominguez, Paloma, Yanik, Hüseyin, Group, GCCR, Hummel, Thomas, Hayes, John, Reed, Danielle, Niv, Masha, Munger, Steven, Parma, Valentina, Arizona State University [Tempe] (ASU), Institute of Neuroscience and Medicine [Jülich] (INM-1), Mersin University, National Institutes of Health [Bethesda] (NIH), AbScent, Pennsylvania State University (Penn State), Penn State System, National Institute of Diabetes and Digestive and Kidney Diseases [Bethesda], Yale University [New Haven], Tennessee State University, University of Illinois at Urbana-Champaign [Urbana], University of Illinois System, Institut de Chimie de Nice (ICN), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Buenos Aires University and GEOG (Grupo de Estudio de Olfato y Gusto), Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), University of Bari Aldo Moro (UNIBA), University of California [Irvine] (UCI), University of California, Utrecht University [Utrecht], Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Monell Chemical Senses Center, Regional Hospital West Jutland [Denmark], University of Helsinki, University of Oslo (UiO), Karunya University, Tata Institute for Fundamental Research (TIFR), Research at Sidra Medicine Research Branch [Doha, Qatar], Indraprastha Institute of Information Technology [New Delhi] (IIIT-Delhi), Sultan Qaboos University (SQU), San Diego State University (SDSU), Goethe-University Frankfurt am Main, State University of Londrina = Universidade Estadual de Londrina, University of Queensland [Brisbane], Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), University College of London [London] (UCL), University of Graz, Howard University, Geneva University Hospital (HUG), Cliniques Universitaires Saint-Luc [Bruxelles], Aristotle University of Thessaloniki, Scuola Internazionale Superiore di Studi Avanzati / International School for Advanced Studies (SISSA / ISAS), University of Gastronomic Sciences of Pollenzo (UNISG), Stockholm University, University of East Anglia [Norwich] (UEA), Towson University [Towson, MD, United States], University of Maryland System, A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences [Moscow] (RAS), Universita degli Studi di Padova, Biruni University, Centre de recherche en neurosciences de Lyon (CRNL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet [Saint-Étienne] (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Hospital General de Barrio Obrero [Asunción, Paraguay] (Public Hospital Barrio Obrero ), Private practice [Milan], DreamAir Llc, Oregon State University (OSU), Cancer Center Karolinska [Karolinska Institutet] (CCK), Karolinska Institutet [Stockholm], University of Insubria, Varese, Computational Biology Center (IBM T.J. Watson Research Center), IBM, Institute for Research in Fundamental Sciences [Tehran] (IPM), Instituto de Investigación Sanitaria de Navarra [Pamplona, Spain] (IdiSNA), University of Extremadura, Technische Universität Dresden = Dresden University of Technology (TU Dresden), The Hebrew University of Jerusalem (HUJ), University of Florida [Gainesville] (UF), Temple University [Philadelphia], Pennsylvania Commonwealth System of Higher Education (PCSHE), Non-byline authors (to be listed as collaborators in PubMed under the GCCR Group Author): Sanne Boesveldt, Jasper H.B. de Groot, Caterina Dinnella, Jessica Freiherr, Tatiana Laktionova, Sajidxa Mariño, Erminio Monteleone, Alexia Nunez-Parra, Olagunju Abdulrahman, Marina Ritchie, Thierry Thomas-Danguin, Julie Walsh-Messinger, Rashid Al Abri, Rafieh Alizadeh, Emmanuelle Bignon, Elena Cantone, Maria Paola Cecchini, Jingguo Chen, Maria Dolors Guàrdia, Kara C. Hoover, Noam Karni, Marta Navarro, Alissa A. Nolden, Patricia Portillo Mazal, Nicholas R. Rowan, Atiye SarabiJamab, Nicholas S. Archer, Ben Chen, Elizabeth A. Di Valerio, Emma L. Feeney, Johannes Frasnelli, Mackenzie E. Hannum, Claire Hopkins, Hadar Klein, Coralie Mignot, Carla Mucignat, Yuping Ning, Elif E. Ozturk, Mei Peng, Ozlem Saatci, Elizabeth A. Sell, Carol H. Yan, Raul Alfaro, Cinzia Cecchetto, Gérard Coureaud, Riley D. Herriman, Jeb M. Justice, Pavan Kumar Kaushik, Sachiko Koyama, Jonathan B. Overdevest, Nicola Pirastu, Vicente A. Ramirez, S. Craig Roberts, Barry C. Smith, Hongyuan Cao, Hong Wang, Patrick Balungwe Birindwa, Marius Baguma, Karl-Franzens-Universität [Graz, Autriche], Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association, The Pennsylvania State University, University of Tennessee, University of Buenos Aires [Argentina], Università degli studi di Bari Aldo Moro (UNIBA), Goethe University of Frankfurt am Main, Wageningen University and Research [Wageningen] (WUR), Radboud university [Nijmegen], Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), A.N. Severtsov Institute of Ecology and Evolution RAS, 119071, Russia., RespiraLibre - Centro de Otorrinolaringología, Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Partenaires INRAE, Universidad de Chile = University of Chile [Santiago] (UCHILE), Federal University of Technology of Akure (FUTA), Centre des Sciences du Goût et de l'Alimentation [Dijon] (CSGA), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Bourgogne Franche-Comté [COMUE] (UBFC), University of Dayton, Iran University of Medical Sciences, University of Naples Federico II, University of Verona (UNIVR), Head and Neck Surgery, Hospital of Xi'an Jiaotong University, Institute of Agrifood Research and Technology (IRTA), University of Alaska [Fairbanks] (UAF), Hadassah Hebrew University Medical Center [Jerusalem], University of Southern Queensland (USQ), University of Massachusetts, Instituto Universitario del Hospital Italiano [Buenos Aires, Argentina], Johns Hopkins University School of Medicine [Baltimore], Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), The First Affiliated Hospital of Guangzhou Medical University (GMU), University College Dublin [Dublin] (UCD), Université du Québec à Trois-Rivières (UQTR), Guy's and St Thomas' Hospitals, University of Padova [Padova, Italy], Kilis Yedi Aralik University, University of Otago [Dunedin, Nouvelle-Zélande], Sancaktepe Education and Research Hospital, Hospital of the University of Pennsylvania (HUP), Perelman School of Medicine, University of Pennsylvania [Philadelphia]-University of Pennsylvania [Philadelphia], UC San Diego Health, University ofFlorida, Tata Institute of Fundamental Research, Indiana University [Bloomington], Indiana University System, Columbia University Irving Medical Center (CUIMC), University of Edinburgh, University of California [Merced], University of Stirling, University of London [London], Florida State University [Panama City], Université catholique de Bukavu, Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Karunya Institute of Technology and Sciences, Sidra Medicine, School of Exercise and Nutritional Sciences, Howard University College of Medicine, Geneva University Hospitals, Geneva University , Geneva , Switzerland., CHU Genève, General Hospital Papageorgiou, University of Toulouse, University of Padova, Lyon Neuroscience Research center, IBM T.J. Watson Research Center, Navarrabiomed-IdiSNA, Temple University, Julien, Sabine, Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Universitad de Buenos Aires = University of Buenos Aires [Argentina], Università degli studi di Bari Aldo Moro = University of Bari Aldo Moro (UNIBA), University of California [Irvine] (UC Irvine), University of California (UC), Karl-Franzens-Universität Graz, Universidad de Extremadura - University of Extremadura (UEX), Radboud University [Nijmegen], Università degli Studi di Firenze = University of Florence (UniFI), University of Naples Federico II = Università degli studi di Napoli Federico II, Università degli studi di Verona = University of Verona (UNIVR), Institut de Recerca i Tecnologia Agroalimentàries = Institute of Agrifood Research and Technology (IRTA), Università degli Studi di Padova = University of Padua (Unipd), University of Pennsylvania-University of Pennsylvania, School of Medicine [Univ California San Diego] (UC San Diego), University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC)-University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC), Centre de recherche en neurosciences de Lyon - Lyon Neuroscience Research Center (CRNL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Tata Institute of Fundamental Research [Bangalore], University of California [Merced] (UC Merced), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Sidra Medicine [Doha, Qatar], Universitá degli Studi dell’Insubria = University of Insubria [Varese] (Uninsubria), and Universitá degli Studi dell’Insubria

Subjects
Adult, Male, medicine.medical_specialty, Coronavirus disease 2019 (COVID-19), Cross-sectional study, Visual analogue scale, Anosmia, Audiology, Logistic regression, AcademicSubjects/SCI01180, Article, Odds, 03 medical and health sciences, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Hyposmia, Humans, Medicine, [SDV.MHEP.OS]Life Sciences [q-bio]/Human health and pathology/Sensory Organs, 030223 otorhinolaryngology, SARS-CoV-2, business.industry, [SCCO.NEUR]Cognitive science/Neuroscience, COVID-19, Middle Aged, Prognosis, Smell, [SDV.AEN] Life Sciences [q-bio]/Food and Nutrition, Cross-Sectional Studies, [SDV.MHEP.OS] Life Sciences [q-bio]/Human health and pathology/Sensory Organs, Smell loss, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Female, Original Article, Self Report, medicine.symptom, business, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, 030217 neurology & neurosurgery, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

BackgroundCOVID-19 has heterogeneous manifestations, though one of the most common symptoms is a sudden loss of smell (anosmia or hyposmia). We investigated whether olfactory loss is a reliable predictor of COVID-19.MethodsThis preregistered, cross-sectional study used a crowdsourced questionnaire in 23 languages to assess symptoms in individuals self-reporting recent respiratory illness. We quantified changes in chemosensory abilities during the course of the respiratory illness using 0-100 visual analog scales (VAS) for participants reporting a positive (C19+; n=4148) or negative (C19-; n=546) COVID-19 laboratory test outcome. Logistic regression models identified singular and cumulative predictors of COVID-19 status and post-COVID-19 olfactory recovery.ResultsBoth C19+ and C19-groups exhibited smell loss, but it was significantly larger in C19+ participants (mean±SD, C19+: -82.5±27.2 points; C19-: -59.8±37.7). Smell loss during illness was the best predictor of COVID-19 in both single and cumulative feature models (ROC AUC=0.72), with additional features providing negligible model improvement. VAS ratings of smell loss were more predictive than binary chemosensory yes/no-questions or other cardinal symptoms, such as fever or cough. Olfactory recovery within 40 days was reported for ∼50% of participants and was best predicted by time since illness onset.ConclusionsAs smell loss is the best predictor of COVID-19, we developed the ODoR-19 tool, a 0-10 scale to screen for recent olfactory loss. Numeric ratings ≤2 indicate high odds of symptomatic COVID-19 (4

Published
2020

15. Variable interplay of UV-induced DNA damage and repair at transcription factor binding sites

Author

Radhakrishnan Sabarinathan, Abel Gonzalez-Perez, Nuria Lopez-Bigas, Joan Frigola, Institut Català de la Salut, [Frigola J] Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain. Thoracic Tumors & Head and Neck Cancer Group, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain. [Sabarinathan R] National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India. [Gonzalez-Perez A] Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain. Research Program on Biomedical Informatics, Universitat Pompeu Fabra,Barcelona, Catalonia, Spain. [Lopez-Bigas N] Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain. Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain. Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain, and Vall d'Hebron Barcelona Hospital Campus

Subjects
Mutation rate, Skin Neoplasms, Neoplasms::Neoplasms by Histologic Type::Neoplasms::Neoplasms by Histologic Type::Neoplasms::Neoplasms by Histologic Type::Nevi and Melanomas::Melanoma [DISEASES], DNA Repair, AcademicSubjects/SCI00010, Ultraviolet Rays, DNA repair, DNA damage, Radiació - Efectes fisiològics, Genome Integrity, Repair and Replication, Biology, medicine.disease_cause, Other subheadings::/radiation effects [Other subheadings], 03 medical and health sciences, Genetic Phenomena::DNA Damage [PHENOMENA AND PROCESSES], 0302 clinical medicine, Genetics, medicine, Humans, Binding site, Transcription factor, Melanoma, Otros calificadores::/efectos de la radiación [Otros calificadores], 030304 developmental biology, 0303 health sciences, Mutation, Binding Sites, Whole Genome Sequencing, Mutagenesis, ADN - Dany, Chromosome Mapping, DNA, Neoplasm, fenómenos genéticos::daño del ADN [FENÓMENOS Y PROCESOS], 3. Good health, Cell biology, DNA binding site, Pyrimidine Dimers, neoplasias::neoplasias por tipo histológico::neoplasias::neoplasias por tipo histológico::neoplasias::neoplasias por tipo histológico::nevos y melanomas::melanoma [ENFERMEDADES], 030217 neurology & neurosurgery, DNA Damage, Transcription Factors
Abstract

Llocs d’unió; Dany en l'ADN; Factor de transcripció Sitios de unión; Daño en el ADN; Factor de transcripcion Binding sites; Dna damage; Transcription factor An abnormally high rate of UV-light related mutations appears at transcription factor binding sites (TFBS) across melanomas. The binding of transcription factors (TFs) to the DNA impairs the repair of UV-induced lesions and certain TFs have been shown to increase the rate of generation of these lesions at their binding sites. However, the precise contribution of these two elements to the increase in mutation rate at TFBS in these malignant cells is not understood. Here, exploiting nucleotide-resolution data, we computed the rate of formation and repair of UV-lesions within the binding sites of TFs of different families. We observed, at certain dipyrimidine positions within the binding site of TFs in the Tryptophan Cluster family, an increased rate of formation of UV-induced lesions, corroborating previous studies. Nevertheless, across most families of TFs, the observed increased mutation rate within the entire DNA region covered by the protein results from the decreased repair efficiency. While the rate of mutations across all TFBS does not agree with the amount of UV-induced lesions observed immediately after UV exposure, it strongly agrees with that observed after 48 h. This corroborates the determinant role of the impaired repair in the observed increase of mutation rate. N.L.-B. acknowledges funding from the European Research Council [consolidator grant 682398]; Spanish Ministry of Economy and Competitiveness [SAF2015-66084-R, MINECO/FEDER to U.E.]; IRB Barcelona is a recipient of a Severo Ochoa Centre of Excellence Award from the Spanish Ministry of Economy and Competitiveness (MINECO; Government of Spain) and is supported by CERCA (Generalitat de Catalunya); R.S. acknowledges funding support from the National Centre for Biological Sciences (NCBS-TIFR), Bangalore, India. Funding for open access charge: Spanish Ministry of Economy and Competitiveness.

Published
2020

16. Natural Selection beyond Life? A Workshop Report

Author

Christophe Malaterre, Etienne Rajon, Sylvain Charlat, Michael Lachmann, Maria Ferreira Ruiz, Nicolas Lartillot, Sandeep Krishna, Olivier Rivoire, Louis Le Sergeant d'Hendecourt, Zorana Zeravcic, Pierrick Bourrat, Matteo Smerlak, Thomas Heams, André Ariew, Philippe Huneman, Philippe Nghe, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), University of Missouri [Columbia] (Mizzou), University of Missouri System, The University of Sydney, Universität Bielefeld = Bielefeld University, Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut d'Histoire et de Philosophie des Sciences et des Techniques (IHPST), Université Paris 1 Panthéon-Sorbonne (UP1)-Centre National de la Recherche Scientifique (CNRS), Tata Institute of Fundamental Research [Bangalore], Santa Fe Institute, Physique des interactions ioniques et moléculaires (PIIM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Centre interuniversitaire de recherche sur la science et la technologie (CIRST), Université de Montréal (UdeM)-Université du Québec à Montréal = University of Québec in Montréal (UQAM), Chimie-Biologie-Innovation (UMR 8231) (CBI), Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Max Planck Institute for Mathematics in the Sciences (MPI-MiS), Max-Planck-Gesellschaft, Gulliver (UMR 7083), scientific committee of the 'Institut d'Etudes Scientifiques de Cargese' (IESC), 'Mission pour les Initiatives Transverses' (MITI) of the CNRS, 'Groupement de Recherche' Sapienv GDR CNRS 3770, Université Paris-Saclay-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Tata Institute of Fundamental Research, Université du Québec à Montréal = University of Québec in Montréal (UQAM)-Université de Montréal (UdeM), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), and Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris)

Subjects
individuality, Science, Physical system, Subject (philosophy), Context (language use), Variation (game tree), Biology, origins of life, General Biochemistry, Genetics and Molecular Biology, [SHS.HISPHILSO]Humanities and Social Sciences/History, Philosophy and Sociology of Sciences, 03 medical and health sciences, 0302 clinical medicine, Lead (geology), evolutionary, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, exobiology, 0303 health sciences, Natural selection, biology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], philosophy of biology, evolutionary biology, other, Paleontology, natural selection, levels of selection, Epistemology, Living systems, Philosophy of biology, Space and Planetary Science, Perspective, physics, 030217 neurology & neurosurgery
Abstract

Natural selection is commonly seen not just as an explanation for adaptive evolution, but as the inevitable consequence of “heritable variation in fitness among individuals”. Although it remains embedded in biological concepts, such a formalisation makes it tempting to explore whether this precondition may be met not only in life as we know it, but also in other physical systems. This would imply that these systems are subject to natural selection and may perhaps be investigated in a biological framework, where properties are typically examined in light of their putative functions. Here we relate the major questions that were debated during a three-day workshop[1] devoted to discussing whether natural selection may take place in non-living physical systems. We start this report with a brief overview of research fields dealing with “life-like” or “proto-biotic” systems, where mimicking evolution by natural selection in test tubes stands as a major objective. We contend the challenge may be as much conceptual as technical. Taking the problem from a physical angle, we then discuss the framework of dissipative structures. Although life is viewed in this context as a particular case within a larger ensemble of physical phenomena, this approach does not provide general principles from which natural selection could be derived. Turning back to evolutionary biology, we ask to what extent the most general formulations of the necessary conditions or signatures of natural selection may be applicable beyond biology. In our view, such a cross-disciplinary jump is in large part impeded by reliance on individuality as a central yet implicit and loosely defined concept. Overall, these discussions thus lead us to conjecture that understanding, in physico-chemical terms, how individuality emerges and how it can be recognised, will be essential in the search for instances of evolution by natural selection outside of living systems. [1] Natural Selection Beyond Life? Observing the physico-chemical world through Darwinian glasses; 12-15 November 2019 - Institut d'Etudes Scientifiques, Cargèse, France

Published
2021

17. Gene Regulation and Species-Specific Evolution of Free Flight Odor Tracking in Drosophila

Author

Benjamin Houot, Stéphane Fraichard, Jean-François Ferveur, Claude Everaerts, Nitesh Saxena, Laurie Cazalé-Debat, Sanjay P. Sane, Centre des Sciences du Goût et de l'Alimentation [Dijon] (CSGA), Centre National de la Recherche Scientifique (CNRS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB), Swedish University of Agricultural Sciences (SLU), Université Bourgogne Franche-Comté [COMUE] (UBFC), National Centre for Biological Sciences [TIFR] (NCBS), Tata Institute for Fundamental Research (TIFR), Centre National de la Recherche Scientifique (INSB) Burgundy Regional Council (PARI) Universite de Bourgogne ANR (Gustaile) CEFIPRA 5103-A CONICYT MEC 80140013, Centre des Sciences du Goût et de l'Alimentation [Dijon] ( CSGA ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS ), Evolution et Diversité Biologique ( EDB ), Institut de Recherche pour le Développement ( IRD ) -Université Paul Sabatier - Toulouse 3 ( UPS ) -Centre National de la Recherche Scientifique ( CNRS ), UMR 5548, Centre National de la Recherche Scientifique ( CNRS ), International Centre for Theoretical Sciences, Tata Institute of Fundamental Research, Bangalore, Tata Institute of Fundamental Research [Bombay] ( TIFR ), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Swedish University of Agricultural Sciences, and National Center for Biological Sciences, Tata Institute of Fundamental Research

Subjects
Fatty Acid Desaturases, Male, 0301 basic medicine, Fat body, melanogaster, coordination, D. buzzatii, consequences, Receptors, Odorant, Pheromones, D. suzukii, flies, Drosophila Proteins, Gene Regulatory Networks, fat body, Mating, Regulation of gene expression, biology, sex-pheromones, Anatomy, Biological Evolution, oenocyte, modulation, Drosophila, Female, Free flight, Zimbabwe, Genetic Speciation, system, D. virilis, Evolution, Molecular, 03 medical and health sciences, Sex Factors, Species Specificity, desaturase gene, Molecular evolution, desat1, expression, Genetics, Animals, Molecular Biology, Gene, Ecology, Evolution, Behavior and Systematics, [SDV.GEN]Life Sciences [q-bio]/Genetics, fungi, biology.organism_classification, 030104 developmental biology, Gene Expression Regulation, Odor, Evolutionary biology, Flight, Animal, sexual dimorphism, Odorants, [ SDV.GEN ] Life Sciences [q-bio]/Genetics
Abstract

Running title: flight evolution in Drosophila This is an invited contribution to the special issue on Genetics of Adaptation based on a symposium of the same name at the National Centre for Biological Sciences (TIFR, Bangalore, India) in November 2016; International audience; The flying ability of insects has coevolved with the development of organs necessary to take-off from the ground, generate, and modulate lift during flight in complex environments. Flight orientation to the appropriate food source and mating partner depends on the perception and integration of multiple chemical signals. We used a wind tunnel-based assay to investigate the natural and molecular evolution of free flight odor tracking in Drosophila. First, the comparison of female and male flies of several populations and species revealed substantial sex-, inter-, and intra-specific variations for distinct flight features. In these flies, we compared the molecular structure of desat1, a fast-evolving gene involved in multiple aspects of Drosophila pheromonal communication. We manipulated desat1 regulation and found that both neural and nonneural tissues affect distinct flight features. Together, our data suggest that desat1 is one of the genes involved in the evolution of free-flight odor tracking behaviors in Drosophila.

Published
2018

18. Large spontaneous exchange bias in a weak ferromagnet Pb6Ni9(TeO6)5

Author

Tanmoy Chakrabarty, B. Koteswararao, Binoy Krishna Hazra, Tathamay Basu, P. L. Paulose, S. Srinath, P. V. Srinivasarao, University of Hyderabad, Sri Venkateswara University, Tata Institute of Fundamental Research [Bangalore], Laboratoire de cristallographie et sciences des matériaux (CRISMAT), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche sur les Matériaux Avancés (IRMA), Normandie Université (NU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Rouen Normandie (UNIROUEN), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Acharya Nagarjuna University, Department of Science and Technology in India [IFA14-PH-92], Tata Inst Fundamental Res, AUTRES, École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), and Normandie Université (NU)-Institut de Chimie du CNRS (INC)

Subjects
Electronic properties and materials, Materials science, Science, FOS: Physical sciences, 02 engineering and technology, Dielectric, 01 natural sciences, Article, Magnetic properties and materials, 0103 physical sciences, [CHIM.CRIS]Chemical Sciences/Cristallography, [CHIM]Chemical Sciences, Author Correction, 010306 general physics, Condensed Matter - Materials Science, Multidisciplinary, Spins, Condensed matter physics, Doping, Materials Science (cond-mat.mtrl-sci), [CHIM.MATE]Chemical Sciences/Material chemistry, Coercivity, 021001 nanoscience & nanotechnology, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Exchange bias, Ferromagnetism, Isothermal magnetization, Medicine, 0210 nano-technology
Abstract

We report the magnetic and dielectric behavior of Pb6Ni9(TeO6)5, a new compound comprising the honeycomb-like layers of S=1 spins, through detailed structural, magnetic and dielectric investigation. An antiferromagnetic-type transition at 25 K (TN) with weak-ferromagnetic behavior is revealed. Interestingly, a large value of coercive field of 1.32 T at 2 K is observed. The isothermal magnetization after zero-field-cooled condition, it exhibits the presence of large spontaneous exchange bias (SEB) with a magnitude of 0.19 T at 2 K; which is rare in single bulk materials, especially without external doping. The value of |HEB| further enhances to 0.24 T under 16 T field-cooled condition, confirming the presence of large exchange bias in the material. In addition, the dielectric constant shows an anomaly at the onset of TN, indicating the presence of magnetodielectric coupling., 16 pages, 6 figures, 2 supplimentory figures, under revision of Scientific Reports

Published
2017

19. Complex nature of magnetic field induced ferroelectricity in GdCrTiO5

Author

Basu, T., Adroja, D. T., Kolb, F., von Nidda, H. -A. Krug, Ruff, A., Hemmida, M., Hillier, A. D., Telling, M., Sampathkumaran, E. V., Loidl, A., Krohns, S., Universität Augsburg [Augsburg], Tata Inst Fundamental Res, AUTRES, Laboratoire de Microélectronique et de Physique des Semiconducteurs (LaMIPS), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-NXP Semiconductors [France]-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU), ISIS Facility, STFC Rutherford Appleton Laboratory (RAL), Science and Technology Facilities Council (STFC)-Science and Technology Facilities Council (STFC), University of the Witwatersrand [Johannesburg] (WITS), ISIS, BMBF [ENREKON 03EK3015], DFG via the Transregional Collaborative Research Center [TRR 80], Tata Institute of Fundamental Research [Bangalore], Laboratoire de cristallographie et sciences des matériaux (CRISMAT), Normandie Université (NU)-Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche sur les Matériaux Avancés (IRMA), Normandie Université (NU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Rouen Normandie (UNIROUEN), and Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Condensed Matter - Materials Science, Ferroelectricity, Strongly Correlated Electrons (cond-mat.str-el), Multiferroics, Magnetism, Materials Science (cond-mat.mtrl-sci), FOS: Physical sciences, Magnetic insulators, [CHIM.MATE]Chemical Sciences/Material chemistry, SQUID, Transport techniques, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Muon spin relaxation & rotation, Susceptibility measurements, Condensed Matter - Strongly Correlated Electrons, Condensed Matter::Materials Science, Pyroelectricity, Magnetoelectric effect, Electron spin resonance, Magnetization measurements, [CHIM.CRIS]Chemical Sciences/Cristallography, [CHIM]Chemical Sciences, ddc:530, Condensed Matter::Strongly Correlated Electrons
Abstract

This work shows an unconventional route for spin-driven ferroelectricity originating from a metastable magnetic field-induced canting of chromium sublattice in the presence of gadolinium moments in GdCrTiO5 at low temperatures. Compared to the isostructural neodymium compound, significant differences of magnetism and magnetoelectric effects are seen. We present the results of thorough investigations of temperature and magnetic field dependent magnetization as well as ac and dc magnetic susceptibility. These bulk measurements are complemented by local-probe spectroscopy utilizing electron-spin resonance and muon-spin rotation/relaxation for probing the chromium moments. Ferroelectric order is inferred from pyro- and magnetocurrent measurements. GdCrTiO5 shows a pyrocurrent signal around 10 K, only if the system is cooled in an applied magnetic field exceeding 10 kOe. A distinct spin-driven ferroelectric order is revealed in this state for temperatures below 10 K, which can be switched by changing magnetic-field direction and the polarity of the electric field. But, the magnetic measurements reveal no clear signature of long-range magnetic ordering. The presence of such meta-magnetoelectric-type behaviour in the absence of any meta-magnetic behavior is rare in the literature. Our microscopic spectroscopy results indicate significant changes of the magnetic properties around 10 K. Probably there is an exchange frustration between Gd and Cr moments, which prevents long-range magnetic ordering at further high temperature. Below 10 K, weak magnetic ordering occurs by minimizing frustration due to lattice distortion, which helps in magnetodielectric coupling. However, the non-polar distortion attains appreciable values after application of magnetic fields above 10 kOe to break the spatial inversion symmetry, which creates ferroelectricity., accepted in PRB

Published
2017

20. Quantum dot-loaded monofunctionalized DNA icosahedra for single-particle tracking of endocytic pathways

Author

Ved Prakash, Chloé Grazon, Ludger Johannes, Prabal K. Maiti, Himanshu Joshi, Dhiraj Bhatia, Christian Wunder, Senthil Arumugam, Brice Nadal, Yamuna Krishnan, Benoit Dubertret, Valérie Chambon, Michel Nasilowski, Chimie biologique des membranes et ciblage thérapeutique (CBMCT - UMR 3666 / U1143), Centre National de la Recherche Scientifique (CNRS)-Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC), Université Paris sciences et lettres (PSL), Tata Institute of Fundamental Research, Laboratoire de Physique et d'Etude des Matériaux (UMR 8213) (LPEM), Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Indian Institute of Science, University of Chicago, NEXDOT, Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Tata Institute of Fundamental Research [Bangalore], Nexdot, and Grazon, Chloé

Subjects
Galectin 3, Endocytic cycle, 02 engineering and technology, Shiga Toxins, 01 natural sciences, chemistry.chemical_compound, Mice, [CHIM] Chemical Sciences, General Materials Science, Physics, [CHIM.MATE]Chemical Sciences/Material chemistry, 021001 nanoscience & nanotechnology, Condensed Matter Physics, Atomic and Molecular Physics, and Optics, Endocytosis, Molecular Imaging, 0210 nano-technology, Molecular probe, [CHIM.INOR] Chemical Sciences/Inorganic chemistry, [CHIM.POLY] Chemical Sciences/Polymers, Biomedical Engineering, Bioengineering, Nanotechnology, Endosomes, [CHIM.INOR]Chemical Sciences/Inorganic chemistry, 010402 general chemistry, Article, Cricetulus, Folic Acid, Dynamic light scattering, Microscopy, Electron, Transmission, Quantum Dots, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Animals, [CHIM]Chemical Sciences, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Electrical and Electronic Engineering, [CHIM.MATE] Chemical Sciences/Material chemistry, Ligand, technology, industry, and agriculture, DNA, Fibroblasts, equipment and supplies, Dynamic Light Scattering, 0104 chemical sciences, [CHIM.POLY]Chemical Sciences/Polymers, chemistry, Quantum dot, Surface modification, Biosensor
Abstract

International audience; Functionalization of quantum dots (QDs) with a single biomolecular tag using traditional approaches in bulk solution has met with limited success. DNA polyhedra consist of an internal void bounded by a well-defined three-dimensional structured surface. The void can house cargo and the surface can be functionalized with stoichiometric and spatial precision. Here, we show that monofunctionalized QDs can be realized by encapsulating QDs inside DNA icosahedra and functionalizing the DNA shell with an endocytic ligand. We deployed the DNA-encapsulated QDs for real-time imaging of three different endocytic ligands-folic acid, galectin-3 (Gal3) and the Shiga toxin B-subunit (STxB). Single-particle tracking of Gal3- or STxB-functionalized QD-loaded DNA icosahedra allows us to monitor compartmental dynamics along endocytic pathways. These DNA-encapsulated QDs, which bear a unique stoichiometry of endocytic ligands, represent a new class of molecular probes for quantitative imaging of endocytic receptor dynamics.

Published
2016

21. An integrated structural model of the DNA damage-responsive H3K4me3 binding WDR76:SPIN1 complex with the nucleosome.

Author

Liu X, Zhang Y, Wen Z, Hao Y, Banks CAS, Cesare J, Bhattacharya S, Arvindekar S, Lange JJ, Xie Y, Garcia BA, Slaughter BD, Unruh JR, Viswanath S, Florens L, Workman JL, and Washburn MP

Subjects
Humans, Protein Binding, Cell Cycle Proteins metabolism, Cell Cycle Proteins chemistry, Cell Cycle Proteins genetics, Carrier Proteins metabolism, Carrier Proteins chemistry, Models, Molecular, ATPases Associated with Diverse Cellular Activities, DNA Helicases, Histones metabolism, Histones chemistry, Nucleosomes metabolism, DNA Damage
Abstract

Serial capture affinity purification (SCAP) is a powerful method to isolate a specific protein complex. When combined with cross-linking mass spectrometry and computational approaches, one can build an integrated structural model of the isolated complex. Here, we applied SCAP to dissect a subpopulation of WDR76 in complex with SPIN1, a histone reader that recognizes trimethylated histone H3 lysine4 (H3K4me3). In contrast to a previous SCAP analysis of the SPIN1:SPINDOC complex, histones and the H3K4me3 mark were enriched with the WDR76:SPIN1 complex. Next, interaction network analysis of copurifying proteins and microscopy analysis revealed a potential role of the WDR76:SPIN1 complex in the DNA damage response. Since we detected 149 pairs of cross-links between WDR76, SPIN1, and histones, we then built an integrated structural model of the complex where SPIN1 recognized the H3K4me3 epigenetic mark while interacting with WDR76. Finally, we used the powerful Bayesian Integrative Modeling approach as implemented in the Integrative Modeling Platform to build a model of WDR76 and SPIN1 bound to the nucleosome., Competing Interests: Competing interests statement:The authors declare no competing interest.

Published
2024
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22. On the road to losing connectivity: Faecal samples provide genome-wide insights into anthropogenic impacts on two large herbivore species in central India.

Author

Tyagi A, Yadav N, Pandit A, and Ramakrishnan U

Subjects
Animals, India, Herbivory genetics, Genetics, Population, Gene Flow, Conservation of Natural Resources, Anthropogenic Effects, Genetic Variation, Feces, Polymorphism, Single Nucleotide genetics, Ecosystem
Abstract

Humans have impacted most of the planet, and the ensuing fragmentation results in small, isolated habitat patches posing a risk of genetic diversity loss, inbreeding, and genetic load. Understanding how natural and anthropogenic landscape features affect gene flow among habitat patches is critical for maintaining connectivity. Genome-wide data are required to comprehend the impacts of recent fragmentation, which can be challenging when only non-invasive samples are available. Here, we build upon advancements in conservation genomics to address connectivity of two large herbivores, gaur (Bos gaurus) and sambar (Rusa unicolor) in central India. Given their habitat associations, we expected these species to respond similarly to habitat fragmentation. We used faecal-DNA and methylation-based host-DNA enrichment with modified ddRAD protocol to generate genome-wide single-nucleotide polymorphism (SNP) data for 124 gaur and 99 sambar individuals. Our findings reveal that gaur populations in central India are fragmented, displaying high genetic differentiation, with drift significantly affecting small populations like Umred Karhandla Wildlife Sanctuary. Although sambar shows low genetic structure, another small population, Bor Tiger Reserve is genetically differentiated. Our results suggest that although land cover change and roads restrict animal movement, the extent of this impact varies across the two species. We show that different species respond differently to landscape features, even with similar habitat associations. We highlight small and isolated populations requiring urgent conservation intervention. Such multi-species approaches enhance our understanding of cross-species connectivity patterns. We suggest shifting from single-species to multi-species holistic conservation approach in rapidly developing landscapes to better manage co-occurring endangered species., (© 2024 The Author(s). Molecular Ecology published by John Wiley & Sons Ltd.)

Published
2024
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23. Plasticity of the proteasome-targeting signal Fat10 enhances substrate degradation.

Author

Negi H, Ravichandran A, Dasgupta P, Reddy S, and Das R

Subjects
Humans, Ubiquitin metabolism, Animals, Protein Conformation, Mice, Ubiquitins, Proteasome Endopeptidase Complex metabolism, Proteolysis
Abstract

The proteasome controls levels of most cellular proteins, and its activity is regulated under stress, quiescence, and inflammation. However, factors determining the proteasomal degradation rate remain poorly understood. Proteasome substrates are conjugated with small proteins (tags) like ubiquitin and Fat10 to target them to the proteasome. It is unclear if the structural plasticity of proteasome-targeting tags can influence substrate degradation. Fat10 is upregulated during inflammation, and its substrates undergo rapid proteasomal degradation. We report that the degradation rate of Fat10 substrates critically depends on the structural plasticity of Fat10. While the ubiquitin tag is recycled at the proteasome, Fat10 is degraded with the substrate. Our results suggest significantly lower thermodynamic stability and faster mechanical unfolding in Fat10 compared to ubiquitin. Long-range salt bridges are absent in the Fat10 structure, creating a plastic protein with partially unstructured regions suitable for proteasome engagement. Fat10 plasticity destabilizes substrates significantly and creates partially unstructured regions in the substrate to enhance degradation. NMR-relaxation-derived order parameters and temperature dependence of chemical shifts identify the Fat10-induced partially unstructured regions in the substrate, which correlated excellently to Fat10-substrate contacts, suggesting that the tag-substrate collision destabilizes the substrate. These results highlight a strong dependence of proteasomal degradation on the structural plasticity and thermodynamic properties of the proteasome-targeting tags., Competing Interests: HN, AR, PD, SR, RD No competing interests declared, (© 2024, Negi et al.)

Published
2024
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24. Insect Flight: State of the Field and Future Directions.

Author

Treidel LA, Deem KD, Salcedo MK, Dickinson MH, Bruce HS, Darveau CA, Dickerson BH, Ellers O, Glass JR, Gordon CM, Harrison JF, Hedrick TL, Johnson MG, Lebenzon JE, Marden JH, Niitepõld K, Sane SP, Sponberg S, Talal S, Williams CM, and Wold ES

Abstract

The evolution of flight in an early winged insect ancestral lineage is recognized as a key adaptation explaining the unparalleled success and diversification of insects. Subsequent transitions and modifications to flight machinery, including secondary reductions and losses, also play a central role in shaping the impacts of insects on broadscale geographic and ecological processes and patterns in the present and future. Given the importance of insect flight, there has been a centuries-long history of research and debate on the evolutionary origins and biological mechanisms of flight. Here, we revisit this history from an interdisciplinary perspective, discussing recent discoveries regarding the developmental origins, physiology, biomechanics, and neurobiology and sensory control of flight in a diverse set of insect models. We also identify major outstanding questions yet to be addressed and provide recommendations for overcoming current methodological challenges faced when studying insect flight, which will allow the field to continue to move forward in new and exciting directions. By integrating mechanistic work into ecological and evolutionary contexts, we hope that this synthesis promotes and stimulates new interdisciplinary research efforts necessary to close the many existing gaps about the causes and consequences of insect flight evolution., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology.)

Published
2024
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25. Generating controlled gust perturbations using vortex rings.

Author

Gupta D, Sane SP, and Arakeri JH

Subjects
Animals, Diptera physiology, Swimming physiology, Flight, Animal physiology
Abstract

To understand the locomotory mechanisms of flying and swimming animals, it is often necessary to develop assays that enable us to measure their responses to external gust perturbations. Typically, such measurements have been carried out using a variety of gusts which are difficult to control or characterize owing to their inherently turbulent nature. Here, we present a method of generating discrete gusts under controlled laboratory conditions in the form of a vortex rings which are well-characterized and highly controllable. We also provide the theoretical guidelines underlying the design of gust generators for specific applications. As a case study, we tested the efficacy of this method to study the flight response of freely-flying soldier flies Hermetia illucens. The vortex ring based method can be used to generate controlled gusts to study diverse phenomena ranging from a natural flight in insects to the artificial flight of insect-sized drones and micro-aerial vehicles., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Gupta et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Published
2024
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26. Emergent dynamics due to chemo-hydrodynamic self-interactions in active polymers.

Author

Kumar M, Murali A, Subramaniam AG, Singh R, and Thutupalli S

Abstract

The field of synthetic active matter has, thus far, been led by efforts to create point-like, isolated (yet interacting) self-propelled objects (e.g. colloids, droplets, microrobots) and understanding their collective dynamics. The design of flexible, freely jointed active assemblies from autonomously powered sub-components remains a challenge. Here, we report freely-jointed active polymers created using self-propelled droplets as monomeric units. Our experiments reveal that the self-shaping chemo-hydrodynamic interactions between the monomeric droplets give rise to an emergent rigidity (the acquisition of a stereotypical asymmetric C-shape) and associated ballistic propulsion of the active polymers. The rigidity and propulsion of the chains vary systematically with their lengths. Using simulations of a minimal model, we establish that the emergent polymer dynamics are a generic consequence of quasi two-dimensional confinement and auto-repulsive trail-mediated chemical interactions between the freely jointed active droplets. Finally, we tune the interplay between the chemical and hydrodynamic fields to experimentally demonstrate oscillatory dynamics of the rigid polymer propulsion. Altogether, our work highlights the possible first steps towards synthetic self-morphic active matter., (© 2024. The Author(s).)

Published
2024
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27. Effect of disorder on phases across two-dimensional thermal melting.

Author

Jami P, Chaudhuri P, Dasgupta C, and Ghosal A

Abstract

We study melting in a two-dimensional system of classical particles with Gaussian-core interactions in disordered environments. The pure system validates the conventional two-step melting with a hexatic phase intervening between the solid and the liquid. This picture is modified in the presence of pinning impurities. A random distribution of pinning centers forces a hexaticlike low-temperature phase that transits into a liquid at a single melting temperature T_{m}^{RP}. In contrast, pinning centers located at randomly chosen sites of a perfect crystal anchor a solid at low temperatures which undergoes a direct transition to the liquid at T_{m}^{CP}. Thus, the two-step melting is lost in either case of disorder. We discuss the characteristics of melting depending on the nature of the impurities.

Published
2024
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29. Design approaches for 3D cell culture and 3D bioprinting platforms.

Author

Sreepadmanabh M, Arun AB, and Bhattacharjee T

Abstract

The natural habitat of most cells consists of complex and disordered 3D microenvironments with spatiotemporally dynamic material properties. However, prevalent methods of in vitro culture study cells under poorly biomimetic 2D confinement or homogeneous conditions that often neglect critical topographical cues and mechanical stimuli. It has also become increasingly apparent that cells in a 3D conformation exhibit dramatically altered morphological and phenotypical states. In response, efforts toward designing biomaterial platforms for 3D cell culture have taken centerstage over the past few decades. Herein, we present a broad overview of biomaterials for 3D cell culture and 3D bioprinting, spanning both monolithic and granular systems. We first critically evaluate conventional monolithic hydrogel networks, with an emphasis on specific experimental requirements. Building on this, we document the recent emergence of microgel-based 3D growth media as a promising biomaterial platform enabling interrogation of cells within porous and granular scaffolds. We also explore how jammed microgel systems have been leveraged to spatially design and manipulate cellular structures using 3D bioprinting. The advent of these techniques heralds an unprecedented ability to experimentally model complex physiological niches, with important implications for tissue bioengineering and biomedical applications., Competing Interests: The authors have no conflicts to disclose., (© 2024 Author(s).)

Published
2024
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30. The Thermodynamic Properties of Fat10ylated Proteins Are Regulated by the Fat10ylation Site.

Author

Ravichandran A and Das R

Abstract

Degradation of proteins by the proteasome is crucial in regulating their levels in the cell. Post-translational modifications, such as ubiquitylation and Fat10ylation, trigger proteasomal degradation of the substrate proteins. While ubiquitylation regulates multiple cellular pathways, Fat10ylation functions explicitly in the inflammatory response pathway. At the proteasome, ubiquitin is recycled after being cleaved from the substrate, while Fat10 is degraded simultaneously with its substrate. Although the thermodynamic properties of the substrate are critical for effective proteasomal degradation, they remain poorly understood for the Fat10-proteasome pathway. We studied the thermodynamic properties of the Fat10∼substrate conjugate to uncover mechanistic details of the pathway. First, the mechanical unfolding of Fat10∼substrate was studied by molecular dynamics simulations, which suggested that the unfolding pathway and unfolding energy of the substrate depend on the site of Fat10 modification. We also investigated different pathways for the entry of the Fat10∼substrate into the proteasome core. Our analysis supports a model where the entry of Fat10, followed by the substrate, is the energetically preferred pathway. Further, we studied Fat10's effect on the thermodynamic properties of distinct substrates, considering their size, flexibility, and surface properties. The results uncovered significant entropic destabilization of substrates due to Fat10ylation, particularly in smaller substrates. For larger substrates, multi-monoFat10ylation is necessary to induce destabilization. Our study further reveals that Fat10 modification at negative patches on substrate surfaces is essential for optimal destabilization and subsequent degradation. These findings provide atomistic insights into the degradation mechanisms in the Fat10 proteasome pathway with potential implications for therapeutic interventions., Competing Interests: The authors declare no competing financial interest., (© 2024 The Authors. Published by American Chemical Society.)

Published
2024
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31. Temporal effects of sugar intake on fly local search and honey bee dance behaviour.

Author

Shakeel M and Brockmann A

Subjects
Animals, Bees physiology, Feeding Behavior physiology, Sugars, Time Factors, Diptera physiology, Flight, Animal physiology, Animal Communication
Abstract

Honey bees communicate flight navigational information of profitable food to nestmates via their dance, a small-scale walking pattern, inside the nest. Hungry flies and honey bee foragers exhibit a sugar-elicited search involving path integration that bears a resemblance to dance behaviour. This study aimed to investigate the temporal dynamics of the initiation of sugar-elicited search and dance behaviour, using a comparative approach. Passive displacement experiments showed that feeding and the initiation of search could be spatially and temporally dissociated. Sugar intake increased the probability of initiating a search but the actual onset of walking triggers the path integration system to guide the search. When prevented from walking after feeding, flies and bees maintained their motivation for a path integration-based search for a duration of 3 min. In flies, turning and associated characters were significantly reduced during this period but remained higher than in flies without sugar stimulus. These results suggest that sugar elicits two independent behavioural responses: path integration and increased turning, with the initiation and duration of path integration system being temporally restricted. Honey bee dance experiments demonstrated that the motivation of foragers to initiate dance persisted for 15 min, while the number of circuits declined after 3 min following sugar ingestion. Based on these findings, we propose that food intake during foraging increases the probability to initiate locomotor behaviours involving the path integration system in both flies and honey bees, and this ancestral connection might have been co-opted and elaborated during the evolution of dance communication by honey bees., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Published
2024
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32. Chromosome organization shapes replisome dynamics in Caulobacter crescentus.

Author

Zhang C, Joseph AM, Casini L, Collier J, Badrinarayanan A, and Manley S

Subjects
DNA, Bacterial metabolism, DNA, Bacterial genetics, Chromosome Segregation, Caulobacter crescentus metabolism, Caulobacter crescentus genetics, DNA Replication, Chromosomes, Bacterial metabolism, Chromosomes, Bacterial genetics, Bacterial Proteins metabolism, Bacterial Proteins genetics
Abstract

DNA replication in bacteria takes place on highly compacted chromosomes, where segregation, transcription, and repair must occur simultaneously. Within this dynamic environment, colocalization of sister replisomes has been observed in many bacterial species, driving the hypothesis that a physical linker may tether them together. However, replisome splitting has also been reported in many of the same species, leaving the principles behind replisome organization a long-standing puzzle. Here, by tracking the replisome β-clamp subunit in live Caulobacter crescentus, we find that rapid DNA segregation can give rise to a second focus which resembles a replisome, but does not replicate DNA. Sister replisomes can remain colocalized, or split apart to travel along DNA separately upon disruption of chromosome inter-arm alignment. Furthermore, chromosome arm-specific replication-transcription conflicts differentially modify replication speed on the two arms, facilitate the decoupling of the two replisomes. With these observations, we conclude that the dynamic chromosome organization flexibly shapes the organization of sister replisomes, and we outline principles which can help to reconcile previously conflicting models of replisome architecture., (© 2024. The Author(s).)

Published
2024
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33. A geometrical model of cell fate specification in the mouse blastocyst.

Author

Raju A and Siggia ED

Subjects
Animals, Mice, Signal Transduction, Fibroblast Growth Factors metabolism, Gene Expression Regulation, Developmental, Endoderm cytology, Endoderm metabolism, Germ Layers cytology, Germ Layers metabolism, Cell Lineage, Models, Biological, Blastocyst metabolism, Blastocyst cytology, Cell Differentiation
Abstract

The lineage decision that generates the epiblast and primitive endoderm from the inner cell mass (ICM) is a paradigm for cell fate specification. Recent mathematics has formalized Waddington's landscape metaphor and proven that lineage decisions in detailed gene network models must conform to a small list of low-dimensional stereotypic changes called bifurcations. The most plausible bifurcation for the ICM is the so-called heteroclinic flip that we define and elaborate here. Our re-analysis of recent data suggests that there is sufficient cell movement in the ICM so the FGF signal, which drives the lineage decision, can be treated as spatially uniform. We thus extend the bifurcation model for a single cell to the entire ICM by means of a self-consistently defined time-dependent FGF signal. This model is consistent with available data and we propose additional dynamic experiments to test it further. This demonstrates that simplified, quantitative and intuitively transparent descriptions are possible when attention is shifted from specific genes to lineages. The flip bifurcation is a very plausible model for any situation where the embryo needs control over the relative proportions of two fates by a morphogen feedback., Competing Interests: Competing interests The authors declare no competing or financial interests., (© 2024. Published by The Company of Biologists Ltd.)

Published
2024
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34. Cryo-EM structures of pannexin 1 and 3 reveal differences among pannexin isoforms.

Author

Hussain N, Apotikar A, Pidathala S, Mukherjee S, Burada AP, Sikdar SK, Vinothkumar KR, and Penmatsa A

Subjects
Cryoelectron Microscopy, Protein Isoforms genetics, Connexins chemistry, Adenosine Triphosphate
Abstract

Pannexins are single-membrane large-pore channels that release ions and ATP upon activation. Three isoforms of pannexins 1, 2, and 3, perform diverse cellular roles and differ in their pore lining residues. In this study, we report the cryo-EM structure of pannexin 3 at 3.9 Å and analyze its structural differences with pannexin isoforms 1 and 2. The pannexin 3 vestibule has two distinct chambers and a wider pore radius in comparison to pannexins 1 and 2. We further report two cryo-EM structures of pannexin 1, with pore substitutions W74R/R75D that mimic the pore lining residues of pannexin 2 and a germline mutant of pannexin 1, R217H at resolutions of 3.2 Å and 3.9 Å, respectively. Substitution of cationic residues in the vestibule of pannexin 1 results in reduced ATP interaction propensities to the channel. The germline mutant R217H in transmembrane helix 3 (TM3), leads to a partially constricted pore, reduced ATP interaction and weakened voltage sensitivity. The study compares the three pannexin isoform structures, the effects of substitutions of pore and vestibule-lining residues and allosteric effects of a pathological substitution on channel structure and function thereby enhancing our understanding of this vital group of ATP-release channels., (© 2024. The Author(s).)

Published
2024
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35. ER-Ca 2+ stores and the regulation of store-operated Ca 2+ entry in neurons.

Author

Chakraborty P and Hasan G

Subjects
Animals, Humans, Stromal Interaction Molecule 1 metabolism, Drosophila metabolism, Neurons metabolism, Endoplasmic Reticulum metabolism, Calcium metabolism, ORAI1 Protein, Mammals metabolism, Calcium Signaling physiology, Membrane Proteins metabolism
Abstract

Key components of endoplasmic reticulum (ER) Ca 2+ release and store-operated Ca 2+ entry (SOCE) are likely expressed in all metazoan cells. Due to the complexity of canonical Ca 2+ entry mechanisms in neurons, the functional significance of ER-Ca 2+ release and SOCE has been difficult to identify and establish. In this review we present evidence of how these two related mechanisms of Ca 2+ signalling impact multiple aspects of neuronal physiology and discuss their interaction with the better understood classes of ion channels that are gated by either voltage changes or extracellular ligands in neurons. Given how a small imbalance in Ca 2+ homeostasis can have strongly detrimental effects on neurons, leading to cell death, it is essential that neuronal SOCE is carefully regulated. We go on to discuss some mechanisms of SOCE regulation that have been identified in Drosophila and mammalian neurons. These include specific splice variants of stromal interaction molecules, different classes of membrane-interacting proteins and an ER-Ca 2+ channel. So far these appear distinct from the mechanisms of SOCE regulation identified in non-excitable cells. Finally, we touch upon the significance of these studies in the context of certain human neurodegenerative diseases., (© 2023 The Authors. The Journal of Physiology © 2023 The Physiological Society.)

Published
2024
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36. A machine-learning tool to identify bistable states from calcium imaging data.

Author

Varma A, Udupa S, Sengupta M, Ghosh PK, and Thirumalai V

Subjects
Mice, Animals, Purkinje Cells physiology, Membrane Potentials physiology, Action Potentials physiology, Calcium, Dietary, Calcium, Zebrafish
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., (© 2024 The Authors. The Journal of Physiology published by John Wiley & Sons Ltd on behalf of The Physiological Society.)

Published
2024
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37. Cysteine-free cone snail venom peptides: Classification of precursor proteins and identification of mature peptides.

Author

Vijayasarathy M, Kumar S, Das R, and Balaram P

Subjects
Animals, Mollusk Venoms chemistry, Mollusk Venoms genetics, Mollusk Venoms metabolism, Peptides chemistry, Protein Precursors genetics, Protein Precursors metabolism, Conotoxins chemistry, Conus Snail chemistry
Abstract

The cysteine-free acyclic peptides present in marine cone snail venom have been much less investigated than their disulfide bonded counterparts. Precursor protein sequences derived from transcriptomic data, together with mass spectrometric fragmentation patterns for peptides present in venom duct tissue extracts, permit the identification of mature peptides. Twelve distinct gene superfamiles have been identified with precursor lengths between 64 and 158 residues. In the case of Conus monile, three distinct mature peptides have been identified, arising from two distinct protein precursors. Mature acyclic peptides are often post-translationally modified, with C-terminus amidation, a feature characteristic of neuropeptides. In the present study, 20 acyclic peptides from Conus monile and Conus betulinus were identified. The common modifications of C-terminus amidation, gamma carboxylation of glutamic acid (E to ϒ), N-terminus conversion of Gln (Q) to a pyroglutamyl residue (Z), and hydroxylation of Pro (P) to Hyp (O) are observed in one or more peptides identified in this study. Proteolytic trimming of sequences by cleavage at the C-terminus of Asn (N) residues is established. The presence of an asparagine endopeptidase is strengthened by the identification of legumain-like sequences in the transcriptome assemblies from diverse Conus species. Such sequences may be expected to have a cleavage specificity at Asn-Xxx peptide bonds., (© 2023 European Peptide Society and John Wiley & Sons, Ltd.)

Published
2024
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38. Optimizing representations for integrative structural modeling using Bayesian model selection.

Author

Arvindekar S, Pathak AS, Majila K, and Viswanath S

Subjects
Bayes Theorem, Macromolecular Substances chemistry, Benchmarking
Abstract

Motivation: Integrative structural modeling combines data from experiments, physical principles, statistics of previous structures, and prior models to obtain structures of macromolecular assemblies that are challenging to characterize experimentally. The choice of model representation is a key decision in integrative modeling, as it dictates the accuracy of scoring, efficiency of sampling, and resolution of analysis. But currently, the choice is usually made ad hoc, manually., Results: Here, we report NestOR (Nested Sampling for Optimizing Representation), a fully automated, statistically rigorous method based on Bayesian model selection to identify the optimal coarse-grained representation for a given integrative modeling setup. Given an integrative modeling setup, it determines the optimal representations from given candidate representations based on their model evidence and sampling efficiency. The performance of NestOR was evaluated on a benchmark of four macromolecular assemblies., Availability and Implementation: NestOR is implemented in the Integrative Modeling Platform (https://integrativemodeling.org) and is available at https://github.com/isblab/nestor. Data for the benchmark is at https://www.doi.org/10.5281/zenodo.10360718., (© The Author(s) 2024. Published by Oxford University Press.)

Published
2024
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39. Orai-mediated calcium entry determines activity of central dopaminergic neurons by regulation of gene expression.

Author

Mitra R, Richhariya S, and Hasan G

Subjects
Dopamine, Calcium, Dietary, Histone-Lysine N-Methyltransferase, Cholinergic Agents, Calcium, Dopaminergic Neurons
Abstract

Maturation and fine-tuning of neural circuits frequently require neuromodulatory signals that set the excitability threshold, neuronal connectivity, and synaptic strength. Here, we present a mechanistic study of how neuromodulator-stimulated intracellular Ca 2+ signals, through the store-operated Ca 2+ channel Orai, regulate intrinsic neuronal properties by control of developmental gene expression in flight-promoting central dopaminergic neurons (fpDANs). The fpDANs receive cholinergic inputs for release of dopamine at a central brain tripartite synapse that sustains flight (Sharma and Hasan, 2020). Cholinergic inputs act on the muscarinic acetylcholine receptor to stimulate intracellular Ca 2+ release through the endoplasmic reticulum (ER) localised inositol 1,4,5-trisphosphate receptor followed by ER-store depletion and Orai-mediated store-operated Ca 2+ entry (SOCE). Analysis of gene expression in fpDANs followed by genetic, cellular, and molecular studies identified Orai-mediated Ca 2+ entry as a key regulator of excitability in fpDANs during circuit maturation. SOCE activates the transcription factor trithorax-like (Trl), which in turn drives expression of a set of genes, including Set2 , that encodes a histone 3 lysine 36 methyltransferase (H3K36me3). Set2 function establishes a positive feedback loop, essential for receiving neuromodulatory cholinergic inputs and sustaining SOCE. Chromatin-modifying activity of Set2 changes the epigenetic status of fpDANs and drives expression of key ion channel and signalling genes that determine fpDAN activity. Loss of activity reduces the axonal arborisation of fpDANs within the MB lobe and prevents dopamine release required for the maintenance of long flight., Competing Interests: RM, SR, GH No competing interests declared, (© 2023, Mitra et al.)

Published
2024
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40. Predictive neural computations in the cerebellum contribute to motor planning and faster behavioral responses in larval zebrafish.

Author

Narayanan S, Varma A, and Thirumalai V

Subjects
Animals, Larva physiology, Purkinje Cells physiology, Neurons physiology, Zebrafish physiology, Cerebellum physiology
Abstract

The ability to predict the future based on past experience lies at the core of the brain's ability to adapt behavior. However, the neural mechanisms that participate in generating and updating predictions are not clearly understood. Further, the evolutionary antecedents and the prevalence of predictive processing among vertebrates are even less explored. Here, we show evidence of predictive processing via the involvement of cerebellar circuits in larval zebrafish. We presented stereotyped optic flow stimuli to larval zebrafish to evoke swims and discovered that lesioning the cerebellum abolished prediction-dependent modulation of swim latency. When expectations of optic flow direction did not match with reality, error signals arrive at Purkinje cells via the olivary climbing fibers, whereas granule cells and Purkinje cells encode signals of expectation. Strong neural representations of expectation correlate with faster swim responses and vice versa. In sum, our results show evidence for predictive processing in nonmammalian vertebrates with the involvement of cerebellum, an evolutionarily conserved brain structure.

Published
2024
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41. The motor apparatus of head movements in the Oleander hawkmoth (Daphnis nerii, Lepidoptera).

Author

Prusty AD and Sane SP

Subjects
Animals, Head Movements, Dendritic Spines, Eye, Nerium, Moths
Abstract

Head movements of insects play a vital role in diverse locomotory behaviors including flying and walking. Because insect eyes move minimally within their sockets, their head movements are essential to reduce visual blur and maintain a stable gaze. As in most vertebrates, gaze stabilization behavior in insects requires the integration of both visual and mechanosensory feedback by the neck motor neurons. Although visual feedback is derived from the optic flow over the retina of their compound eyes, mechanosensory feedback is derived from their organs of balance, similar to the vestibular system in vertebrates. In Diptera, vestibular feedback is derived from the halteres-modified hindwings that evolved into mechanosensory organs-and is integrated with visual feedback to actuate compensatory head movements. However, non-Dipteran insects, including Lepidoptera, lack halteres. In these insects, vestibular feedback is obtained from the antennal Johnston's organs but it is not well-understood how it integrates with visual feedback during head movements. Indeed, although head movements are well-studied in flies, the underlying motor apparatus in non-Dipteran taxa has received relatively less attention. As a first step toward understanding compensatory head movements in the Oleander hawkmoth Daphnis nerii, we image the anatomy and architecture of their neck joint sclerites and muscles using X-ray microtomography, and the associated motor neurons using fluorescent dye fills and confocal microscopy. Based on these morphological data, we propose testable hypotheses about the putative function of specific neck muscles during head movements, which can shed light on their role in neck movements and gaze stabilization., (© 2024 Wiley Periodicals LLC.)

Published
2024
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42. A theoretical perspective on Waddington's genetic assimilation experiments.

Author

Raju A, Xue B, and Leibler S

Subjects
Phenotype, Penetrance, Biological Evolution, Epigenesis, Genetic, Adaptation, Physiological, Models, Genetic
Abstract

Genetic assimilation is the process by which a phenotype that is initially induced by an environmental stimulus becomes stably inherited in the absence of the stimulus after a few generations of selection. While the concept has attracted much debate after being introduced by C. H. Waddington 70 y ago, there have been few experiments to quantitatively characterize the phenomenon. Here, we revisit and organize the results of Waddington's original experiments and follow-up studies that attempted to replicate his results. We then present a theoretical model to illustrate the process of genetic assimilation and highlight several aspects that we think require further quantitative studies, including the gradual increase of penetrance, the statistics of delay in assimilation, and the frequency of unviability during selection. Our model captures Waddington's picture of developmental paths in a canalized landscape using a stochastic dynamical system with alternative trajectories that can be controlled by either external signals or internal variables. It also reconciles two descriptions of the phenomenon-Waddington's, expressed in terms of an individual organism's developmental paths, and that of Bateman in terms of the population distribution crossing a hypothetical threshold. Our results provide theoretical insight into the concepts of canalization, phenotypic plasticity, and genetic assimilation., Competing Interests: Competing interests statement:The authors declare no competing interest.

Published
2023
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43. Diffusion controls local versus dispersed inheritance of histones during replication and shapes epigenomic architecture.

Author

Singh A and Chakrabarti S

Subjects
Chromatin genetics, Heterochromatin, Histones genetics, Histones metabolism, Epigenomics
Abstract

The dynamics of inheritance of histones and their associated modifications across cell divisions can have major consequences on maintenance of the cellular epigenomic state. Recent experiments contradict the long-held notion that histone inheritance during replication is always local, suggesting that active and repressed regions of the genome exhibit fundamentally different histone dynamics independent of transcription-coupled turnover. Here we develop a stochastic model of histone dynamics at the replication fork and demonstrate that differential diffusivity of histones in active versus repressed chromatin is sufficient to quantitatively explain these recent experiments. Further, we use the model to predict patterns in histone mark similarity between pairs of genomic loci that should be developed as a result of diffusion, but cannot originate from either PRC2 mediated mark spreading or transcriptional processes. Interestingly, using a combination of CHIP-seq, replication timing and Hi-C datasets we demonstrate that all the computationally predicted patterns are consistently observed for both active and repressive histone marks in two different cell lines. While direct evidence for histone diffusion remains controversial, our results suggest that dislodged histones in euchromatin and facultative heterochromatin may exhibit some level of diffusion within "Diffusion-Accessible-Domains" (DADs), leading to redistribution of epigenetic marks within and across chromosomes. Preservation of the epigenomic state across cell divisions therefore might be achieved not by passing on strict positional information of histone marks, but by maintaining the marks in somewhat larger DADs of the genome., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Singh, Chakrabarti. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Published
2023
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44. Optimizing representations for integrative structural modeling using Bayesian model selection.

Author

Arvindekar S, Pathak AS, Majila K, and Viswanath S

Abstract

Motivation: Integrative structural modeling combines data from experiments, physical principles, statistics of previous structures, and prior models to obtain structures of macromolecular assemblies that are challenging to characterize experimentally. The choice of model representation is a key decision in integrative modeling, as it dictates the accuracy of scoring, efficiency of sampling, and resolution of analysis. But currently, the choice is usually made ad hoc , manually., Results: Here, we report NestOR ( Nest ed Sampling for O ptimizing R epresentation), a fully automated, statistically rigorous method based on Bayesian model selection to identify the optimal coarse-grained representation for a given integrative modeling setup. Given an integrative modeling setup, it determines the optimal representations from given candidate representations based on their model evidence and sampling efficiency. The performance of NestOR was evaluated on a benchmark of four macromolecular assemblies., Availability: NestOR is implemented in the Integrative Modeling Platform (https://integrativemodeling.org) and is available at https://github.com/isblab/nestor., Competing Interests: Conflict of Interest None declared.

Published
2023
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45. Unified treatment of mean-field dynamo and angular-momentum transport in magnetorotational instability-driven turbulence.

Author

Mondal T and Bhat P

Abstract

Magnetorotational instability-driven (MRI-driven) turbulence and dynamo phenomena are analyzed using direct statistical simulations. Our approach begins by developing a unified mean-field model that combines the traditionally decoupled problems of the large-scale dynamo and angular momentum transport in accretion disks. The model consists of a hierarchical set of equations, capturing up to the second-order correlators, while a statistical closure approximation is employed to model the three-point correlators. We highlight the web of interactions that connect different components of stress tensors-Maxwell, Reynolds, and Faraday-through shear, rotation, correlators associated with mean fields, and nonlinear terms. We determine the dominant interactions crucial for the development and sustenance of MRI turbulence. Our general mean-field model for the MRI-driven system allows for a self-consistent construction of the electromotive force, inclusive of inhomogeneities and anisotropies. Within the realm of large-scale magnetic field dynamo, we identify two key mechanisms-the rotation-shear-current effect and the rotation-shear-vorticity effect-that are responsible for generating the radial and vertical magnetic fields, respectively. We provide the explicit (nonperturbative) form of the transport coefficients associated with each of these dynamo effects. Notably, both of these mechanisms rely on the intrinsic presence of large-scale vorticity dynamo within MRI turbulence.

Published
2023
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46. Methyltransferase-independent function of enhancer of zeste homologue 2 maintains tumorigenicity induced by human oncogenic papillomavirus and polyomavirus.

Author

Khattri M, Amako Y, Gibbs JR, Collura JL, Arora R, Harold A, Li MY, Harms PW, Ezhkova E, and Shuda M

Subjects
Humans, Enhancer of Zeste Homolog 2 Protein genetics, Human Papillomavirus Viruses, Methyltransferases, Polyomavirus, Papillomavirus Infections complications, Carcinoma, Merkel Cell metabolism, Oncogene Proteins, Viral genetics, Skin Neoplasms metabolism
Abstract

Merkel cell polyomavirus (MCV) and high-risk human papillomavirus (HPV) are human tumor viruses that cause Merkel cell carcinoma (MCC) and oropharyngeal squamous cell carcinoma (OSCC), respectively. HPV E7 and MCV large T (LT) oncoproteins target the retinoblastoma tumor suppressor protein (pRb) through the conserved LxCxE motif. We identified enhancer of zeste homolog 2 (EZH2) as a common host oncoprotein activated by both viral oncoproteins through the pRb binding motif. EZH2 is a catalytic subunit of the polycomb 2 (PRC2) complex that trimethylates histone H3 at lysine 27 (H3K27me3). In MCC tissues EZH2 was highly expressed, irrespective of MCV status. Loss-of-function studies revealed that viral HPV E6/E7 and T antigen expression are required for Ezh2 mRNA expression and that EZH2 is essential for HPV(+)OSCC and MCV(+)MCC cell growth. Furthermore, EZH2 protein degraders reduced cell viability efficiently and rapidly in HPV(+)OSCC and MCV(+)MCC cells, whereas EZH2 histone methyltransferase inhibitors did not affect cell proliferation or viability within the same treatment period. These results suggest that a methyltransferase-independent function of EZH2 contributes to tumorigenesis downstream of two viral oncoproteins, and that direct targeting of EZH2 protein expression could be a promising strategy for the inhibition of tumor growth in HPV(+)OSCC and MCV(+)MCC patients., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Author(s). Published by Elsevier B.V. All rights reserved.)

Published
2023
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47. Oxidative Folding Catalysts of Conotoxins Derived from the Venom Duct Transcriptome of C. frigidus and C. amadis .

Author

Shekh S, Dhurjad P, Vijayasarathy M, Dolle A, Dhannura S, Sahoo DK, Sonti R, and Gowd KH

Subjects
Animals, Transcriptome, Venoms, Cysteine metabolism, Peptides chemistry, Proline metabolism, Disulfides metabolism, Cystine metabolism, Oxidation-Reduction, Oxidative Stress, Conotoxins chemistry, Conus Snail genetics
Abstract

Two novel redox conopeptides with proline residues outside and within the active site disulfide loop were derived from the venom duct transcriptome of the marine cone snails Conus frigidus and Conus amadis . Mature peptides with possible post-translational modification of 4-trans-hydroxylation of proline, namely, Fr874, Fr890[P1O], Fr890[P2O], Fr906, Am1038, and Am1054, have been chemically synthesized and characterized using mass spectrometry. The estimated reduction potential of cysteine disulfides of synthetic peptides varied from -298 to -328 mV, similar to the active site cysteine disulfide motifs of the redox family of proteins. Fr906/Am1054 exhibited pronounced catalytic activity and assisted in improving the yields of natively folded globular form α-conotoxin ImI. Three-dimensional (3D) structures of the redox conopeptides were optimized using computational methods and verified by 2D-ROESY NMR spectroscopy: C. frigidus peptides adopt an N-terminal helical fold and C. amadis peptides adopt distinct structures based on the Phe4-Pro/Hyp5 peptide bond configuration. The shift in the cis - trans configuration of the Phe4-Pro/Hyp5 peptide bond of Am1038/Am1054 was observed between reduced free thiol and oxidized disulfide forms of the optimized peptides. The report confirms the position-specific effect of hydroxyproline on the oxidative folding of conotoxins and sequence diversity of redox conopeptides in the venom duct of cone snails.

Published
2023
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48. Out-of-time-ordered correlator in the one-dimensional Kuramoto-Sivashinsky and Kardar-Parisi-Zhang equations.

Author

Roy D, Huse DA, and Kulkarni M

Abstract

The out-of-time-ordered correlator (OTOC) has emerged as an interesting object in both classical and quantum systems for probing the spatial spread and temporal growth of initially local perturbations in spatially extended chaotic systems. Here, we study the (classical) OTOC and its "light cone" in the nonlinear Kuramoto-Sivashinsky (KS) equation, using extensive numerical simulations. We also show that the linearized KS equation exhibits a qualitatively similar OTOC and light cone, which can be understood via a saddle-point analysis of the linearly unstable modes. Given the deep connection between the KS (deterministic) and the Kardar-Parisi-Zhang (KPZ, which is stochastic) equations, we also explore the OTOC in the KPZ equation. While our numerical results in the KS case are expected to hold in the continuum limit, for the KPZ case it is valid in a discretized version of the KPZ equation. More broadly, our work unravels the intrinsic interplay between noise/instability, nonlinearity, and dissipation in partial differential equations (deterministic or stochastic) through the lens of OTOC.

Published
2023
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49. Exploring bixin from Bixa orellana L. seeds: quantification and in silico insights into its anti-cancer potential.

Author

Muthusamy K, Ramasamy G, Ravikumar C, Natesan S, Muthurajan R, Uthandi S, Kalyanasundaram K, and Tiwari V

Abstract

Bixin, the key pigment of Bixa orellana L., is an apo-carotenoid found in the seed arils. The present study aimed to quantitatively determine the bixin content of seeds and explore its anti-cancer activity through in silico studies. The bixin content from the seeds of the local genotype, TNMTP8, quantified by RP-HPLC was 4.58 mg per gram. The prediction of pharmacological activity suggested that bixin may serve as a BRAF, MMP9, TNF expression inhibitors, and TP53 expression enhancer. According to molecular docking analysis, bixin interacted with eight different skin cancer targets and had the lowest binding energy compared to the standard drug, 5-fluorouracil. The binding score between bixin and the targets ranged from -4.7 to -8.7 kcal/mol. The targets BRAF and SIRT3 interacted well with bixin, with binding energies as low as -8.3 and -8.7 kcal/mol, respectively. Hence, the dynamic behavior of these two docked complexes throughout a 500 ns trajectory run was investigated further. The Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF) values, and total contacts as a function of time recorded during scrutiny suggest that both complexes were stable. This was validated by post-molecular dynamics analysis using Molecular Mechanics Generalized Born Surface Area (MM-GBSA). Principal component analysis (PCA) was used to analyze the significant differences in motion exhibited by BRAF-Bixin and SIRT3-Bixin. The results showed that bixin is a promising source for potential treatment interventions in skin cancer therapies.Communicated by Ramaswamy H. Sarma.

Published
2023
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50. Validating saliva as a biological sample for cost-effective, rapid and routine screening for SARS-CoV-2.

Author

Ansil BR, George CE, Chandrasingh S, Viswanathan A, Thattai M, Raghu P, Devadiga S, Harikumar AG, Harsha PK, Nair I, Ramakrishnan U, and Mayor S

Subjects
Humans, SARS-CoV-2, Cost-Benefit Analysis, India, Nasopharynx, Specimen Handling, Saliva, COVID-19 diagnosis
Abstract

Purpose: Compared to nasopharyngeal/oropharyngeal swabs (N/OPS-VTM), non-invasive saliva samples have enormous potential for scalability and routine population screening of SARS-CoV-2. In this study, we investigate the efficacy of saliva samples relative to N/OPS-VTM for use as a direct source for RT-PCR based SARS-CoV-2 detection., Methods: We collected paired nasopharyngeal/oropharyngeal swabs and saliva samples from suspected positive SARS-CoV-2 patients and tested using RT-PCR. We used generalized linear models to investigate factors that explain result agreement. Further, we used simulations to evaluate the effectiveness of saliva-based screening in restricting the spread of infection in a large campus such as an educational institution., Results: We observed a 75.4% agreement between saliva and N/OPS-VTM, that increased drastically to 83% in samples stored for less than three days. Such samples processed within two days of collection showed 74.5% test sensitivity. Our simulations suggest that a test with 75% sensitivity, but high daily capacity can be very effective in limiting the size of infection clusters in a workspace. Guided by these results, we successfully implemented a saliva-based screening in the Bangalore Life Sciences Cluster (BLiSC) campus., Conclusion: These results suggest that saliva may be a viable alternate source for SARS-CoV-2 surveillance if samples are processed immediately. Although saliva shows slightly lower sensitivity levels when compared to N/OPS-VTM, saliva collection is logistically advantageous. We strongly recommend the implementation of saliva-based screening strategies for large workplaces and in schools, as well as for population-level screening and routine surveillance as we learn to live with the SARS-CoV-2 virus., Competing Interests: Conflict of Interest The authors declare that they have no conflict of interest., (Copyright © 2023 Indian Association of Medical Microbiologists. Published by Elsevier B.V. All rights reserved.)

Published
2023
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