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2. Full Collection of Personal Narratives

Author

Morris, Austin, P., Lisa, Kerwin, Jeanne, Watson, Jean, Makoff, Eve, Carr, Brent R., One, Anonymous, Prong, Michelle, Hoeksema, Laura J., Wilson, Tracy R., Maynard, Frances Rieth, Katers, Laura A., and Taylor, Maggie

Published
2024
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5. Full Collection of Personal Narratives

Author

Jetpuri, Zaiba, Kornu, Kimbell, Igwe-Kalu, Cecilia, One, Anonymous, Castillo-Anderson, Juliete, Bradley Jr., Calvin, Cuartas, Pablo, Temkin, Sarah M., Mathis, Henriette, Hoskins, Ebony R., Bemanian, Amin, Proctor, Lisa, Vo, Holly, Scott, Maya, Tieder, Alicia Adiele, Gilliam, Courtney, Patneaude, Arika, Simpson, Kara, Thompson, Moneka A., and Miller, Pringl

Published
2022
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6. Full Collection of Personal Narratives

Author

Mozersky, Jessica, Davis, Dena S., Baxter, Sara, Binning, Bernard ‘Bernie’, Bogdan-Lovis, Elizabeth ‘Libby’, Chittooran, Mary (Rina) M., Ferguson, Noël, One, Anonymous, Pearson, Scott, We, Sunnie Songeun, Tumosa, Nina, Tumosa, John, Yarbrough, Sheri L., Zerrenner, Walt, Thew, Janice M., Driver, C. Noelle, Jecker, Nancy S., Levine, Carol, Schwarz, Judith, Cleere, Ashley, Feldman, Sara, Klaus, Karen, Politi, Catherine M., Roberts, Marsha, Weikart, Scott, Miller, Pringl, Leach, Caitlin, and Kaufman, Sharon R.

Published
2020
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13. Full Collection of Personal Narratives

Author

McCarthy, Ryan, Asaro, Joe, Hurst, Daniel J., One, Anonymous, Wik, Susan, Fausch, Kathryn, Two, Anonymous, Douglass, Janet Lynne, Hammonds, Jennifer, Spars, Gretchen M., Howe-Cobb, Sarah, Gumz, Holly, Holloway, Rochelle, Nagel, Marj, Miller, Jessica P., and Black, Lora

Published
2019
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14. Full Collection of Personal Narratives

Author

Ankeney, Tonya, One, Anonymous, Brown, Amy Caruso, Hennessy, Kathleen, Kirkwood, Ken, Kowalcheck, Nora, Kuntz, Ted, Matthews, Kirstin R.W., Mazer, Josh, Mazer, Jennifer, Parker, Liz, Shields, Jane, Taylor, Ginger, Guppy, Michelle M., Marotta, Serese A., and Millan, Ann

Published
2017
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15. Narrative Symposium: Living Organ Donation

Author

Altobelli, Laura, Bauman, Sherri, Flynn, Janice, Heath, Andy, Jacobs, Joseph, Joos, Tim, Lewensten, Amy K., Luebke, Donna L., McDaniel, Sarah A., Olenick, Donald, Post, Laurie E, Young, Vicky, Adams, Blake, One, Anonymous, Sauls, Michael, Wright, Christine, Wyatt, Shannon D., and Yesawich, Cara

Published
2012
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18. Full Collection of Personal Narratives

Author

Jetpuri, Zaiba, primary, Kornu, Kimbell, additional, Igwe-Kalu, Cecilia, additional, One, Anonymous, additional, Castillo-Anderson, Juliete, additional, Bradley Jr., Calvin, additional, Cuartas, Pablo, additional, Temkin, Sarah M., additional, Mathis, Henriette, additional, Hoskins, Ebony R., additional, Bemanian, Amin, additional, Proctor, Lisa, additional, Vo, Holly, additional, Scott, Maya, additional, Tieder, Alicia Adiele, additional, Gilliam, Courtney, additional, Patneaude, Arika, additional, Simpson, Kara, additional, Thompson, Moneka A., additional, and Miller, Pringl, additional

Published
2021
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21. Full Collection of Personal Narratives.

Author

Temkin, Sarah M., Burgess, Nora L., One, Anonymous, Butler, Karyn, Verran, Deborah, Barnett, Marguerite, Wandel, Amy, Emami, Claudia, Two, Anonymous, Chopra, Priya, Wall, Anji, Ganai, Sabha, Stephens, Elizabeth H., Carlisle, Erica M., Stewart, Amy, Newman, Jan B, Newsome, Hillary, John, Preeti R., and Bakke, Katherine

Subjects
EYEWITNESS accounts, COLLECTIONS
Published
2019
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22. Surprised Divide.

Author

One, Anonymous

Subjects
*PEER pressure
Abstract

As our family was gathered in my wife's hospital room, joyfully celebrating the newest addition, the doctor entered the room to check on my wife and said it was time to do the circumcision if we wanted. The hospital photographer came by and took photos of our two kids together and photos of our son swaddled and sleeping soundly in a basket. I NIB policy allows authors to publish anonymously when stories considerably contribute to a symposium but contain highly sensitive information that cannot be de-identified. [Extracted from the article]

Published
2023
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23. Full Collection of Personal Narratives

Author

Ankeney, Tonya, primary, One, Anonymous, additional, Brown, Amy Caruso, additional, Hennessy, Kathleen, additional, Kirkwood, Ken, additional, Kowalcheck, Nora, additional, Kuntz, Ted, additional, Matthews, Kirstin R.W., additional, Mazer, Josh, additional, Mazer, Jennifer, additional, Parker, Liz, additional, Shields, Jane, additional, Taylor, Ginger, additional, Guppy, Michelle M., additional, Marotta, Serese A., additional, and Millan, Ann, additional

Published
2016
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24. The Happy Golden Years, Practicing Medicine on the Prairie.

Author

One, Anonymous

Subjects
*MEDICAL practice, *PRAIRIES, *MEDICAL students, *LGBTQ+ communities
Abstract

My first transgender patient pushed me to expand Patient in public, becoming a hermit would be the Into the emergency room and attached to the patient If another patient needs blood as well?. [Extracted from the article]

Published
2019
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27. Adoption Times Two.

Author

One, Anonymous

Subjects
*ADOPTEES, *FAMILY history (Medicine)
Abstract

A personal narrative is presented in which the author shares experience of medical situations along with her adopted sister and depicts the importance of knowing family medical history.

Published
2018
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28. Autistic Child Undamaged by Vaccines-- A Mother's Story.

Author

One, Anonymous

Abstract

After three years of heartbreaking infertility, our miracle baby was born in January of 2012. I had never seen such a beautiful baby. We had wished for this child for years, and he was finally here. I had plenty of questions and choices as a new parent, but I never questioned immunization or even thought of it as a choice. It's just something that you do. I waited too long and cried too many tears to bring this child into the world; I certainly didn't want him susceptible to preventable diseases. I brought him faithfully to all the well visits, held his hand, and comforted him when he got all his shots. It seems that they were harder on me, as a mother, than they ever were on my son. He never cried for very long afterward, and while he sometimes got sleepy, cranky, or slightly feverish after receiving his scheduled vaccines, he never had any severe reactions to any of them. [ABSTRACT FROM AUTHOR]

Published
2016
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29. Production-based pollution versus deforestation: optimal policy with state-independent and-dependent environmental absorption efficiency restoration process

Author

Marc Leandri, Eugene Khmelnitsky, Fouad El Ouardighi, ESSEC Business School [Cergy-Pontoise], Tel Aviv University [Tel Aviv], Centre d'études sur la mondialisation, les conflits, les territoires et les vulnérabilités (Cemotev), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Tel Aviv University, TAU, and The authors acknowledge helpful comments from one anonymous referee. This research was supported by ESSEC Business School (France) and Tel Aviv University (Israel). The first author dedicates this paper to the memory of Mohamed El Houari, a wonderful mentor and friend.

Subjects
Pollution, Natural resource economics, Process (engineering), media_common.quotation_subject, 0211 other engineering and technologies, General Decision Sciences, Social Welfare, 02 engineering and technology, Management Science and Operations Research, History dependence, Deforestation, 11. Sustainability, Restoration process, Production (economics), 10. No inequality, Environmental absorption efficiency, media_common, 021103 operations research, [INFO.INFO-RO]Computer Science [cs]/Operations Research [cs.RO], 15. Life on land, 13. Climate action, Sustainability, Environmental science, Optimal pollution, Absorption efficiency
Abstract

International audience; An important yet largely unexamined issue is how the interaction between deforestation and pollution affects economic and environmental sustainability.This article seeks to bridge the gap by introducing a dynamic model of pollution accumulation where polluting emissions can be mitigated and the absorption efficiency of pollution sinks can be restored. We assume that emissions are due to a production activity, and we include deforestation both as an additional source of emissions and as a cause of the exhaustion of environmental absorption efficiency. To account for the fact that the switching of natural sinks to a pollution source can be either possible, and in such a case even reversible, or impossible, we consider that restoration efforts can be either independent from or dependent on environmental absorption efficiency, i.e., state-independent versus state-dependent restoration efforts. We determine (i) whether production or deforestation is the most detrimental from environmental and social welfare perspectives, and (ii) how state-dependent restoration process affects pollution accumulation and deforestation policies and the related environmental and social welfare consequences.

Published
2020

30. Clumped isotopes in modern marine bivalves

Author

Damien Huyghe, Mathieu Sebilo, D. Blamart, Marc de Rafélis, Yves-Marie Paulet, Mathieu Daëron, Franck Lartaud, Centre de Géosciences (GEOSCIENCES), MINES ParisTech - École nationale supérieure des mines de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Laboratoire d'Ecogéochimie des environnements benthiques (LECOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Géosciences Environnement Toulouse (GET), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Paléocéanographie (PALEOCEAN), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), E2S UPPA, Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Mines Paris - PSL (École nationale supérieure des mines de Paris), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Pau et des Pays de l'Adour (UPPA), Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), This project was financially supported by the ANR AMOR (Data Model Reconstruction of the Cenozoic Climate). The authors thank Laurent Chauvaud and Erwan Amice (LEMAR, UBO) for the collection of A. colbecki specimens, supported by the MACARBI project (IUEM). The authors are also grateful to the captain and crew of the RV Nereis II from the UMS Service at Sea of the OOB, for their help in acquiring N. cochlear shells. Analytical facilities (a part of the PANOPLY analytical Platform) at LSCE received funding from various sources (Région Ile-de-France, Commissariat à l’Energie Atomique, Institut National des Sciences de l’Univers/Centre National de la Recherche Scientifique, Université de Versailles/St-Quentin-en-Yvelines). Thoughtful comments by Editor W. Guo, S. Petersen, N. Meckler and one anonymous reviewer helped to improve the original version of the manuscript., ANR-16-CE31-0020,AMOR,Reconstruction modèle-données des climats du Cénozoique(2016), Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS), Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO), Université Paris sciences et lettres (PSL), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)

Subjects
Mollusk, 010504 meteorology & atmospheric sciences, Paleoclimate, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, 010502 geochemistry & geophysics, 01 natural sciences, Mineralization (biology), Clumped isotopes, Isotopes of oxygen, chemistry.chemical_compound, Geochemistry and Petrology, Abundance (ecology), Ecosystem, 14. Life underwater, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, Paleo-Climat, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, Abiotic component, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Isotope, Temperature, Oceanography, chemistry, 13. Climate action, [SDU.STU.CL]Sciences of the Universe [physics]/Earth Sciences/Climatology, Environmental science, Carbonate, Seawater
Abstract

International audience; Oxygen-isotope measurements of fossil carbonates remain the most common method for paleoclimatic temperature reconstructions. A well-known limitation of this approach is the influence of the oxygen isotope composition of water in which mineralization occurs, which may vary significantly through space and time, and is often difficult to constrain precisely. Carbonate clumped-isotope thermometry is an alternative approach applicable to many carbonates. It is based on measurements of Δ47 (a tracer of small statistical anomalies in the abundance of rare, doubly-substituted carbonate isotopologues), and requires no independent information on the oxygen-isotope composition of parent waters. Here, we report new calibration observations of clumped isotopes in four species of calcitic marine bivalves (A. colbecki, N. cochlear, S. cucullata, M. gigas) from various ecosystems including coastal and deep-sea environments, with calcification temperatures ranging from −2 °C to 27 °C and very different amplitudes of seasonal temperature variability. At two localities with large seasonal temperature variability, calcification time intervals were constrained using a sclerochronological approach to test whether seasonal gradients of temperature can be accurately quantified based on Δ47 measurements.Our results indicate that the mature bivalves we analyzed have clumped-isotope compositions entirely consistent with earlier calibration studies processed in the I-CDES reference frame and based on biogenic/abiotic/synthetic materials. By contrast, juvenile M. gigas oysters yield substantially lower Δ47 values than expected based on their calcification environments, suggesting that their early growth phase is associated with yet poorly understood isotopic biases affecting both δ18Ο and Δ47 values. The link between seawater temperatures and bivalve Δ47 values is thus potentially applicable to seasonal reconstructions, but only if shell sections formed in cold seasons are precisely identified and precisely sampled, and taking into account that winter calcification is likely to be biased due to reduced growth rate. Moreover, the excellent agreement between our observations and the existing I-CDES calibrations further demonstrates the efficacy of the I-CDES standardization approach, and adds to the evidence that many different types of carbonates conform to statistically indistinguishable relationships between Δ47 and crystallization temperature.

Published
2022

31. Novel genome sequences of cell-fusing agent virus allow comparison of virus phylogeny with the genetic structure of Aedes aegypti populations

Author

Sebastian Lequime, Laura B. Dickson, Jelle Matthijnssens, Julien Guglielmini, Veasna Duong, Sébastien Boyer, Artem Baidaliuk, Andrea Gloria-Soria, Isabelle Moltini-Conclois, Louis Lambrechts, Matthieu Prot, Stéphanie Dabo, Philippe Dussart, Etienne Simon-Loriere, Chenyan Shi, Interactions Virus-Insectes - Insect-Virus Interactions (IVI), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Collège doctoral [Sorbonne universités], Sorbonne Université (SU), Rega Institute for Medical Research [Leuven, België], Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Génomique évolutive des virus à ARN - Evolutionary genomics of RNA viruses, Institut Pasteur [Paris], Unité de Virologie / Virology Unit [Phnom Penh], Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Réseau International des Instituts Pasteur (RIIP), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Yale University [New Haven], The Connecticut Agricultural Experiment Station [New Haven] (CAES), This work was supported by Agence Nationale de la Recherche (grant numbers ANR-16-CE35-0004-01 and ANR-17-ERC2-0016-01), the French Government’s Investissement d’Avenir program Laboratoire d’Excellence Integrative Biology of Emerging Infectious Diseases (grant number ANR-10-LABX-62-IBEID), the INCEPTION program (Investissements d’Avenir grant number ANR-16-CONV-0005), the City of Paris Emergence(s) program in Biomedical Research, and the European Union Seventh Framework Programme (FP7/2007/2011) under Grant Agreement 282378., We thank Catherine Lallemand for assistance with mosquito rearing, and Jeff Powell, Carla Saleh, and Marie Flamand for their insights. We are grateful to Martin Mayanja and Julius Lutwama for providing the original mosquito colony from Uganda. We thank Gordana Rašić, Lícia Natal Fernandes, Bronwyn MacInnis, and Hayden Metsky for providing CFAV sequences. We thank Oliver Pybus, Peter Simmonds, Xavier de Lamballerie, and one anonymous reviewer for their insights and constructive suggestions on earlier versions of the manuscript, ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-17-ERC2-0016,GxG,Base génétique de la spécificité génotype-génotype dans l'interaction naturelle entre un virus et son insecte vecteur(2017), European Project: 282378,EC:FP7:HEALTH,FP7-HEALTH-2011-single-stage,DENFREE(2012), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Collège Doctoral, and Institut Pasteur [Paris] (IP)

Subjects
Viral metagenomics, viruses, insect-specific virus, 030231 tropical medicine, Aedes aegypti, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Microbiology, Arbovirus, Genome, 03 medical and health sciences, 0302 clinical medicine, Phylogenetics, Virology, medicine, 030304 developmental biology, 0303 health sciences, Genetic diversity, biology, Phylogenetic tree, phylogenetic analysis, fungi, virus diseases, biology.organism_classification, medicine.disease, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, Evolutionary biology, Genetic structure, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology
Abstract

Flaviviruses encompass not only medically relevant arthropod-borne viruses (arboviruses) but also insect-specific flaviviruses (ISFs) that are presumably maintained primarily through vertical transmission in the insect host. Interestingly, ISFs are commonly found infecting important arbovirus vectors such as the mosquito Aedes aegypti. Cell-fusing agent virus (CFAV) was the first described ISF of mosquitoes more than four decades ago. Despite evidence for widespread CFAV infections in A.aegypti populations and for CFAV potential to interfere with arbovirus transmission, little is known about CFAV evolutionary history. Here, we generated six novel CFAV genome sequences by sequencing three new virus isolates and subjecting three mosquito samples to untargeted viral metagenomics. We used these new genome sequences together with published ones to perform a global phylogenetic analysis of CFAV genetic diversity. Although there was some degree of geographical clustering among CFAV sequences, there were also notable discrepancies between geography and phylogeny. In particular, CFAV sequences from Cambodia and Thailand diverged significantly, despite confirmation that A.aegypti populations from both locations are genetically close. The apparent phylogenetic discrepancy between CFAV and its A.aegypti host in Southeast Asia indicates that other factors than host population structure shape CFAV genetic diversity. ispartof: VIRUS EVOLUTION vol:6 issue:1 ispartof: location:England status: published

Published
2020

32. Simulation data for the estimation of numerical constants for approximating pairwise evolutionary distances between amino acid sequences

Author

Alexis Criscuolo, Julien Guglielmini, Thomas Bigot, Institut Pasteur [Paris], Département de Biologie Computationnelle - Department of Computational Biology, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors., The authors are obliged to the Bioinformatics and Biostatistics Hub of Institut Pasteur, Paris, France, for support., This work used the computational and storage services (TARS cluster) provided by the IT department at Institut Pasteur, Paris. The authors also thank one anonymous reviewer for its fruitful comments., Institut Pasteur [Paris] (IP), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)

Subjects
lcsh:Computer applications to medicine. Medical informatics, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 03 medical and health sciences, 0302 clinical medicine, Phylogenetics, Agricultural and Biological Science, Nonlinear regression, Statistical physics, Corrected distance, lcsh:Science (General), 030304 developmental biology, Mathematics, Comparative genomics, chemistry.chemical_classification, 0303 health sciences, Sequence, Quantitative Biology::Biomolecules, Multidisciplinary, Substitution (logic), Computer simulation, Quantitative Biology::Genomics, Amino acid, Evolutionary model, Range (mathematics), Uncorrected distance, chemistry, lcsh:R858-859.7, Pairwise comparison, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], 030217 neurology & neurosurgery, [MATH.MATH-NA]Mathematics [math]/Numerical Analysis [math.NA], lcsh:Q1-390
Abstract

Estimating the number of substitution events per site that have occurred during the evolution of a pair of amino acid sequences is a common task in phylogenetics and comparative genomics that often requires quite slow maximum-likelihood procedures when taking into account explicit evolutionary models. Data presented in this article are large sets of numbers of substitution events and associated numbers of observed differences between pairs of aligned amino acid sequences that have been generated through a simulation procedure of sequence evolution under a broad range of evolutionary models. These data are available at https://zenodo.org/record/2653704 (doi:10.5281/zenodo.2653704). They are accompanied in this paper by figures showing the strong relationship between the corresponding evolutionary and uncorrected distances, as well as estimated numerical constants that determine non-linear functions that fit the simulated data. These numerical constants can be useful to quickly estimate pairwise evolutionary distances directly from uncorrected distances between aligned amino acid sequences. Keywords: Amino acid, Evolutionary model, Corrected distance, Uncorrected distance, Computer simulation, Nonlinear regression

Published
2019

33. Virus-mediated archaeal hecatomb in the deep seafloor

Author

David Prangishvili, Mart Krupovic, Cinzia Corinaldesi, Takuro Nunoura, Eugenio Rastelli, Rachel T. Noble, Ricardo Cavicchioli, Antonio Dell'Anno, Roberto Danovaro, Università Politecnica delle Marche [Ancona] (UNIVPM), Stazione Zoologica Anton Dohrn (SZN), University of New South Wales [Canberra Campus] (UNSW), Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), University of North Carolina [Chapel Hill] (UNC), University of North Carolina System (UNC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), We thank J. Middelburg and one anonymous reviewer for useful suggestions. Funding: This study was supported by the Flagship Project RITMARE (Italian Research for the Sea) coordinated by the Italian National Research Council and funded by the Italian Ministry of Education, Universities, and Research within the National Research Program 2011–2013. Further support was provided by the national project EXPLODIVE (A metagenomic approach for exploring microbial diversity and gene flows in deep-sea ecosystems) (FIRB 2008, contract no. I31J10000060001) and by the European Commission Seventh Framework Program Project MIDAS (Managing Impacts of Deep-seA reSource exploitation, grant no. 603418). We would like to thank the captain and crew of the R/V Kairei and operation team of ROV Automatic Bottom Inspection and Sampling Mobile onboard Japan Agency for Marine-Earth Science and Technology cruise KR11-11. The research performed by R.C. was supported by the Australian Research Council., European Project: 603418,EC:FP7:ENV,FP7-ENV-2013-two-stage,MIDAS(2013), and Institut Pasteur [Paris]

Subjects
Archaeal Viruses, 0301 basic medicine, Biogeochemical cycle, Nutrient cycle, MESH: Oceans and Seas, Thaumarchaeota, archaea, viruses, Oceans and Seas, [SDV]Life Sciences [q-bio], Deep-sea ecosystems, 03 medical and health sciences, MESH: Archaeal Viruses, MESH: Ecosystem, Ecosystem, 14. Life underwater, bacteria, Research Articles, biodiversity, virus-host interactions, Multidisciplinary, biology, Ecology, fungi, Marine Ecology, SciAdv r-articles, biology.organism_classification, MESH: Water Microbiology, 030104 developmental biology, 13. Climate action, ecosystem functioning, MESH: Archaea, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, microbial loop, Water Microbiology, Microbial loop, geographic locations, Bacteria, Research Article, Archaea
Abstract

Viruses cause the mortality of a large fraction of deep-sea benthic archaea, thereby influencing overall ecosystem functions., Viruses are the most abundant biological entities in the world’s oceans, and they play a crucial role in global biogeochemical cycles. In deep-sea ecosystems, archaea and bacteria drive major nutrient cycles, and viruses are largely responsible for their mortality, thereby exerting important controls on microbial dynamics. However, the relative impact of viruses on archaea compared to bacteria is unknown, limiting our understanding of the factors controlling the functioning of marine systems at a global scale. We evaluate the selectivity of viral infections by using several independent approaches, including an innovative molecular method based on the quantification of archaeal versus bacterial genes released by viral lysis. We provide evidence that, in all oceanic surface sediments (from 1000- to 10,000-m water depth), the impact of viral infection is higher on archaea than on bacteria. We also found that, within deep-sea benthic archaea, the impact of viruses was mainly directed at members of specific clades of Marine Group I Thaumarchaeota. Although archaea represent, on average, ~12% of the total cell abundance in the top 50 cm of sediment, virus-induced lysis of archaea accounts for up to one-third of the total microbial biomass killed, resulting in the release of ~0.3 to 0.5 gigatons of carbon per year globally. Our results indicate that viral infection represents a key mechanism controlling the turnover of archaea in surface deep-sea sediments. We conclude that interactions between archaea and their viruses might play a profound, previously underestimated role in the functioning of deep-sea ecosystems and in global biogeochemical cycles.

Published
2016

34. Nasal Bone Shape Is under Complex Epistatic Genetic Control in Mouse Interspecific Recombinant Congenic Strains

Author

Evelyne Heyer, Xavier Montagutelli, Michel Baylac, Gaetan Burgio, Eco-Anthropologie et Ethnobiologie (EAE), Muséum national d'Histoire naturelle (MNHN)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Génétique Fonctionnelle de la Souris, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), University of Tasmania [Hobart, Australia] (UTAS), Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), The authors have no support or funding to report., We are very grateful to Isabelle Lanctin for careful breeding of the IRCS, crosses, genotyping and technical help, Marek Szatanik for genotyping and breeding help, Jean Louis Guénet for helpful discussions, Sybille Moulin for early manuscript correction, Raphael Cornette and the morphometrics platform of the Museum National d’Histoire Naturelle for skull preparation and technical help in morphometrics analysis. One anonymous reviewer is greatly acknowledged for his excellent suggestion on this manuscript, which improved its quality., and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Male, 0106 biological sciences, Anatomy and Physiology, Heredity, Mouse, MESH: Nasal Bone, Gene Identification and Analysis, lcsh:Medicine, 01 natural sciences, Genome, Loss of heterozygosity, Mice, Molecular Cell Biology, MESH: Epistasis, Genetic, Nasal Bone, MESH: Animals, lcsh:Science, Musculoskeletal System, Genetics, 0303 health sciences, Multidisciplinary, Chromosome Biology, Strain (biology), Chromosome Mapping, Genomics, Animal Models, MESH: Crosses, Genetic, Fourier analysis, Medicine, Female, Research Article, Quantitative trait loci, Linear discriminant analysis, DNA recombination, Mus spretus, Congenic, Biology, Quantitative trait locus, 010603 evolutionary biology, Molecular Genetics, Mice, Congenic, 03 medical and health sciences, Model Organisms, MESH: Mice, Congenic, MESH: Mice, Inbred C57BL, Animals, Inbred strains, Mammalian genomics, Bone, MESH: Mice, Crosses, Genetic, Alleles, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, Quantitative Traits, Skull, lcsh:R, Computational Biology, Chromosome, Epistasis, Genetic, biology.organism_classification, MESH: Quantitative Trait Loci, MESH: Male, Mice, Inbred C57BL, Epistasis, lcsh:Q, Gene Function, MESH: Chromosome Mapping, Animal Genetics, MESH: Female
Abstract

International audience; Background: Genetic determinism of cranial morphology in the mouse is still largely unknown, despite the localization of putative QTLs and the identification of genes associated with Mendelian skull malformations. To approach the dissection of this multigenic control, we have used a set of interspecific recombinant congenic strains (IRCS) produced between C57BL/6 and mice of the distant species Mus spretus (SEG/Pas). Each strain has inherited 1.3% of its genome from SEG/Pas under the form of few, small-sized, chromosomal segments.Results: The shape of the nasal bone was studied using outline analysis combined with Fourier descriptors, and differential features were identified between IRCS BcG-66H and C57BL/6. An F2 cross between BcG-66H and C57BL/6 revealed that, outof the three SEG/Pas-derived chromosomal regions present in BcG-66H, two were involved. Segments on chromosomes 1~32 Mb) and 18 (~13 Mb) showed additive effect on nasal bone shape. The three chromosomal regions present in BcG-66H were isolated in congenic strains to study their individual effect. Epistatic interactions were assessed in bicongenicstrains.Conclusions: Our results show that, besides a strong individual effect, the QTL on chromosome 1 interacts with genes onchromosomes 13 and 18. This study demonstrates that nasal bone shape is under complex genetic control but can beefficiently dissected in the mouse using appropriate genetic tools and shape descriptors.

Published
2012

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