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459 results on '"National Natural Science Foundation"'

1. Unsupervised Contrastive Learning of Radiomics and Deep Features for Label-Efficient Tumor Classification

Author: Ziteng Zhao, Guanyu Yang, Laboratory of Image Science and Technology [Nanjing] (LIST), Southeast University [Jiangsu]-School of Computer Science and Engineering, Centre de Recherche en Information Biomédicale sino-français (CRIBS), Université de Rennes (UR)-Southeast University [Jiangsu]-Institut National de la Santé et de la Recherche Médicale (INSERM), National Natural Science Foundation National Natural Science Foundation of China (NSFC) [31571001, 61828101], DeBruijne, Cattin, PC, Cotin, Padoy, Speidel, Zheng, Essert, Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Southeast University [Jiangsu]-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: Self-supervised learning, Decision support system, Computer science, Machine learning, computer.software_genre, Convolutional neural network, Tumor heterogeneity, Task (project management), 03 medical and health sciences, 0302 clinical medicine, Radiomics, Representation (mathematics), 030304 developmental biology, 0303 health sciences, Unsupervised contrastive learning, business.industry, Deep learning, Tumor classification, 3. Good health, ComputingMethodologies_PATTERNRECOGNITION, Feature (computer vision), 030220 oncology & carcinogenesis, [SDV.IB]Life Sciences [q-bio]/Bioengineering, Artificial intelligence, business, computer
Abstract: International audience; Background - During the COVID-19 pandemic people were asked to keep interpersonal distance, wash their hands and avoid gatherings of people. But, do people understand how much a change of the distance to a virus infected person means for the exposure to that person's virus? To answer this question, we studied how people perceive virus exposure from an infected person at different distances and lengths of a conversation. Method - An online questionnaire was distributed to 101 participants drawn from the general US population. Participants judged perceived virus exposure at different interpersonal distances to an infected person in a face to face conversation of different lengths of time. A model based on empirical and theoretical studies of dispersion of particles in the air was used to estimate a person's objective virus exposure during different times and distances from a virus source. The model and empirical data show that exposure changes with the square of the distance and linearly with time. Results - A majority (78%) of the participants underestimated the effects on virus exposure following a change of interpersonal distance. The dominating bias was assuming that exposure varies linearly with distance. To illustrate, an approach to a virus source from 6 to 2 feet was judged to give a 3 times higher exposure but, objectively it is 9 times. By way of contrast, perceptions of exposure as a function of the duration of a conversation were unbiased. The COVID-19 pandemic caused by the SARS-CoV2 virus is likely to be followed by other pandemics also caused by airborne Corona or other viruses. Therefore, the results are important for administrators when designing risk communications to the general public and workers in the health care sector about social distancing and infection risks. Conclusions - People quite drastically underestimate the increase in virus exposure following an approach to a virus infected person. They also overestimate exposure after a move away from an infected person. For public health reasons, the correct function connecting distance with virus exposure should be communicated to the general public to avoid deliberate violations of recommended interpersonal distances. Supplementary information - The online version contains supplementary material available at 10.1007/s44155-022-00027-9.
Published: 2021

2. Morphological studies of rose prickles provide new insights

Author: Laurence Hibrand-Saint Oyant, Tatiana Thouroude, Fabienne Simonneau, Fabrice Foucher, Ningning Zhou, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-AGROCAMPUS OUEST, 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), SFR UA 4207 QUAlité et SAnté du Végétal (QUASAV), Université d'Angers (UA)-Université de Nantes (UN)-AGROCAMPUS OUEST, 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)-Ecole supérieure d'Agricultures d'Angers (ESA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), National Natural Science Foundation of China (NSFC), China Scholarship Council, 2017-3109., National Natural Science Foundation of China (NSFC) : 31760585, and China Scholarship Council : [2017]3109.
Subjects: 0106 biological sciences, Population, Gland cell, Plant Science, Horticulture, Biology, 01 natural sciences, Biochemistry, Article, 03 medical and health sciences, Botany, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 1234567890(), education, 030304 developmental biology, 0303 health sciences, Developmental stage, education.field_of_study, Plant morphogenesis, Non-model organisms, Meristem, Trichome, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, 010606 plant biology & botany, Biotechnology
Abstract: Prickles are common structures in plants that play a key role in defense against herbivores. In theRosagenus, prickles are widely present with great diversity in terms of form and density. For cut rose production, prickles represent an important issue, as they can damage the flower and injure workers. Our objectives were to precisely describe the types of prickles that exist in roses, their tissues of origin and their development. We performed a detailed histological analysis of prickle initiation and development in a rose F1 population. Based on the prickle investigation of 110 roses, we proposed the first categorization of prickles in theRosagenus. They are mainly divided into two categories, nonglandular prickles (NGPs) and glandular prickles (GPs), and subcategories were defined based on the presence/absence of hairs and branches. We demonstrated that NGPs and GPs both originate from multiple cells of the ground meristem beneath the protoderm. For GPs, the gland cells originate from the protoderm of the GP at the early developmental stage. Our findings clearly demonstrate that prickles are not modified trichomes (which originate from the protoderm). These conclusions are different from the current mainstream hypothesis. These results provide a foundation for further studies on prickle initiation and development in plants.
Published: 2021

3. Predicting the effect of confinement on the COVID-19 spread using machine learning enriched with satellite air pollution observations

Author: Xu Tang, Jianmin Chen, Tun Lu, Haidong Kan, Philippe Ciais, Renhe Zhang, Ivan A. Janssens, Rong Wang, Jordi Sardans, Lin Wang, Xiaofan Xing, Josep Peñuelas, Xiangrong Wang, Didier A. Hauglustaine, Ruipu Yang, Yves Balkanski, Yijing Wang, Weibing Wang, Lidia Morawska, Guy Brasseur, Junji Cao, Yuankang Xiong, Nico Bauer, Dongsheng Li, Yifei Deng, Olivier Boucher, Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Fudan University [Shanghai], Microsoft Research Asia, Institute of Atmospheric Physics [Beijing] (IAP), Chinese Academy of Sciences [Beijing] (CAS), CREAF - Centre for Ecological Research and Applied Forestries, 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), Potsdam Institute for Climate Impact Research (PIK), University of Antwerp (UA), Max Planck Institute for Meteorology (MPI-M), Max-Planck-Gesellschaft, International Laboratory for Air Quality and Health [Brisbane], Queensland University of Technology [Brisbane] (QUT), ANR-15-CE04-0005, European Space Agency, ESA: 725546, ESRIN/4000123002/18/I-NB, National Natural Science Foundation of China, NSFC: 18107, 41877506, Generalitat de Catalunya: AGAUR-2020PANDE00117, ACKNOWLEDGMENTS. We thank H. J. Yu for important comments and J. H. Pan for help in compiling the epidemiological data. This work was supported by the National Natural Science Foundation of China (41877506), the Fudan’s Wangdao Undergraduate Research Opportunities Program (18107), the Chinese Thousand Youth Talents Program, the PolEASIA-ANR project (ANR-15-CE04-0005), and the Australia-China Centre for Air Quality Science and Management. J.P. and J.S. acknowledge financial support from the Catalan Government grant AGAUR-2020PANDE00117. P.C. acknowledges support from the European Space Agency Climate Change Initiative ESA-CCI RECCAP2 project (ESRIN/4000123002/18/I-NB) and the Observation-based system for monitoring and verification of greenhouse gases project (VERIFY, grant 725546)., 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), National Natural Science Foundation of China, Fudan University, Agence Nationale de la Recherche (France), Generalitat de Catalunya, European Space Agency, Xing, Xiaofan [0000-0002-0334-6408], Wang, Rong [0000-0003-1962-0165], Wang, Weibing [0000-0002-4497-5251], Peñuelas, Josep [0000-0002-7215-0150], Ciais, Philippe [0000-0001-8560-4943], Bauer, Nico [0000-0002-0211-4162], Morawska, Lidia [0000-0002-0594-9683], Sardans, Jordi [0000-0003-2478-0219], Wang, Lin [0000-0002-4905-3432], Chen, Jianmin [0000-0001-5859-3070], Zhang, Renhe [0000-0001-7750-8679], Xing, Xiaofan, Wang, Rong, Wang, Weibing, Peñuelas, Josep, Ciais, Philippe, Bauer, Nico, Morawska, Lidia, Sardans, Jordi, Wang, Lin, Chen, Jianmin, and Zhang, Renhe
Subjects: China, 2019-20 coronavirus outbreak, 010504 meteorology & atmospheric sciences, Coronavirus disease 2019 (COVID-19), [SDV]Life Sciences [q-bio], Air pollution, Satellite observation, Pandemic management, medicine.disease_cause, 7. Clean energy, 01 natural sciences, Surrogate data, Troposphere, 03 medical and health sciences, Machine learning, medicine, Humans, Baseline (configuration management), Biology, 030304 developmental biology, 0105 earth and related environmental sciences, 0303 health sciences, Multidisciplinary, Scenario based, COVID-19, 3. Good health, Socioeconomic Factors, 13. Climate action, Climatology, Physical Sciences, Environmental science, Satellite, Engineering sciences. Technology
Abstract: The real-time monitoring of reductions of economic activity by containment measures and its effect on the transmission of the coronavirus (COVID-19) is a critical unanswered question. We inferred 5,642 weekly activity anomalies from the meteorology-adjusted differences in spaceborne tropospheric NO2 column concentrations after the 2020 COVID-19 outbreak relative to the baseline from 2016 to 2019. Two satellite observations reveal reincreasing economic activity associated with lifting control measures that comes together with accelerating COVID-19 cases before the winter of 2020/2021. Application of the near-real-time satellite NO2 observations produces a much better prediction of the deceleration of COVID-19 cases than applying the Oxford Government Response Tracker, the Public Health and Social Measures, or human mobility data as alternative predictors. A convergent cross-mapping suggests that economic activity reduction inferred from NO2 is a driver of case deceleration in most of the territories. This effect, however, is not linear, while further activity reductions were associated with weaker deceleration. Over the winter of 2020/2021, nearly 1 million daily COVID-19 cases could have been avoided by optimizing the timing and strength of activity reduction relative to a scenario based on the real distribution. Our study shows how satellite observations can provide surrogate data for activity reduction during the COVID-19 pandemic and monitor the effectiveness of containment to the pandemic before vaccines become widely available., This work was supported by the National Natural Science Foundation of China (41877506), the Fudan’s Wangdao Undergraduate Research Opportunities Program (18107), the Chinese Thousand Youth Talents Program, the PolEASIA-ANR project (ANR15-CE04-0005), and the Australia-China Centre for Air Quality Science and Management. J.P. and J.S. acknowledge financial support from the Catalan Government grant AGAUR-2020PANDE00117. P.C. acknowledges support from the European Space Agency Climate Change Initiative ESA-CCI RECCAP2 project (ESRIN/4000123002/18/I-NB) and the Observation-based system for monitoring and verification of greenhouse gases project (VERIFY, grant 725546).
Published: 2021

4. Efficacy of Thymosin Alpha 1 in the Treatment of COVID-19: A Multicenter Cohort Study

Author: Jean-Louis Teboul, Huibin Feng, Qianghong Xu, Jiao Liu, Lidi Zhang, Zhenliang Wen, Djillali Annane, Tao Wang, Yanfei Shen, Zhongyi Li, Jun Guo, Yongan Liu, Xuan Dong, Wei Zhu, Wenzhe Li, Dechang Chen, Yizhu Chen, Zhixiong Wu, Limin Chen, Hangxiang Du, Sisi Huang, Hypertension pulmonaire : physiopathologie et innovation thérapeutique (HPPIT), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Infection et inflammation (2I), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut National de la Santé et de la Recherche Médicale (INSERM), National Natural Science Foundation of China, NSFC: 81571943, 81873944, 81971869, This work was supported by the National Natural Science Foundation of China [81873944, 81971869, and 81571943]., Shanghai Jiao Tong University School of Medicine, Zhejiang Hospital [Hangzhou], Fudan University [Shanghai], Hubei Polytechnic University (HBPU), Wuhan Jinyintan Hospital [Wuhan, China] (WJH), Huazhong University of Science and Technology [Wuhan] (HUST), Wuhan University [China], Hypertension arterielle pulmonaire physiopathologie et innovation thérapeutique, Centre Chirurgical Marie Lannelongue (CCML)-Institut National de la Santé et de la Recherche Médicale (INSERM), Hôpital Bicêtre, Hôpital Raymond Poincaré [AP-HP], and HAL UVSQ, Équipe
Subjects: 0301 basic medicine, Male, ARDS, Thymalfasin, Organ Dysfunction Scores, efficacy, law.invention, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, law, Immunology and Allergy, 030212 general & internal medicine, Hospital Mortality, non-recovery, Original Research, [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Respiratory Distress Syndrome, Mortality rate, Incidence (epidemiology), Confounding, Acute kidney injury, Middle Aged, thymosin alpha 1, Prognosis, Intensive care unit, 3. Good health, Intensive Care Units, Treatment Outcome, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.IMM]Life Sciences [q-bio]/Immunology, Female, disease severity, [SDV.IMM.IMM] Life Sciences [q-bio]/Immunology/Immunotherapy, Cohort study, Adult, medicine.medical_specialty, Immunology, Risk Assessment, 03 medical and health sciences, Internal medicine, medicine, Humans, Aged, Retrospective Studies, business.industry, COVID-19, Retrospective cohort study, [SDV.IMM.IMM]Life Sciences [q-bio]/Immunology/Immunotherapy, RC581-607, Length of Stay, medicine.disease, COVID-19 Drug Treatment, 030104 developmental biology, Logistic Models, Immunologic diseases. Allergy, business
Abstract: BackgroundThymosin alpha 1 (Tα1) is widely used to treat patients with COVID-19 in China; however, its efficacy remains unclear. This study aimed to explore the efficacy of Tα1 as a COVID-19 therapy.MethodsWe performed a multicenter cohort study in five tertiary hospitals in the Hubei province of China between December 2019 and March 2020. The patient non-recovery rate was used as the primary outcome.ResultsAll crude outcomes, including non-recovery rate (65/306 vs. 290/1,976, p = 0.003), in-hospital mortality rate (62/306 vs. 271/1,976, p = 0.003), intubation rate (31/306 vs. 106/1,976, p = 0.001), acute respiratory distress syndrome (ARDS) incidence (104/306 vs. 499/1,976, p = 0.001), acute kidney injury (AKI) incidence (26/306 vs. 66/1,976, p < 0.001), and length of intensive care unit (ICU) stay (14.9 ± 12.7 vs. 8.7 ± 8.2 days, p < 0.001), were significantly higher in the Tα1 treatment group. After adjusting for confounding factors, Tα1 use was found to be significantly associated with a higher non-recovery rate than non-Tα1 use (OR 1.5, 95% CI 1.1–2.1, p = 0.028). An increased risk of non-recovery rate associated with Tα1 use was observed in the patient subgroups with maximum sequential organ failure assessment (SOFA) scores ≥2 (OR 2.0, 95%CI 1.4–2.9, p = 0.024), a record of ICU admission (OR 5.4, 95%CI 2.1–14.0, p < 0.001), and lower PaO2/FiO2 values (OR 1.9, 95%CI 1.1–3.4, p = 0.046). Furthermore, later initiation of Tα1 use was associated with a higher non-recovery rate.ConclusionTα1 use in COVID-19 patients was associated with an increased non-recovery rate, especially in those with greater disease severity.
Published: 2021
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5. Plasma Metabolomics for Discovery of Early Metabolic Markers of Prostate Cancer Based on Ultra-High-Performance Liquid Chromatography-High Resolution Mass Spectrometry

Author: Mohamed N. Triba, Adrien Rossary, Serge Hercberg, Aicha Demidem, L. Lécuyer, Pilar Galan, Philippe Savarin, Xinyu Liu, Tony Lionel Palama, Mathilde Touvier, Mélanie Deschasaux-Tanguy, Guowang Xu, Marie-Paule Vasson, Zhicheng Liu, Xiangping Lin, Université Sorbonne Paris Nord, Chinese Academy of Agricultural Sciences (CAAS), Equipe 3: EREN- Equipe de Recherche en Epidémiologie Nutritionnelle (CRESS - U1153), Université Sorbonne Paris Nord-Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS (U1153 / UMR_A_1125 / UMR_S_1153)), Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Nutrition Humaine (UNH), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Anhui University [Hefei], Centre Jean Perrin [Clermont-Ferrand] (UNICANCER/CJP), UNICANCER, French Ministry of Higher Education, Research and InnovationNational Natural Science Foundation of China (NSFC)21934006Appeared in source as:National Natural Science Foundation of China21876169Appeared in source as:National Natural Science Foundation of China, ROSSI, Sabine, and Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0301 basic medicine, Oncology, Cancer Research, medicine.medical_specialty, [SDV.CAN]Life Sciences [q-bio]/Cancer, Article, 03 medical and health sciences, Prostate cancer, chemistry.chemical_compound, 0302 clinical medicine, Metabolomics, [SDV.CAN] Life Sciences [q-bio]/Cancer, Liquid chromatography–mass spectrometry, Internal medicine, Partial least squares regression, Medicine, Carnitine, RC254-282, Receiver operating characteristic, business.industry, Cholesterol, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, biomarkers, medicine.disease, prostate cancer, metabolomics, 3. Good health, LC-MS, 030104 developmental biology, multivariate analysis, chemistry, 030220 oncology & carcinogenesis, Cohort, business, medicine.drug
Abstract: Background: The prevention and early screening of PCa is highly dependent on the identification of new biomarkers. In this study, we investigated whether plasma metabolic profiles from healthy males provide novel early biomarkers associated with future risk of PCa. Methods: Using the Supplémentation en Vitamines et Minéraux Antioxydants (SU.VI.MAX) cohort, we identified plasma samples collected from 146 PCa cases up to 13 years prior to diagnosis and 272 matched controls. Plasma metabolic profiles were characterized using ultra-high-performance liquid chromatography-high resolution mass spectrometry (UHPLC-HRMS). Results: Orthogonal partial least squares discriminant analysis (OPLS-DA) discriminated PCa cases from controls, with a median area under the receiver operating characteristic curve (AU-ROC) of 0.92 using a 1000-time repeated random sub-sampling validation. Sparse Partial Least Squares Discriminant Analysis (sPLS-DA) identified the top 10 most important metabolites (p &lt, 0.001) discriminating PCa cases from controls. Among them, phosphate, ethyl oleate, eicosadienoic acid were higher in individuals that developed PCa than in the controls during the follow-up. In contrast, 2-hydroxyadenine, sphinganine, L-glutamic acid, serotonin, 7-keto cholesterol, tiglyl carnitine, and sphingosine were lower. Conclusion: Our results support the dysregulation of amino acids and sphingolipid metabolism during the development of PCa. After validation in an independent cohort, these signatures may promote the development of new prevention and screening strategies to identify males at future risk of PCa.
Published: 2021

6. A GWAS in Latin Americans identifies novel face shape loci, implicating VPS13B and a Denisovan introgressed region in facial variation

Author: Tábita Hünemeier, Andres Ruiz-Linares, Samuel Canizales-Quinteros, Christel Thauvin-Robinet, Betty Bonfante, Juan Camilo Chacón-Duque, Laurence Duplomb, Charlotte Montillot, Sagnik Palmal, Javier Mendoza-Revilla, Justin Cotney, Laurence Faivre, Seth M. Weinberg, Victor Acuña-Alonzo, Emma Wentworth, Philip H. Jones, Claudia Jaramillo, Caroline Costedoat, Morgane Dubied, David J. Balding, Manfred Kayser, Pierre Faux, Francisco Rothhammer, Mirsha Sánchez-Quinto, Carla Gallo, Paola Everardo-Martínez, Macarena Fuentes-Guajardo, Evie Stergiakouli, Pirro G. Hysi, Ziyi Xiong, Giovanni Poletti, Ceferino Varón-González, Rodrigo Barquera, Maria Cátira Bortolini, Laurence J. Howe, Lauriane Poloni, Rolando González-José, Valeria Villegas, Malena Hurtado, Kaustubh Adhikari, William Arias, Vanessa Granja, Lavinia Schuler-Faccini, Virginia Ramallo, John R. Shaffer, Timothy C. Cox, Tim D. Spector, Gabriel Bedoya, Hugo Villamil-Ramírez, Caio Cesar Silva de Cerqueira, Fan Liu, Binnaz Yalcin, Jorge Gómez-Valdés, Nicolas Navarro, Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL), Universidad Peruana Cayetano Heredia (UPCH), Génétique Evolutive Humaine - Human Evolutionary Genetics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Equipe GAD (LNC - U1231), Lipides - Nutrition - Cancer [Dijon - U1231] (LNC), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Agro Dijon, 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 Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Agro Dijon, 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), University of Connecticut Health Center [Farmington], Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), University College of London [London] (UCL), Erasmus University Medical Center [Rotterdam] (Erasmus MC), Universidad de Tarapaca, The Natural History Museum [London] (NHM), Universidad de Antioquia = University of Antioquia [Medellín, Colombia], National School of Anthropology and History [Mexico City, Mexico] (NSAH), Max Planck Institute for the Science of Human History (MPI-SHH), Max-Planck-Gesellschaft, Universidad Nacional Autónoma de México = National Autonomous University of Mexico (UNAM), Instituto Nacional de Medicina Genomica, Scientific Police of São Paulo State [Ourinhos, Brazil], Universidade de São Paulo = University of São Paulo (USP), Universidade Federal do Rio Grande do Sul [Porto Alegre] (UFRGS), Centro Nacional Patagónico (CENPAT), Beijing Genomics Institute [Shenzhen] (BGI), University of Chinese Academy of Sciences [Beijing] (UCAS), University of Pittsburgh (PITT), Pennsylvania Commonwealth System of Higher Education (PCSHE), University of Bristol [Bristol], King‘s College London, FHU TRANSLAD (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), University of Melbourne, University of Missouri [Kansas City] (UMKC), University of Missouri System, The Open University [Milton Keynes] (OU), Fudan University [Shanghai], Work leading to this publication was funded by grants from the National Natural Science Foundation of China (#31771393), the Scientific and Technology Committee of Shanghai Municipality (18490750300), the Ministry of Science and Technology of China (2020YFE0201600), the Shanghai Municipal Science and Technology Major Project (2017SHZDZX01) and the 111 Project (B13016), the Leverhulme Trust (F/07 134/DF), BBSRC (BB/I021213/1), the Excellence Initiative of Aix-Marseille University–A*MIDEX (a French 'Investissements d’Avenir' program), Universidad de Antioquia (CODI sostenibilidad de grupos 2013-2014 and MASO 2013-2014), Conselho Nacional de Desenvolvimento Científico e Tecnológico, Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul (Apoio a Núcleos de Excelência Program), Fundação de Aperfeiçoamento de Pessoal de Nível Superior, the National Institute of Dental and Craniofacial Research (R01-DE027023, U01-DE020078, R01-DE016148, and X01-HG007821), and a Santander Research and Scholarship Award. B.B. is supported by a doctoral scholarship from Ecole Doctorale 251 Aix-Marseille Université., ANR-11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011), Biogéosciences [UMR 6282] [Dijon] (BGS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, École pratique des hautes études (EPHE), Laboratorios de Investigación y Desarrollo (LID), Unit of Human Evolutionary Genetics, Centre de génétique - Centre de référence des maladies rares, anomalies du développement et syndromes malformatifs (CHU de Dijon), Department of Genetics and Genome Sciences, University of Connecticut (UCONN), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, Department of Genetic Identification, Departamento de Tecnología Médica, Division of Vertebrates and Anthropology, Genética Molecular (GENMOL), Molecular Genetics Laboratory, National School of Anthropology and History, Department of Archaeogenetics [Jena] (DAG), Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Forensic Science, Universidad Nacional Autónoma de México (UNAM), Unidad de Genomica de Poblaciones Aplicada a la Salud, Universidad Nacional Autónoma de México (UNAM)-Instituto Nacional de Medicina Genomica, Scientific Police of São Paulo State, Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo (USP), Departamento de Genética, Universidade Federal do Rio Grande do Sul [Porto Alegre] (UFRGS)-Instituto de Biociencias, Instituto Patagónico de Ciencias Sociales y Humanas, Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), Key Laboratory of Genomic and Precision Medicine [Beijing, China], Beijing Genomics Institute [Shenzhen] (BGI)-University of Chinese Academy of Sciences [Beijing] (UCAS), Center for Craniofacial and Dental Genetics, University of Pittsburgh School of Medicine, Pennsylvania Commonwealth System of Higher Education (PCSHE)-Pennsylvania Commonwealth System of Higher Education (PCSHE), Department of Human Genetics, Department of Anthropology, Medical Research Council Integrative Epidemiology Unit, University of the West of England [Bristol] (UWE Bristol), School of Oral and Dental Sciences, Department of Twin Research & Genetic Epidemiology, King's College London, Facultad de Medicina & Instituto de Alta Investigacion, Universidad de Tarapaca-Universidade de Chile, Melbourne Integrative Genomics, School of Mathematics and Statistics, University of Melbourne-University of Melbourne, Department of Oral and Craniofacial Sciences, University of Missouri System-University of Missouri System, School of Mathematics and Statistics [Milton Keynes], Faculty of Science, Technology, Engineering and Mathematics [Milton Keynes], The Open University [Milton Keynes] (OU)-The Open University [Milton Keynes] (OU), State Key Laboratory of Genetics Engineering & MOE Key Laboratory of Contemporary Anthropology, Fudan University [Shanghai]-School of Life Sciences, Work leading to this publication was funded by grantsfrom the National Natural Science Foundation of China (#31771393), the Scientific andTechnology Committee of Shanghai Municipality (18490750300), the Ministry ofScience and Technology of China (2020YFE0201600), the Shanghai Municipal Scienceand Technology Major Project (2017SHZDZX01) and the 111 Project (B13016), theLeverhulme Trust (F/07 134/DF), BBSRC (BB/I021213/1), the Excellence Initiative ofAix-Marseille University–A*MIDEX (a French 'Investissements d’Avenir' program),Universidad de Antioquia (CODI sostenibilidad de grupos 2013-2014 and MASO 2013-2014), Conselho Nacional de Desenvolvimento Científico e Tecnológico,Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul (Apoio a Núcleos deExcelência Program), Fundação de Aperfeiçoamento de Pessoal de Nível Superior, theNational Institute of Dental and Craniofacial Research (R01-DE027023, U01-DE020078,R01-DE016148, and X01-HG007821), and a Santander Research and Scholarship Award.B.B. is supported by a doctoral scholarship from Ecole Doctorale 251 Aix-MarseilleUniversité., and Genetic Identification
Subjects: haplotype, Latin Americans, [SDV]Life Sciences [q-bio], [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Vesicular Transport Proteins, Genome-wide association study, Genome-wide association studies, Regulatory sequences, purl.org/becyt/ford/1 [https], Mice, 0302 clinical medicine, Native Americans, single nucleotide polymorphism, GWAS, 10. No inequality, Two-dimensional profiles, Research Articles, Mammals, 0303 health sciences, Multidisciplinary, biology, adult, article, SciAdv r-articles, Genomic regions, Hispanic or Latino, craniofacial development, VPS13B, GENÉTICA, Phenotype, American Indian, regulatory sequence, HUMAN POPULATION, Research Article, Morphology, Latin americans, Genotype, animal experiment, introgression, Introgression, Polymorphism, Single Nucleotide, Homo denisovan, 03 medical and health sciences, male, Animals, Humans, controlled study, human, Craniofacial, Facial feature, purl.org/becyt/ford/1.6 [https], Denisovan, Gene, mouse, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, nonhuman, genome-wide association study, Haplotype, face, Human Genetics, Single nucleotide polymorphisms, biology.organism_classification, photography, thickness, purl.org/pe-repo/ocde/ford#3.01.02 [https], facies, DENOSIVAN HAPLOTYPE, Evolutionary biology, Anthropology, Face, 030217 neurology & neurosurgery, purl.org/pe-repo/ocde/ford#1.06.07 [https], Genome-Wide Association Study
Abstract: We carried out a genome-wide association study in Latin Americans and identified novel face morphology loci.., To characterize the genetic basis of facial features in Latin Americans, we performed a genome-wide association study (GWAS) of more than 6000 individuals using 59 landmark-based measurements from two-dimensional profile photographs and ~9,000,000 genotyped or imputed single-nucleotide polymorphisms. We detected significant association of 32 traits with at least 1 (and up to 6) of 32 different genomic regions, more than doubling the number of robustly associated face morphology loci reported until now (from 11 to 23). These GWAS hits are strongly enriched in regulatory sequences active specifically during craniofacial development. The associated region in 1p12 includes a tract of archaic adaptive introgression, with a Denisovan haplotype common in Native Americans affecting particularly lip thickness. Among the nine previously unidentified face morphology loci we identified is the VPS13B gene region, and we show that variants in this region also affect midfacial morphology in mice.
Published: 2021

7. Accounting for mesophyll conductance substantially improves 13 C‐based estimates of intrinsic water‐use efficiency

Author: Xiao Ying Gong, Xu Ming Wang, Hans Schnyder, Rudi Schäufele, Wei Ting Ma, Guillaume Tcherkez, Yusheng Yang, College of Geographical Science, Fujian Normal University, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-AGROCAMPUS OUEST, 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), National Natural Science Foundation of China (NSFC) : NSFC 31870377, National Natural Science Foundation of Guangdong Province : 2018A030313450, and German Research Foundation (DFG) : SCHN 557/7-1 : SCHN 557/9-1.
Subjects: 0106 biological sciences, 0301 basic medicine, Stomatal conductance, Physiology, mesophyll conductance, Soil science, Plant Science, Photosynthesis, 01 natural sciences, transpiration, 03 medical and health sciences, stable isotope, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 13 C discrimination, water-use efficiency, Water-use efficiency, Transpiration, Mathematics, photosynthesis, Stable isotope ratio, drought stress, Conductance, use efficiency, 15. Life on land, Herbaceous plant, Evergreen, C-13 discrimination, 030104 developmental biology, 13. Climate action, stomatal conductance, water&#8208, 010606 plant biology & botany
Abstract: International audience; Carbon isotope discrimination (Delta) has been used widely to infer intrinsic water-use efficiency (iWUE) of C-3 plants, a key parameter linking carbon and water fluxes. Despite the essential role of mesophyll conductance (g(m)) in photosynthesis and Delta, its effect on Delta-based predictions of iWUE has generally been neglected.Here, we derive a mathematical expression of iWUE as a function of Delta that includes g(m) (iWUE(mes)) and exploits the g(m)-stomatal conductance (g(sc)) relationship across drought-stress levels and plant functional groups (deciduous or semideciduous woody, evergreen woody and herbaceous species) in a global database. iWUE(mes) was further validated with an independent dataset of online-Delta and CO2 and H2O gas exchange measurements with seven species.Drought stress reduced g(sc) and g(m) by nearly one-half across all plant functional groups, but had no significant effect on the g(sc) : g(m) ratio, with a well supported value of 0.79 +/- 0.07 (95% CI, n = 198). g(m) was negatively correlated to iWUE. Incorporating the g(sc) : g(m) ratio greatly improved estimates of iWUE, compared with calculations that assumed infinite g(m).The inclusion of the g(sc) : g(m) ratio, fixed at 0.79 when g(m) was unknown, proved desirable to eliminate significant errors in estimating iWUE from Delta across various C-3 vegetation types.
Published: 2021

8. Macroevolution of defense syndromes in Ficus (Moraceae)

Author: Jin Chen, Doyle McKey, Jin Zhao, Simon T. Segar, Chinese Academy of Sciences [Beijing] (CAS), Harper Adams University, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), National Natural Science Foundation of China (NSFC) : U1402264, National Natural Science Foundation of China (NSFC) : 31300369, Chinese Academy of Sciences, and CAS 135 program : 2017XTBG-T01
Subjects: 0106 biological sciences, Ficus, life form, Macroevolution, phylogeny, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Ecology, Evolution, Behavior and Systematics, trade&#8208, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, macroevolution, biology, off, Ecology, herbivory, phylogenetic generalized linear mixed model, 15. Life on land, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Moraceae, biology.organism_classification, defense syndrome, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; Recursive adaptations and counter-adaptations of plant-feeding insects are thought to have driven chemical and physical diversity in plant defenses. Among existing theories on defensive diversity, the syndromes hypothesis predicts that plants may evolve suites of covarying defense traits along evolutionary arms races with herbivores. We use the large, phenotypically diverse angiosperm genus Ficus (Moraceae) to test the major predictions of this hypothesis: (1) plant species will form distinctive combinations of defensive traits; (2) these traits will be correlated within each syndrome. Trait combinations need not map well onto phylogenies because plant species can converge onto similar trait values, but strong phylogenetic signal driven by selection (as opposed to drift) suggests roles for escalation and coevolution. Finally, Ficus species with complementary combinations of defenses will be less susceptible to insect damage and harbor distinct insect communities. We quantified susceptibility to insect herbivory and nine leaf traits related to resource acquisition and defense in 36 Ficus species growing in a common-garden setting in dry and wet seasons over 2 yr. We recovered a set of three syndromes defined by relatively small sets of trait combinations. Broadly speaking, these syndromes grouped fig species with different life forms. For example, epiphytic figs had nutrient-poor, tough, tannin-rich leaves, while free-standing trees tended to have leaves covered in trichomes and full of alkaloid-rich latex. When season and species identity were accounted for, the combination of two traits, higher C:N and higher latex tannin content, provided significantly stronger defense than did either trait taken singly. Several individual traits (C:N, latex tannin, and trichome density) were significantly negatively correlated with herbivore damage, while alkaloid content was positively correlated (perhaps as a result of feeding by adapted herbivores). Several defensive traits influenced insect herbivore community structure. Finally, traits followed different evolutionary trajectories. While latex tannin, C:N, and leaf tannin fit a Brownian-motion model of evolution, the first two escalating across Ficus phylogeny, others appeared to have more limited phylogenetic signal or tended to de-escalate. Overall, the patterns we detected support the concept of coordinated defense syndromes, demonstrating that evolutionary arms races can drive combinations of traits in this genus.
Published: 2021

9. Hybrid-Domain Neural Network Processing for Sparse-View CT Reconstruction

Author: Dianlin Hu, Tianling Lv, Limin Luo, Feng Juan, Qianlong Zhao, Guotao Quan, Jin Liu, Yikun Zhang, Chen Yang, Southeast University [Jiangsu], Centre de Recherche en Information Biomédicale sino-français (CRIBS), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Southeast University [Jiangsu]-Institut National de la Santé et de la Recherche Médicale (INSERM), Anhui Polytechnic University, Shanghai United Imaging Healthcare Co Ltd, State's Key Project of Research and Development Plan [2017YFA0104302, 2017YFC0109202, 2017YFC0107900], National Natural Science Foundation National Natural Science Foundation of China (NSFC) [81530060, 61871117], Science and Technology Program of Guangdong [2018B030333001], and Université de Rennes (UR)-Southeast University [Jiangsu]-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: sparse-view computed tomography (SVCT) reconstruction, Computer science, Streak, 02 engineering and technology, Iterative reconstruction, 030218 nuclear medicine & medical imaging, Convolution, 03 medical and health sciences, 0302 clinical medicine, Nondestructive testing, 0202 electrical engineering, electronic engineering, information engineering, Medical imaging, Radiology, Nuclear Medicine and imaging, Projection (set theory), Instrumentation, Artificial neural network, business.industry, Pattern recognition, Deep learning, Atomic and Molecular Physics, and Optics, 020201 artificial intelligence & image processing, [SDV.IB]Life Sciences [q-bio]/Bioengineering, Artificial intelligence, hybrid-domain processing, business, residual learning, Interpolation
Abstract: International audience; X-ray computed tomography (CT) is one of the most widely used tools in medical imaging, industrial nondestructive testing, lesion detection, and other applications. However, decreasing the projection number to lower the X-ray radiation dose usually leads to severe streak artifacts. To improve the quality of the images reconstructed from sparse-view projection data, we developed a hybrid-domain neural network (HDNet) processing for sparse-view CT (SVCT) reconstruction in this study. The HDNet decomposes the SVCT reconstruction problem into two stages and each stage focuses on one mission, which reduces the learning difficulty of the entire network. Experiments based on the simulated and clinical datasets are performed to demonstrate the performance of the proposed method. Compared with other competitive algorithms, quantitative and qualitative results show that the proposed method makes a great improvement on artifact suppression, tiny structure restoration, and contrast retention.
Published: 2021

10. SPECIAL: Single-Shot Projection Error Correction Integrated Adversarial Learning for Limited-Angle CT

Author: Yang Chen, Yikun Zhang, Jinglin Zhang, Shouhua Luo, Jin Liu, Dianlin Hu, Qiegen Liu, Limin Luo, Guotao Quan, Changping Du, Southeast University [Jiangsu], Centre de Recherche en Information Biomédicale sino-français (CRIBS), Université de Rennes (UR)-Southeast University [Jiangsu]-Institut National de la Santé et de la Recherche Médicale (INSERM), Anhui Polytechnic University, Hebei University of Technology [Tianjin], Shanghai United Imaging Healthcare Co Ltd, Nanchang University, State's Key Project of Research and Development Plan [2017YFC0109202, 2017YFA0104302], National Natural Science Foundation National Natural Science Foundation of China (NSFC) [61871117], Science and Technology Program of Guangdong [2018B030333001], Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Southeast University [Jiangsu]-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: Computer science, Iterative reconstruction, Limited-angle CT reconstruction, 030218 nuclear medicine & medical imaging, Domain (software engineering), 03 medical and health sciences, Consistency (database systems), 0302 clinical medicine, enhanced adversarial learning, Computer vision, Projection (set theory), Image restoration, Artifact (error), measurement consistency, business.industry, Computer Science Applications, Computational Mathematics, 030220 oncology & carcinogenesis, Signal Processing, [SDV.IB]Life Sciences [q-bio]/Bioengineering, Enhanced Data Rates for GSM Evolution, Artificial intelligence, Error detection and correction, business, high-frequency constraint, projection correction
Abstract: International audience; Limited-angle CT is an indispensable tool for some practical applications when the projection data can be only collected within a limited-angle range due to the constraints of scanning conditions. However, the limited-angle scanning mode will lead to severely degraded images with excessive artifacts. Meanwhile, existing methods fail to reconstruct satisfactory images in limited-angle CT because of the unguaranteed measurement consistency caused by serious projection missing. In this paper, we developed a method termed Single-shot Projection Error Correction Integrated Adversarial Learning (SPECIAL) progressive-improvement strategy, which could effectively combine the complementary information contained in the image domain and projection domain, and greatly improve the reconstructions at the expense of small computational cost. Specifically, enhanced adversarial learning is used in different stages to remove artifacts without losing high-frequency component. A projection error correction module is used to boost the performance in high-attenuation tissue restoration. Compared with other competitive algorithms, quantitative and qualitative results show that the proposed method could make a promising improvement on artifact removal, edge preservation and tiny structure restoration.
Published: 2021

11. The Venom of the Ectoparasitoid Wasp Pachycrepoideus vindemiae (Hymenoptera: Pteromalidae) Induces Apoptosis of Drosophilamelanogaster Hemocytes

Author: Marylène Poirié, Gongyin Ye, Qi Fang, Hongwei Yao, Jean-Luc Gatti, Lei Yang, Bin Wan, Liming Qiu, Jiao Zhang, State Key Laboratory of Rice Biology, Chinese Academy of Agricultural Sciences (CAAS), Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA), Major International (Regional) Joint Research Project of National Natural Science Foundation 31620103915, National Key R&D Program of China 2017YFD0200400, Natural Science Foundation of Zhejiang Province LY18C140001, National Natural Science Foundation of China (NSFC) 31830074, Program for Chinese Innovation Team in Key Areas of Science and Technology of Ministry of Science and Technology of the People's Republic of China 2016RA4008, and Program for Chinese Outstanding Talents in Agricultural Scientific Research of Ministry of Agriculture and Rural Affairs of the People's Republic of China
Subjects: 0106 biological sciences, [SDV]Life Sciences [q-bio], venom, Venom, Vacuole, 01 natural sciences, complex mixtures, 03 medical and health sciences, Pachycrepoideus vindemiae, Melanogaster, Envenomation, lcsh:Science, Drosophila melanogaster, ectoparasitoid, Caspase, 030304 developmental biology, 0303 health sciences, biology, apoptosis, biology.organism_classification, cell immunity, 3. Good health, Cell biology, 010602 entomology, Vacuolization, Apoptosis, Insect Science, biology.protein, lcsh:Q
Abstract: The pupal ectoparasitoid Pachycrepoideus vindemiae injects venom into its fly hosts prior to oviposition. We have shown that this venom causes immune suppression in Drosophila melanogaster pupa but the mechanism involved remained unclear. Here, we show using transgenic D. melanogaster with fluorescent hemocytes that the in vivo number of plasmatocytes and lamellocytes decreases after envenomation while it has a limited effect on crystal cells. After in vitro incubation with venom, the cytoskeleton of plasmatocytes underwent rearrangement with actin aggregation around the internal vacuoles, which increased with incubation time and venom concentration. The venom also decreased the lamellocytes adhesion capacity and induced nucleus fragmentation. Electron microscopy observation revealed that the shape of the nucleus and mitochondria became irregular after in vivo incubation with venom and confirmed the increased vacuolization with the formation of autophagosomes-like structures. Almost all venom-treated hemocytes became positive for TUNEL assays, indicating massive induced apoptosis. In support, the caspase inhibitor Z-VAD-FMK attenuated the venom-induced morphological changes suggesting an involvement of caspases. Our data indicate that P. vindemiae venom inhibits D. melanogaster host immunity by inducing strong apoptosis in hemocytes. These assays will help identify the individual venom component(s) responsible and the precise mechanism(s)/pathway(s) involved.
Published: 2020

12. Contribution of land use to the interannual variability of the land carbon cycle

Author: Chao Yue, Philippe Ciais, Alexander A. Nassikas, Richard A. Houghton, 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), Northwest A and F University, ICOS-ATC (ICOS-ATC), 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), Woods Hole Research Center, Partenaires INRAE, European Research Council, ERC: ERC-2013-SyG-610028 'IMBALANCE-P Chinese Academy of Sciences, CAS: XDB40000000 European Commission, EC: 603542 National Natural Science Foundation of China, NSFC: 41971132, C.Y. and P.C. acknowledge funding from the European Commission project LUC4C (grant no. 603542) and from the European Research Council through Synergy grant ERC-2013-SyG-610028 'IMBALANCE-P'. C.Y. is also supported by the Strategic Priority Research Program of Chinese Academy of Sciences (grant no. XDB40000000) and by the National Natural Science Foundation of China (grant no. 41971132). We acknowledge the help by Junzhi Ye in compiling the forest biomass growth database., European Project: 610028,EC:FP7:ERC,ERC-2013-SyG,IMBALANCE-P(2014), 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), and 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)
Subjects: 0301 basic medicine, Biosphere model, 010504 meteorology & atmospheric sciences, Science, [SDV]Life Sciences [q-bio], General Physics and Astronomy, 01 natural sciences, Article, General Biochemistry, Genetics and Molecular Biology, Carbon cycle, 03 medical and health sciences, 11. Sustainability, Tropical climate, Ecosystem, lcsh:Science, skin and connective tissue diseases, 0105 earth and related environmental sciences, Multidisciplinary, Land use, business.industry, Environmental resource management, Carbon sink, General Chemistry, Vegetation, Biogeochemistry, 15. Life on land, Climate resilience, 030104 developmental biology, 13. Climate action, Environmental science, lcsh:Q, sense organs, business, Climate sciences
Abstract: Understanding the driving mechanisms of the interannual variability (IAV) of the net land carbon balance (Snet) is important to predict future climate–carbon cycle feedbacks. Past studies showed that the IAV of Snet was correlated with tropical climate variation and controlled by semiarid vegetation. But today’s land ecosystems are also under extensive human land use and management. Here, we report a previously hidden role of land use in driving the IAV of Snet by using an improved biosphere model. We found that managed land accounted for 30–45% of the IAV of Snet over 1959–2015, while the contribution of intact land is reduced by more than half compared with previous assessments of the global carbon budget. Given the importance of land use in modulating future land climate–carbon cycle feedbacks, climate mitigation efforts should strive to reduce land-use emissions and enhance the climate resilience of carbon sinks over managed land., Terrestrial carbon uptake as high inter-annual variability which can be used to help understand future responses to climate change. Here the authors’ modeling reveals a large portion of this variability is driven by human land use changes and management, and not captured by other models.
Published: 2020

13. Temporally downsampled cerebral CT perfusion image restoration using deep residual learning

Author: Dan Tong, Baosheng Li, Shijie Wang, Lu Zhang, Haichen Zhu, Limin Luo, Weiwen Wu, Hui Tang, Jian Zhu, Yang Chen, Jonchère, Laurent, Southeast University [Jiangsu], Jilin University (JLU), Institut d'Électronique et des Technologies du numéRique (IETR), Université de Nantes (UN)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Laboratory of Image Science and Technology [Nanjing] (LIST), Southeast University [Jiangsu]-School of Computer Science and Engineering, Chongqing University [Chongqing], Nanjing Southeast University (SEU), Centre de Recherche en Information Biomédicale sino-français (CRIBS), Université de Rennes (UR)-Southeast University [Jiangsu]-Institut National de la Santé et de la Recherche Médicale (INSERM), Shandong University, 81530060, National Natural Science Foundation of China, 31571001, National Natural Science Foundation of China, Université de Nantes (UN)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-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)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Nanjing Southeast University, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Southeast University [Jiangsu]-Institut National de la Santé et de la Recherche Médicale (INSERM), and Nantes Université (NU)-Université de Rennes 1 (UR1)
Subjects: Computer science, media_common.quotation_subject, Perfusion Imaging, 0206 medical engineering, Acute ischemic stroke, Biomedical Engineering, Health Informatics, Perfusion scanning, 02 engineering and technology, Signal-To-Noise Ratio, Residual, Convolutional neural network, 030218 nuclear medicine & medical imaging, Brain Ischemia, 03 medical and health sciences, 0302 clinical medicine, Deep Learning, medicine, Image Processing, Computer-Assisted, CT perfusion imaging, Contrast (vision), Humans, Radiology, Nuclear Medicine and imaging, Stroke, Image restoration, media_common, [SDV.IB] Life Sciences [q-bio]/Bioengineering, Low-dose CT, Deep residual CNN, business.industry, Pattern recognition, General Medicine, medicine.disease, 020601 biomedical engineering, Computer Graphics and Computer-Aided Design, 3. Good health, Computer Science Applications, Cerebral blood flow, Cerebrovascular Circulation, Surgery, [SDV.IB]Life Sciences [q-bio]/Bioengineering, Computer Vision and Pattern Recognition, Artificial intelligence, Neural Networks, Computer, business, Tomography, X-Ray Computed, Algorithms, Interpolation
Abstract: International audience; Purpose - Acute ischemic stroke is one of the most causes of death all over the world. Onset to treatment time is critical in stroke diagnosis and treatment. Considering the time consumption and high price of MR imaging, CT perfusion (CTP) imaging is strongly recommended for acute stroke. However, too much CT radiation during CTP imaging may increase the risk of health problems. How to reduce CT radiation dose in CT perfusion imaging has drawn our great attention. Methods - In this study, the original 30-pass CTP images are downsampled to 15 passes in time sequence, which equals to 50% radiation dose reduction. Then, a residual deep convolutional neural network (DCNN) model is proposed to restore the downsampled 15-pass CTP images to 30 passes to calculate the parameters such as cerebral blood flow, cerebral blood volume, mean transit time, time to peak for stroke diagnosis and treatment. The deep restoration CNN is implemented simply and effectively with 16 successive convolutional layers which form a wide enough receptive field for input image data. 18 patients' CTP images are employed as training set and the other six patients' CTP images are treated as test dataset in this study. Results - Experiments demonstrate that our CNN can restore high-quality CTP images in terms of structural similarity index (SSIM) and peak signal-to-noise ratio (PSNR). The average SSIM and PSNR for test images are 0.981 and 56.25, and the SSIM and PSNR of regions of interest are 0.915 and 42.44, respectively, showing promising quantitative level. In addition, we compare the perfusion maps calculated from the restored images and from the original images, and the average perfusion results of them are extremely close. Areas of hypoperfusion of six test cases could be detected with comparable accuracy by radiologists. Conclusion - The trained model can restore the temporally downsampled 15-pass CTP to 30 passes very well. According to the contrast test, sufficient information cannot be restored with, e.g., simple interpolation method and deep convolutional generative adversarial network, but can be restored with the proposed CNN model. This method can be an optional way to reduce radiation dose during CTP imaging.
Published: 2020

14. A wavelet transform-based photon starvation artifacts suppression algorithm in CT imaging

Author: Baosheng Li, Yang Chen, Baodong Liu, Cunfeng Wei, Shilei Hao, Jin Liu, Jian Zhu, Southeast University [Jiangsu], Anhui Polytechnic University, Centre de Recherche en Information Biomédicale sino-français (CRIBS), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Southeast University [Jiangsu]-Institut National de la Santé et de la Recherche Médicale (INSERM), University of Chinese Academy of Sciences [Beijing] (UCAS), Shandong University, State's Key Project of Research and Development Plan [2017YFA0104302, 2017YFC0109202], National Natural Science Foundation National Natural Science Foundation of China (NSFC) [81530060, 61871117], Science and Technology Program of Guangdong [2018B030333001], National Key RandD Program of China [2017YFF0107201], CAS Interdisciplinary Innovation Team [JCTD-2019-02], and Université de Rennes (UR)-Southeast University [Jiangsu]-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: Anisotropic diffusion, Streak, Wavelet Analysis, Image processing, 030218 nuclear medicine & medical imaging, 03 medical and health sciences, 0302 clinical medicine, Wavelet, Optics, streak artifact, Image Processing, Computer-Assisted, Humans, Radiology, Nuclear Medicine and imaging, Projection (set theory), wavelet transform, Physics, Photons, Radiological and Ultrasound Technology, Noise (signal processing), business.industry, Phantoms, Imaging, Wavelet transform, anisotropic diffusion, Filter (signal processing), photon starvation, artifact suppression, 030220 oncology & carcinogenesis, [SDV.IB]Life Sciences [q-bio]/Bioengineering, business, Artifacts, Tomography, X-Ray Computed, Algorithms, CT
Abstract: International audience; In computed tomography, high attenuation occurs when x-rays pass through a dense region or a long path in the scanning object. In this case, only limited photons reach the detector, which causes photon starvation artifacts. The artifacts usually appear as streaks along the directions with high attenuation. It might lower the discrimination of minor structures and lead to misdiagnosis. Applying a local filter to the projection data adaptively is a common solution, however, if the parameters of projection-based filter are not well selected, new artifacts and noise might appear in the final image. In this paper, a post image processing technique was developed to suppress the photon starvation streak artifacts. Based on the directional characteristics of streaks, a semi-adaptive anisotropic diffusion filter was applied to the high frequency sub-bands after wavelet transformation (WASA). Qualitative and quantitative experiments were performed on phantom data and clinical data to prove the effectiveness of this method for photon starvation artifact suppression.
Published: 2020

15. Short-lived climate forcers have long-term climate impacts via the carbon–climate feedback

Author: Philippe Ciais, Xinyue Li, Yunman Han, Bengang Li, Yves Balkanski, Bo Fu, S. L. Piao, Thomas Gasser, Shu Tao, S. Peng, Luchao Han, Wei Li, Tianya Yin, Jie An, Jing Xu, 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), National Natural Science Foundation of China, NSFC: 41988101, 2019QZKK0208, 41830641, 41771495, This study is supported by the National Natural Science Foundation of China grant nos. 41771495, 41830641 and 41988101 and the Second Tibetan Plateau Scientific Expedition and Research Program grant no. 2019QZKK0208., and 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)
Subjects: [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 0303 health sciences, 010504 meteorology & atmospheric sciences, Climate system, chemistry.chemical_element, Climate change, Carbon sink, 15. Life on land, Environmental Science (miscellaneous), Radiative forcing, Atmospheric sciences, 01 natural sciences, Term (time), 03 medical and health sciences, chemistry, 13. Climate action, Climate impact, Environmental science, Earth system model, Carbon, Social Sciences (miscellaneous), 030304 developmental biology, 0105 earth and related environmental sciences
Abstract: Short-lived climate forcers (SLCFs) like methane, ozone and aerosols have a shorter atmospheric lifetime than CO2 and are often assumed to have a short-term effect on the climate system: should their emissions cease, so would their radiative forcing (RF). However, via their climate impact, SLCFs can affect carbon sinks and atmospheric CO2, causing additional climate change. Here, we use a compact Earth system model to attribute CO2 RF to direct CO2 emissions and to climate–carbon feedbacks since the pre-industrial era. We estimate the climate–carbon feedback contributed 93 ± 50 mW m−2 (~5%) to total RF of CO2 in 2010. Of this, SLCF impacts were −13 ± 50 mW m−2, made up of cooling (−115 ± 43 mW m−2) and warming (102 ± 26 mW m−2) terms that largely cancel. This study illustrates the long-term impact that short-lived species have on climate and indicates that past (and future) change in atmospheric CO2 cannot be attributed only to CO2 emissions. Short-lived climate forcers (SLCFs) are thought to have short-term impacts relative to CO2. A compact Earth system model estimates SLCFs have caused substantial, long-term impacts via carbon–climate feedbacks since the pre-industrial era but species-dependent impacts of opposite sign largely cancel.
Published: 2020

16. Lymphoid Tissue in Teleost Gills: Variations on a Theme

Author: Geert F. Wiegertjes, Louis Du Pasquier, Alf Seljenes Dalum, Yaqing Zhang, Erling Olaf Koppang, Julien Rességuier, Pierre Boudinot, Department of Biosciences [Oslo], Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO), Norwegian University of Life Sciences (NMBU), University of Basel (Unibas), Wageningen University and Research [Wageningen] (WUR), Virologie et Immunologie Moléculaires (VIM (UR 0892)), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), China Scholarship Council, CSC Wageningen UR, WUR 144642 Norges MiljÃ¸- og Biovitenskapelige Universitet, NMBU National Natural Science Foundation of China, NSFC, and Funding: This research was funded by the Norwegian Research Counsil (FRIMEDBIO‐No 144642), and by institutional grants from INRAE, Norwegian University of Life Sciences and WUR. Yaqing Zhang was funded by the China Scholarship Council, National Natural Science Foundation of China.
Subjects: 0301 basic medicine, Gill, Gills, animal structures, Evolution, [SDV]Life Sciences [q-bio], Zoology, Celbiologie en Immunologie, zap70, Ilt, General Biochemistry, Genetics and Molecular Biology, Article, Structural variation, 03 medical and health sciences, Common carp, 0302 clinical medicine, Immune system, Aquaculture and Fisheries, Immunity, Cypriniformes, evolution, 14. Life underwater, Zebrafish, lcsh:QH301-705.5, fish, gills, General Immunology and Microbiology, biology, Aquacultuur en Visserij, Zap70, biology.organism_classification, ilt, 030104 developmental biology, Lymphatic system, Fish, Cell Biology and Immunology, lcsh:Biology (General), WIAS, General Agricultural and Biological Sciences, 030215 immunology
Abstract: International audience; In bony fish, the gill filaments are essential for gas exchanges, but also are vulnerable to infection by water‐borne microorganisms. Omnipresent across fish, gill‐associated lymphoid tissues (GIALT) regulate interactions with local microbiota and halt infection by pathogens. A special GIALT structure has recently been found in Salmonids, the interbranchial lymphoid tissue (ILT). However, the structural variation of GIALT across bony fish remains largely unknown. Here, we show how this critical zone of interaction evolved across fishes. By labeling a conserved T‐cell epitope on tissue sections, we find that several basal groups of teleosts possess typical ILT, while modern teleosts have lymphoepithelium of different shape and size at the base of primary gill filaments. Within Cypriniformes, neither body size variation between two related species, zebrafish and common carp, nor morphotype variation, did have a drastic effect on the structure of ILT. Thereby this study is the first to describe the presence of ILT in zebrafish. The ILT variability across fish orders seems to represent different evolutionary solutions to balancing trade‐offs between multiple adaptations of jaws and pharyngeal region, and immune responses. Our data point to a wide structural variation in gill immunity between basal groups and modern teleosts.
Published: 2020

17. Human activities aggravate nitrogen-deposition pollution to inland water over China

Author: Tiantian Yang, Feng Zhou, Yanlong Jia, Tao Yang, Philippe Ciais, Xudong Zhou, Guirui Yu, Chiyuan Miao, Butterbach-Bahl Klaus, Yang Gao, Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), 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), ICOS-ATC (ICOS-ATC), 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), National Natural Science Foundation of China, NSFC: 41871080, 41922003 Youth Innovation Promotion Association of the Chinese Academy of Sciences National Key Research and Development Program of China, NKRDPC: 2016YFC0500202, This work was supported by the National Natural Science Foundation of China (41922003 and 41871080), the National Key R&D Program of China (2016YFC0500202) and the Youth Innovation Promotion Association of the CAS. The authors thank all anonymous reviewers for their helpful remarks., 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), and 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)
Subjects: 0301 basic medicine, Nitrogen deposition, Pollution, dam, 010504 meteorology & atmospheric sciences, AcademicSubjects/SCI00010, media_common.quotation_subject, 01 natural sciences, N deposition, 03 medical and health sciences, Pollution in China, ddc:550, Leaching (agriculture), water area, China, 0105 earth and related environmental sciences, media_common, Multidisciplinary, Water area, human activity, 15. Life on land, 6. Clean water, Earth sciences, 030104 developmental biology, 13. Climate action, [SDU]Sciences of the Universe [physics], Environmental chemistry, Soil water, Earth Sciences, Environmental science, Terrestrial ecosystem, N concentration, AcademicSubjects/MED00010, Research Article
Abstract: In the past three decades, China has built more than 87 000 dams with a storage capacity of ≈6560 km3 and the total surface area of inland water has increased by 6672 km2. Leaching of N from fertilized soils to rivers is the main source of N pollution in China, but the exposure of a growing inland water area to direct atmospheric N deposition and N leaching caused by N deposition on the terrestrial ecosystem, together with increased N deposition and decreased N flow, also tends to raise N concentrations in most inland waters. The contribution of this previously ignored source of N deposition to freshwaters is estimated in this study, as well as mitigation strategies. The results show that the annual amounts of N depositions ranged from 4.9 to 16.6 kg · ha−1 · yr−1 in the 1990s to exceeding 20 kg · ha−1 · yr−1 in the 2010s over most of regions in China, so the total mass of ΔN (the net contribution of N deposition to the increase in N concentration) for lakes, rivers and reservoirs change from 122.26 Gg N · yr−1 in the 1990s to 237.75 Gg N · yr−1 in the 2010s. It is suggested that reducing the N deposition from various sources, shortening the water-retention time in dams and decreasing the degree of regulation for rivers are three main measures for preventing a continuous increase in the N-deposition pollution to inland water in China.
Published: 2020

18. SISTER: Spectral-Image Similarity-Based Tensor With Enhanced-Sparsity Reconstruction for Sparse-View Multi-Energy CT

Author: Weiwen Wu, Dianlin Hu, Limin Luo, Jin Liu, Yang Chen, Gouenou Coatrieux, Yanbo Zhang, Moran Xu, Rongjun Ge, Centre de Recherche en Information Biomédicale sino-français (CRIBS), Université de Rennes (UR)-Southeast University [Jiangsu]-Institut National de la Santé et de la Recherche Médicale (INSERM), Nanjing Southeast University (SEU), Chongqing University [Chongqing], University of Massachusetts [Lowell] (UMass Lowell), University of Massachusetts System (UMASS), Anhui University [Hefei], Laboratoire de Traitement de l'Information Medicale (LaTIM), Université de Brest (UBO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Hospitalier Régional Universitaire de Brest (CHRU Brest)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut Brestois Santé Agro Matière (IBSAM), Université de Brest (UBO), Département lmage et Traitement Information (IMT Atlantique - ITI), IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Postgraduate Research and Practice Innovation Program of Jiangsu Province [KYCX17 0104], China Scholarship Council China Scholarship Council [201706090248], State's Key Project of Research and Development Plan [2017YFA0104302, 2017YFC0109202, 2018YFA0704102], National Natural Science Foundation National Natural Science Foundation of China (NSFC) [61871117, 61828101, 31571001], Science and Technology Program of Guangdong [2018B030333001], Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Southeast University [Jiangsu]-Institut National de la Santé et de la Recherche Médicale (INSERM), Nanjing Southeast University, Université de Brest (UBO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Hospitalier Régional Universitaire de Brest (CHRU Brest)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), and IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique)
Subjects: Computer science, 02 engineering and technology, Iterative reconstruction, 030218 nuclear medicine & medical imaging, L-0-norm of image gradient, 03 medical and health sciences, 0302 clinical medicine, tensor decomposition, Similarity (network science), Tensor (intrinsic definition), 0202 electrical engineering, electronic engineering, information engineering, Cluster analysis, sparse view reconstruction, Image gradient, business.industry, Multi-energy CT, non-local similarity, Pattern recognition, Computer Science Applications, Computational Mathematics, Feature (computer vision), Signal Processing, 020201 artificial intelligence & image processing, [SDV.IB]Life Sciences [q-bio]/Bioengineering, Noise (video), Artificial intelligence, business, Energy (signal processing)
Abstract: International audience; Multi-energy computed tomography (MCT) has a great potential in material decomposition, tissue characterization, lesion detection, and other applications. However, the severe noise that exists within projections makes it difficult to obtain high-quality MCT images. To overcome this limitation, we propose a method termed Spectral-Image Similarity-based Tensor with Enhanced-sparsity Reconstruction (SISTER) method. SISTER utilizes the non-local feature similarity in the spatial-spectral domain by clustering similar spatial-spectral patches within non-local window to a 4th-order tensor group. Compared with the image gradient L-0-norm with tensor dictionary learning (L0TDL) method, by adopting tensor decomposition rather than tensor dictionary learning, SISTER overcomes the instability of tensor dictionary. Besides, in our SISTER method the weight coefficients update strategy is also optimized. Both numerical simulation and preclinical dataset were performed to evaluate and validate the performance of SISTER. Qualitative and quantitative results show that the proposed method can lead to a promising improvement of edge preservation, finer feature recovery, and noise suppression.
Published: 2020

19. A facile route to synthesize CdSe/ZnS thick-shell quantum dots with precisely controlled green emission properties: towards QDs based LED applications

Author: Jun Miao, Rui Lu, Ziming Zhou, Bin Xie, Junjie Hao, Kai Wang, Marie-Hélène Delville, Haochen Liu, Jiaji Cheng, Bingxin Zhao, Institut de Chimie de la Matière Condensée de Bordeaux (ICMCB), Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Department of Electrical and Electronic Engineering, Southern University of Science and Technology of China (SUSTech), The Institute of Applied Physics and Materials Engineering, University of Macau (UMac), School of Materials Science and Engineering, Hubei University, and This work is supported by National Key Research and Development Program of China administrated by the Ministry of Science and Technology of China (No. 2016YFB0401702 and No. 2017YFE0120400), National Natural Science Foundation of China (No. 61674074 and 61405089), Shenzhen Innovation Project (No. JCYJ20160301113537474, No. JSGG20170823160757004), Development and Reform Commission of Shenzhen Project (No. [2017]1395), Shenzhen Peacock Team Project (No. KQTD2016030111203005), Shenzhen Key Laboratory for Advanced Quantum Dot Displays and Lighting (No. ZDSYS201707281632549), Guangdong University Key Laboratory for Advanced Quantum Dot Displays and Lighting (No. 2017KSYS007), Distinguished Young Scholar of National Natural Science Foundation of Guangdong (No. 2017B030306010), Tianjin New Materials Science and Technology Key Project (No.16ZXCLGX00040), Zhonghuan Quantum Co., Ltd (18YFZCGX00580), and also thanks the start-up fund from Southern University of Science and Technology.
Subjects: 0301 basic medicine, Materials science, Science, Quantum yield, engineering.material, Green emission, Article, Ion, 03 medical and health sciences, 0302 clinical medicine, Coating, Lattice (order), Electronic devices, Multidisciplinary, Energy, business.industry, [CHIM.MATE]Chemical Sciences/Material chemistry, Full width at half maximum, 030104 developmental biology, Quantum dot, engineering, Optoelectronics, Medicine, Luminescence, business, 030217 neurology & neurosurgery
Abstract: In recent, the quantum yield (QY) and stability of green quantum dots (QDs) have been significantly improved. However, most of the progresses were achieved by using alloyed QDs, and the control of green emission QDs still remains challenging. Herein, we report a novel method for synthesizing thick-shell structure quantum dots (TSQDs) with saturated green-emitting where tri-n-octylphosphine (TOP) was used as both ligand and solvent to extract the redundant ions from the QDs surface and remove the lattice imperfections before any surface inorganic layer-by-layer coating. The as-prepared TSQDs demonstrate enhanced luminescent properties including high QY reaching up to 75%, full width at half maximum (FWHM) remaining close to 26 nm and tunable precise emission properties (532 nm), which can be utilized to perform 91% of the International Telecommunication Union (ITU) Recommendation BT. 2020 (Rec. 2020) for high definition and color gamut displays.
Published: 2019

20. Archaeal community structure in sediments from a seamount in the Mariana Volcanic Arc

Author: Cong Xu, Hongmiao Pan, Tian Xiao, Wenyan Zhang, Jia Liu, Xuegang Li, Yi Dong, Long-Fei Wu, Key Laboratory of Experimental Marine Biology [Qingdao], Chinese Academy of Sciences [Qingdao], Chinese Academy of Sciences [Beijing] (CAS), Center for Ocean Mega-Science [Qingdao], Chinese Academy of Sciences [Changchun Branch] (CAS), International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms ( LIA-MagMC), Chinese Academy of Sciences [Beijing] (CAS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de chimie bactérienne (LCB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), and Supported by the National Natural Science Foundation of China (Nos. 41806178, 41776130, 41776131), the Strategic Priority Research Programs (No. XDA11030202.2), the National Natural Science Foundation of China—Shandong Joint Fund (Nos. U1706208, U1606404), and a grant for LIA-MagMC, from the Centre National de la Recherche Scientifique
Subjects: Thaumarchaeota, [SDV]Life Sciences [q-bio], Seamount, Oceanography, 03 medical and health sciences, Nitrosopumilales, seamount, archaeal diversity, 14. Life underwater, 030304 developmental biology, Water Science and Technology, 0303 health sciences, geography, geography.geographical_feature_category, biology, Volcanic arc, 030306 microbiology, Community structure, biology.organism_classification, Species richness, community structure, Geology, Hydrothermal vent, Archaea
Abstract: International audience; Seamounts are subsurface mountains in the ocean. Examination of the abundance and distribution of Archaea in seamount ecosystems may provide a better understanding of their ecological functions. Most studies of marine archaeal assemblages in seamount area have focused on hydrothermal vents or ferromanganese crusts. We investigated the archaeal communities from a seamount of the Mariana Volcanic Arc, in the tropical western Pacific Ocean by using high-throughput sequencing. Thaumarchaeota was dominant in the sediments of all sample stations. Community diversity and species richness were greatest at stations near the top of the seamount, and lowest at the deepest station. One sample station on the steep southeast slope that faced the Yap-Mariana trench had a unique composition of Archaea. In summary, depth has an important influence on archaeal community structure, and the geographic properties and sediment characteristics may explain the unique distribution patterns of Archaea in this seamount. This study provides a foundation for future research on Archaea in seamounts.
Published: 2019

21. In Vitro Seeding Activity of Glycoform-Deficient Prions from Variably Protease-Sensitive Prionopathy and Familial CJD Associated with PrPV180I Mutation

Author: Tetsuyuki Kitamoto, Yong-Sun Kim, Yue Lang, Jan P. M. Langeveld, Ling Xu, Hyoung Gon Lee, Jiyan Ma, Jiachun Feng, Pingping Shen, Wen-Quan Zou, Romany Abskharon, Robert B. Petersen, Qingzhong Kong, Li Cui, Brian S. Appleby, Zerui Wang, Johnny Dang, Alise Adornato, Jue Yuan, Jiafeng Chen, Mohammed Moudjou, Jilin University (JLU), Case Western Reserve University [Cleveland], Van Andel Research Institute, Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892)), Institut National de la Recherche Agronomique (INRA), Tohoku University Graduate School of Medicine, The University of Texas at San Antonio (UTSA), Graduate School of Hallym University, Wageningen University and Research Centre (WUR), Central Michigan University College of Medicine Foundation Sciences, Partenaires INRAE, China Center for Diseases Control and Prevention, CJD Foundation, National Institutes of Health (NIH) [NS062787, NS087588, NS109532, NS088604], Centers for Disease Control and Prevention [UR8/CCU515004], National Natural Science Foundation of China (NNSFC) [81,801,207], NNSFC [81,671,186], The first hospital of Jilin University, Center for Neurodegenerative Science, Van Andel Research Institute, Tohoku University [Sendai], Department of Biology (Texas State University), Texas State University, Hallym University College of Medicine, Wageningen BioVeterinary Research, Wageningen University and Research [Wageningen] (WUR), National Prion Disease Pathology Surveillance Center, Department of Neurology University Hospitals of Cleveland Case Western Reserve University Cleveland, United States Department of Health & Human Services National Institutes of Health (NIH) - USA NS062787NS087588 NS109532 NS088604, United States Department of Health & Human Services Centers for Disease Control & Prevention - USA UR8/CCU515004, National Natural Science Foundation of China 81801207, National Natural Science Foundation of China 81671186, and ProdInra, Migration
Subjects: 0301 basic medicine, Gene isoform, Transgene, [SDV]Life Sciences [q-bio], animal diseases, Neuroscience (miscellaneous), Prion disease, Variably protease-sensitive prionopathy, Brain homogenate, Article, Serial protein misfolding cyclic amplification (sPMCA), 03 medical and health sciences, Cellular and Molecular Neuroscience, 0302 clinical medicine, medicine, Variably protease-sensitive prionopathy (VPSPr), Prion protein, Polymorphism, ComputingMilieux_MISCELLANEOUS, Host Pathogen Interaction & Diagnostics, Humanized transgenic mice, Chemistry, Bacteriologie, Bacteriology, Human brain, Bacteriology, Host Pathogen Interaction & Diagnostics, Molecular biology, Host Pathogen Interactie & Diagnostiek, In vitro, nervous system diseases, [SDV] Life Sciences [q-bio], 030104 developmental biology, medicine.anatomical_structure, Neurology, nervous system, Bacteriologie, Host Pathogen Interactie & Diagnostiek, Prion, Real-time quaking-induced conversion (RT-QuIC), Protein Misfolding Cyclic Amplification, 030217 neurology & neurosurgery
Abstract: Both sporadic variably protease-sensitive prionopathy (VPSPr) and familial Creutzfeldt-Jakob disease linked to the prion protein (PrP) V180I mutation (fCJDV180I) have been found to share a unique pathological prion protein (PrPSc) that lacks the protease-resistant PrPSc glycosylated at residue 181 because two of four PrP glycoforms are apparently not converted into the PrPSc from their cellular PrP (PrPC). To investigate the seeding activity of these unique PrPSc molecules, we conducted in vitro prion conversion experiments using serial protein misfolding cyclic amplification (sPMCA) and real-time quaking-induced conversion (RT-QuIC) assays with different PrPC substrates. We observed that the seeding of PrPSc from VPSPr or fCJDV180I in the sPMCA reaction containing normal human or humanized transgenic (Tg) mouse brain homogenates generated PrPSc molecules that unexpectedly exhibited a dominant diglycosylated PrP isoform along with PrP monoglycosylated at residue 181. The efficiency of PrPSc amplification was significantly higher in non-CJDMM than in non-CJDVV human brain homogenate, whereas it was higher in normal TgVV than in TgMM mouse brain homogenate. PrPC from the mixture of normal TgMM and Tg mouse brain expressing PrPV180I mutation (Tg180) but not TgV180I alone was converted into PrPSc by seeding with the VPSPr or fCJDV180I. The RT-QuIC seeding activity of PrPSc from VPSPr and fCJDV180I was significantly lower than that of sCJD. Our results suggest that the formation of glycoform-selective prions may be associated with an unidentified factor in the affected brain and the glycoform-deficiency of PrPSc does not affect the glycoforms of in vitro newly amplified PrPSc. Electronic supplementary material The online version of this article (10.1007/s12035-018-1459-0) contains supplementary material, which is available to authorized users.
Published: 2019

22. K + Efflux Antiporters 4, 5, and 6 Mediate pH and K + Homeostasis in Endomembrane Compartments

Author: Ligang Fan, Hong Zhao, Quan-Sheng Qiu, Xiaojiao Li, Jinbo Shen, Liwen Jiang, Xiaojie Zhu, José M. Pardo, Xiaomeng Su, Imelda Mendoza, Irene Villalta, Francisco J. Quintero, Xiao Zhang, Ting Pan, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Institut de recherche sur la biologie de l'insecte UMR7261 (IRBI), Université de Tours-Centre National de la Recherche Scientifique (CNRS), Universidad de Castilla-La Mancha (UCLM), 31571464,31371438,31070222, National Natural Science Foundation of China, 2013CB429904, the National Basic Research Program of China, 20130211110001, the Research Fund for the Doctoral Program of Higher Education of China (RFDP), BIO2015-70946-R,BFU2015-64671-R, the Spanish Ministry MINECO co-financed by the European Regional Development Fund, PJ01318205, SSAC, Ministerio de Economía y Competitividad (España), National Basic Research Program (China), Rural Development Administration (South Korea), National Natural Science Foundation of China, and Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Physiology, Endosome, Antiporter, [SDV]Life Sciences [q-bio], Mutant, Transport, Plant Science, Vacuole, 03 medical and health sciences, symbols.namesake, Arabidopsis, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Biogenetics, Endomembrane system, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, ComputingMilieux_MISCELLANEOUS, Membranes, biology, Chemistry, 4. Education, Golgi apparatus, biology.organism_classification, 3. Good health, Cell biology, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, 030104 developmental biology, Ion homeostasis, symbols
Abstract: KEA4, KEA5, and KEA6 are members of the Arabidopsis thaliana K+ efflux antiporter (KEA) family that share high sequence similarity, but whose function remains unknown. Here, we show their gene expression pattern, subcellular localization, and physiological function in Arabidopsis. KEA4, KEA5, and KEA6 had a similar tissue expression pattern and the three KEA proteins localized to the Golgi, the trans-Golgi network (TGN), and the pre-vacuolar compartment (PVC)/multivesicular bodies (MVB), suggesting overlapping roles of these proteins in the endomembrane system. Phenotypic analyses of single, double, and triple mutants confirmed functional redundancy. The triple mutant kea4 kea5 kea6 had small rosettes, short seedlings, and was sensitive to low K+ availability and to the sodicity imposed by high salinity. Also, the kea4 kea5 kea6 mutant plants had a reduced luminal pH in the Golgi, TGN, PVC, and vacuole, in accordance with the K/H exchange activity of KEA proteins. Genetic analysis indicated that KEA4, KEA5, KEA6 and endosomal Na+/H+exchanger (NHX) 5 and NHX6 acted coordinately to facilitate the endosomal pH homeostasis and salt tolerance. Neither cancelling nor overexpressing the vacuolar antiporters NHX1 and NHX2 in the kea4 kea5 kea6 mutant background altered the salt-sensitive phenotype. The NHX1 and NHX2 proteins in the kea4 kea5 kea6 mutant background could not suppress the acidity of the endomembrane system but brought the vacuolar pH close to wild-type values. Together, these data signify that KEA4, KEA5, and KEA6 are endosomal K+ transporters functioning in maintaining pH and ion homeostasis in the endomembrane network., This work was supported by the National Natural Science Foundation of China (31571464, 31371438, and 31070222 to Q.-S.Q.), the National Basic Research Program of China (973 project, 2013CB429904 to Q.-S.Q.), and the Research Fund for the Doctoral Program of Higher Education of China (20130211110001 to Q.-S.Q.). F.J.Q. and J.M.P. were supported by grants from the Spanish Ministry MINECO cofinanced by the European Regional Development Fund (BIO2015-70946-R and BFU2015-64671-R) and by the Rural Development Administration, Republic of Korea, SSAC (PJ01318205).
Published: 2018

23. The Novel Microwave Temperature Vegetation Drought Index (MTVDI) Captures Canopy Seasonality across Amazonian Tropical Evergreen Forests

Author: Liyang Liu, Fanxi Gong, Xiuzhi Chen, Yongxian Su, Guangqing Huang, Xueqin Yang, 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), Applied Basic Research Foundation of Yunnan Province: 2020A151501091, 2020GDASYL-20200102002 GML2019ZD0301 National Natural Science Foundation of China, NSFC: 41907289, 31971458, 41971275, This research was funded by the National Natural Science Foundation of China, grant numbers 31971458, 41971275 and 41907289, the Key Special Project for Introduced Talents Team of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), grant number GML2019ZD0301, the Guangdong Basic and Applied Basic Research Foundation, grant number 2020A151501091, the GDAS Special Project of Science and Technology Development, grant number 2020GDASYL-20200102002., and 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)
Subjects: Canopy, 010504 meteorology & atmospheric sciences, Vapour Pressure Deficit, Microwave Temperature Vegetation Drought Index (MTVDI), Science, tropical evergreen forests, canopy growth index, photosynthesis seasonality, tropical phenology, Amazon, Atmospheric sciences, 01 natural sciences, 03 medical and health sciences, Dry season, medicine, 030304 developmental biology, 0105 earth and related environmental sciences, 0303 health sciences, Vegetation, Enhanced vegetation index, 15. Life on land, Evergreen, Seasonality, medicine.disease, Evergreen forest, 13. Climate action, [SDE]Environmental Sciences, General Earth and Planetary Sciences, Environmental science
Abstract: International audience; Despite its perennial canopy, the Amazonian tropical evergreen forest shows significant canopy growth seasonality, which has been represented by optical satellite-based observations. In this paper, a new Microwave Temperature–Vegetation Drought Index (MTVDI) based on Advanced Microwave Scanning Radiometer for the Earth Observing System (AMSR-E) sensors was used to capture the canopy seasonality from 2003 to 2010 in comparison with four climatic dryness indicators (Palmer Drought Severity Index (PDSI), Climatological Water Deficit (CWD), Terrestrial Water Storage (TWS), Vapor Pressure Deficit (VPD)) and two photosynthesis proxies (Enhanced Vegetation Index (EVI) and Solar-Induced chlorophyll Fluorescence (SIF)), respectively. Our results suggest that the MTVDI shows opposite seasonal variability with two photosynthesis proxies and performs better than the four climatic dryness indicators in reflecting the canopy photosynthesis seasonality of tropical forests in the Amazon. Besides, the MTVDI captures wet regions that show green-up during the dry season with mean annual precipitation higher than 2000 mm per year. The MTVDI provides a new way for monitoring the canopy seasonality of tropical forests from microwave signals.
Published: 2021

24. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

Author: Jingqui Dai, Alexey V. Melnik, Jenan J. Kharbush, Kenji L. Kurita, Robert A. Keyzers, Katrina M. Waters, Mario Sandoval-Calderón, Ajit Jadhav, Clifford A. Kapono, Charles B. Larson, Evgenia Glukhov, Danielle VanLeer, Daniel P. Demarque, Lars Jelsbak, Yi Zeng, Eve A. Granatosky, Kit Pogliano, Maryam Elfeki, Marcelino Gutiérrez, Jeramie D. Watrous, Katherine R. Duncan, Laura M. Sanchez, Jeremy Carver, Brendan M. Duggan, Thomas O. Metz, Julia A. Vorholt, Pep Charusanti, Paul Shinn, Nuno Bandeira, Pavel A. Pevzner, Amy C. Sims, Nobuhiro Koyama, David Gonzalez, Xueting Liu, Denise Brentan Silva, Venkat R. Macherla, Pieter C. Dorrestein, Andrew R. Johnson, Jörn Piel, Michael J. Meehan, Delphine Parrot, Jehad Almaliti, Don D. Nguyen, Louis-Félix Nothias, Wenyuan Shi, Max Crüsemann, Cristopher A. Boya P., Philip G. Williams, Erin E. Carlson, Ronnie G. Gavilan, Yao Peng, Roland D. Kersten, Jennifer E. Kyle, Bertrand Aigle, Yu-Liang Yang, Mingxun Wang, Amina Bouslimani, Lixin Zhang, Ram P. Neupane, Chih-Chuang Liaw, Tyler Peryea, Eric J. N. Helfrich, Kristian Fog Nielsen, Hans-Ulrich Humpf, Robert A. Quinn, Rolf Müller, Paul R. Jensen, Hailey Houson, Eduardo Esquenazi, Kathleen Dorrestein, Vanessa V. Phelan, Bernhard O. Palsson, Lisa Vuong, Cheng-Chih Hsu, Sophie Tomasi, Trent R. Northen, Laura A. Pace, Marc Litaudon, Samantha J. Mascuch, Chen Zhang, Maria Maansson, Ashley M. Sidebottom, Vinayak Agarwal, Ricardo Pianta Rodrigues da Silva, Ellis C. O’Neill, Tal Luzzatto-Knaan, Florian Ryffel, Oliver B. Vining, Andrés M. C. Rodríguez, Andreas Klitgaard, Enora Briand, Brian T. Murphy, Neha Garg, Norberto Peporine Lopes, Ralph S. Baric, William H. Gerwick, Pierre-Marie Allard, Daniel Torres-Mendoza, Jeffrey S. McLean, Stefan Jenkins, Lena Gerwick, Theodore Alexandrov, Roger G. Linington, Egle Pociute, Christian Sohlenkamp, Joshua R. Gurr, Matthew F. Traxler, Wei-Ting Liu, Rob Knight, Anne Lamsa, Anna Edlund, Bradley S. Moore, Prasad Phapale, Hosein Mohimani, Karin Kleigrewe, Charlotte Frydenlund Michelsen, Lucas Miranda Marques, Niclas Engene, Jean-Luc Wolfender, Thomas Hoffman, Rachel J. Dutton, Dac-Trung Nguyen, Paul D. Boudreau, Dimitrios J. Floros, Kerry L. McPhail, Carla Porto, Brian E. Sedio, Computer Science and Engineering, University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC), Collaborative Mass Spectrometry Innovation Center, KDDI R&D Laboratories Inc. [Saitama], Shandong University of Science and Technology, 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), Dynamique des Génomes et Adaptation Microbienne (DynAMic), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Metacohorts Consortium, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Universidade Estadual de Campinas = University of Campinas (UNICAMP), Unité mixte de physique CNRS/Thales (UMPhy CNRS/THALES), THALES [France]-Centre National de la Recherche Scientifique (CNRS), Department of Civil Engineering, University of Siegen, Institut de Chimie des Substances Naturelles (ICSN), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de recherches sur la catalyse et l'environnement de Lyon (IRCELYON), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique de l'ENS Lyon (Phys-ENS), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Skaggs School of Pharmacy and Pharmaceutical Sciences [San Diego], CNPq, Conselho Nacional de Desenvolvimento Científico e Tecnológico, 2014/01884-2, FAPESP, São Paulo Research Foundation, DAAD, German Academic Exchange Service, K12 GM068524, NIH, National Institutes of Health, RCSA, Research Corporation for Science Advancement, K99DE024543, NIH, National Institutes of Health, PQ 480 306385/2011-2, CNPq, Conselho Nacional de Desenvolvimento Científico e Tecnológico, T32 GM075762, NIH, National Institutes of Health, U01TW006634-06, NIH, National Institutes of Health, U19-AI106772, NIAID, National Institute of Allergy and Infectious Diseases, U19-AI106772, NIH, National Institutes of Health, DFG, Deutsche Forschungsgemeinschaft, 2013/16496-5, FAPESP, São Paulo Research Foundation, 2014/50265-3, FAPESP, São Paulo Research Foundation, 1F32GM089044, NIH, National Institutes of Health, 1R01DE023810-01, NIH, National Institutes of Health, 1R01GM095373, NIH, National Institutes of Health, 200020-146200, FNS, French Norwegian Foundation, 2012/18031-7, FAPESP, São Paulo Research Foundation, NIAID, National Institute of Allergy and Infectious Diseases, K01 GM103809, NIH, National Institutes of Health, 31125002, NSFC, National Natural Science Foundation of China, 5R21AI085540, NIH, National Institutes of Health, 81102369, NSFC, National Natural Science Foundation of China, CN-12-552, CONACYT, Consejo Nacional de Ciencia y Tecnología, DEB 1010816, NSF, National Science Foundation, Wolfender, Jean-Luc, University of California-University of California, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-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)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), University of Campinas [Campinas] (UNICAMP), Centre National de la Recherche Scientifique (CNRS)-THALES, Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), École normale supérieure - Lyon (ENS Lyon)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, 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)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Rennes-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Unité mixte de physique CNRS/Thalès (UMP CNRS/THALES), THALES-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS),Saarland Universitätscampus E8.1, 66123 Saarbrücken, Germany.
Subjects: 0301 basic medicine, Internationality, Computer science, Information Dissemination/methods, Information Storage and Retrieval, Bioinformatics, Mass spectrometry data, 01 natural sciences, Applied Microbiology and Biotechnology, Knowledge base, Data driven, Ms libraries, Data Curation, Data Curation/methods, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, ddc:615, Natural products, 3. Good health, Identification (information), Molecular networking, Molecular Medicine, Knowledge based systems, Raw data, Biotechnology, Biological Products/chemistry/classification, Biomedical Engineering, Chemical, Bioengineering, Mass spectrometry, Article, Databases, Open Access, 03 medical and health sciences, Knowledge-based systems, Computational platforms and environments, TA164, MEDICINA, Tandem mass, High through-put characterization, Mass Spectrometry/statistics & numerical data, Biological Products, Data curation, Information Dissemination, Information Storage and Retrieval/methods, Spectrometry, 010405 organic chemistry, business.industry, Data science, 0104 chemical sciences, Data sharing, 030104 developmental biology, ZA, Database Management Systems, business, Databases, Chemical
Abstract: International audience; The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.
Published: 2016

25. Histone variants H2A.Z and H3.3 coordinately regulate PRC2-dependent H3K27me3 deposition and gene expression regulation in mES cells

Author: Baowen Zhuo, Xia Li, Guohong Li, Michel Wassef, Liping Dong, Jicheng Zhao, Juan Yu, Luyuan Chang, Qianfei Wang, Min Wang, Cuifang Liu, Haizhen Long, Ping Chen, Zengqi Wen, Xueqing Xu, Yan Wang, Raphaël Margueron, National Laboratory of Biomacromolecules [Pékin, Chine], CAS Center for Excellence in Biomacromolecules [Pékin, Chine], Institute of Biophysics [Pékin, Chine], Chinese Academy of Sciences [Beijing] (CAS)-Chinese Academy of Sciences [Beijing] (CAS)-Institute of Biophysics [Pékin, Chine], Chinese Academy of Sciences [Beijing] (CAS)-Chinese Academy of Sciences [Beijing] (CAS), University of Chinese Academy of Sciences [Beijing] (UCAS), Génétique et Biologie du Développement, Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Baoan Maternal and Child Health Hospital [Shenzhen, Chine], Jinan University [Canton, Chine] (JNU), Key Laboratory of Genomic and Precision Medicine [Pékin, Chine], Beijing Genomics Institute [Shenzhen] (BGI), This work was supported by grants to GL from the National Natural Science Foundation of China (31630041, 31525013 and 31521002), the Ministry of Science and Technology of China (2017YFA0504200, 2015CB856200), and the Chinese Academy of Sciences (CAS) Strategic Priority Research Program (XDB19040202), to PC from the National Natural Science Foundation of China (31471218) and the Youth Innovation Promotion Association CAS (2015071), and to XX from the Sanming Project of Medicine in Shenzhen (SZSM201406007). The work was also supported by the CAS Key Research Program on Frontier Science (QYZDY-SSW-SMC020) and HHMI international research scholar grant (55008737) to GL. Work in RM Lab is supported by an ERC-StG grant (REPODDID)., European Project: 281447,EC:FP7:ERC,ERC-2011-StG_20101109,REPODDID(2012), Bodescot, Myriam, and Regulation of Polycomb Complex (PRC2) during development and in diseases - REPODDID - - EC:FP7:ERC2012-02-01 - 2017-01-31 - 281447 - VALID
Subjects: 0301 basic medicine, animal structures, Physiology, Plant Science, macromolecular substances, [SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, General Biochemistry, Genetics and Molecular Biology, Cell Line, Histones, Mice, 03 medical and health sciences, Structural Biology, Transcription (biology), Gene expression, Animals, Gene silencing, lcsh:QH301-705.5, Gene, Ecology, Evolution, Behavior and Systematics, Regulation of gene expression, biology, Polycomb Repressive Complex 2, Mouse Embryonic Stem Cells, Promoter, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Cell Biology, Chromatin, Cell biology, 030104 developmental biology, lcsh:Biology (General), Gene Expression Regulation, biology.protein, General Agricultural and Biological Sciences, PRC2, Developmental Biology, Biotechnology
Abstract: International audience; BACKGROUND:The hierarchical organization of eukaryotic chromatin plays a central role in gene regulation, by controlling the extent to which the transcription machinery can access DNA. The histone variants H3.3 and H2A.Z have recently been identified as key regulatory players in this process, but the underlying molecular mechanisms by which they permit or restrict gene expression remain unclear. Here, we investigated the regulatory function of H3.3 and H2A.Z on chromatin dynamics and Polycomb-mediated gene silencing.RESULTS:Our ChIP-seq analysis reveals that in mouse embryonic stem (mES) cells, H3K27me3 enrichment correlates strongly with H2A.Z. We further demonstrate that H2A.Z promotes PRC2 activity on H3K27 methylation through facilitating chromatin compaction both in vitro and in mES cells. In contrast, PRC2 activity is counteracted by H3.3 through impairing chromatin compaction. However, a subset of H3.3 may positively regulate PRC2-dependent H3K27 methylation via coordinating depositions of H2A.Z to developmental and signaling genes in mES cells. Using all-trans retinoic acid (tRA)-induced gene as a model, we show that the dynamic deposition of H2A.Z and H3.3 coordinately regulates the PRC2-dependent H3K27 methylation by modulating local chromatin structure at the promoter region during the process of turning genes off.CONCLUSIONS:Our study provides key insights into the mechanism of how histone variants H3.3 and H2A.Z function coordinately to finely tune the PRC2 enzymatic activity during gene silencing, through promoting or impairing chromosome compaction respectively.
Published: 2018

26. Bacterial conjugated linoleic acid production and their applications

Author: Yong Q. Chen, Catherine Stanton, R. Paul Ross, Wei Chen, Hao Zhang, He Gao, Bo Yang, Haiqin Chen, National Natural Science Foundation of China, National Natural Science Foundation of Jiangsu Province, Fundamental Research Funds for the Central Universities, Jiangsu Province 'Collaborative Innovation Center for Food Safety and Quality Control', BK20150141, JUSRP51702A, and JUSRP11733
Subjects: 0301 basic medicine, Conjugated linoleic acid, Linoleic acid, 030106 microbiology, CLA bioconversion mechanism, Biochemistry, 03 medical and health sciences, Propionibacterium acnes, chemistry.chemical_compound, Microbial cell factories, Biosynthesis, Animals, Humans, Linoleic Acids, Conjugated, biology, Bacteria, integumentary system, Fungi, food and beverages, Cell Biology, Bacterial CLA-producers, biology.organism_classification, Food supplement, chemistry, lipids (amino acids, peptides, and proteins), Heterologous expression, Lactobacillus plantarum
Abstract: peer-reviewed Conjugated linoleic acid (CLA) has been shown to exert various potential physiological properties including anti-carcinogenic, anti-obesity, anti-cardiovascular and anti-diabetic activities, and consequently has been considered as a promising food supplement. Bacterial biosynthesis of CLA is an attractive approach for commercial production due to its high isomer-selectivity and convenient purification process. Many bacterial species have been reported to convert free linoleic acid (LA) to CLA, hitherto only the precise CLA-producing mechanisms in Propionibacterium acnes and Lactobacillus plantarum have been illustrated completely, prompting the development of recombinant technology used in CLA production. The purpose of the article is to review the bacterial CLA producers as well as the recent progress on describing the mechanism of microbial CLA-production. Furthermore, the advances and potential in the heterologous expression of CLA genetic determinants will be presented.
Published: 2017

27. Calredoxin represents a novel type of calcium-dependent sensor-responder connected to redox regulation in the chloroplast

Author: Martin Scholz, Ratana Charoenwattanasatien, Jan Niklas Offenborn, Dimitris Petroutsos, Christian Fufezan, Michael Hippler, Risa Mutoh, Stefan Schulze, Genji Kurisu, Hideaki Tanaka, Kaiyao Huang, Gai Liu, André Nordhues, Philipp Gäbelein, Ana Karina Hochmal, Karen Zinzius, Giovanni Finazzi, Institute for Plant Biochemistry and Biotechnology, Westfälische Wilhelms-Universität Münster = University of Münster (WWU), Institute for Protein Research [Osaka], Osaka University [Osaka], Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Guizhou Institute of Technology, Physiologie cellulaire et végétale (LPCV), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Centre de recherches Paul Pascal (CRPP), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Deutsche Forschungsgemeinschaft (DFG)HI 739/9-1 FOR964, Funding Program for Next Generation World-Leading Researchers from the Cabinet Office of Japan, GS016, International Joint Research Promotion Program, International Collaborative Research Program, Osaka University, Marie Curie ITN Accliphot, HFSP grants, National Natural Science Foundation of China 31171287, DFG FOR964, Deutsche Forschungsgemeinschaft (DFG, HI 739/9-1, FOR964)), Funding Program for Next Generation World-Leading Researchers (GS016) from the Cabinet Office of Japan, International Joint Research Promotion Program and International Collaborative Research Program, Osaka University, (G.K. and M.H.)., Marie Curie ITN Accliphot (G.F.), HFSP grants (G.F.), National Natural Science Foundation of China (31171287) (K.H.), DFG (FOR964) (J.K.), Westfälische Wilhelms-Universität Münster (WWU), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Centre National de la Recherche Scientifique (CNRS), and Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG)
Subjects: 0301 basic medicine, Models, Molecular, Protein Conformation, alpha-Helical, Protein Folding, Redox signaling, Chloroplasts, Thioredoxin reductase, [SDV]Life Sciences [q-bio], General Physics and Astronomy, Chlamydomonas reinhardtii, Gene Expression, Crystallography, X-Ray, Protein structure, Thioredoxins, Stress acclimation, Gene Expression Regulation, Plant, Calcium-binding protein, Cloning, Molecular, Photosynthesis, ComputingMilieux_MISCELLANEOUS, Plant Proteins, Multidisciplinary, chloroplaste, biology, Subcellular localization, food and beverages, Plants, Genetically Modified, Recombinant Proteins, 3. Good health, Cell biology, Biochemistry, Thioredoxin domain, Thioredoxin, Oxidation-Reduction, Protein Binding, Signal Transduction, Calmodulin, Algae, CRX, Science, Calredoxin, Chloroplast, General Biochemistry, Genetics and Molecular Biology, Article, Electron transfer, Electron Transport, 03 medical and health sciences, transfert d'électrons, Escherichia coli, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Protein Interaction Domains and Motifs, acclimatation, Binding Sites, Protein, Crystal structure, Chlamydomonas, fungi, Calcium-Binding Proteins, stress oxydatif, General Chemistry, Peroxiredoxins, biology.organism_classification, 030104 developmental biology, Oxidative stress, biology.protein, Calcium, Protein Conformation, beta-Strand, Peroxiredoxin
Abstract: Calcium (Ca2+) and redox signalling play important roles in acclimation processes from archaea to eukaryotic organisms. Herein we characterized a unique protein from Chlamydomonas reinhardtii that has the competence to integrate Ca2+- and redox-related signalling. This protein, designated as calredoxin (CRX), combines four Ca2+-binding EF-hands and a thioredoxin (TRX) domain. A crystal structure of CRX, at 1.6 Å resolution, revealed an unusual calmodulin-fold of the Ca2+-binding EF-hands, which is functionally linked via an inter-domain communication path with the enzymatically active TRX domain. CRX is chloroplast-localized and interacted with a chloroplast 2-Cys peroxiredoxin (PRX1). Ca2+-binding to CRX is critical for its TRX activity and for efficient binding and reduction of PRX1. Thereby, CRX represents a new class of Ca2+-dependent ‘sensor-responder' proteins. Genetically engineered Chlamydomonas strains with strongly diminished amounts of CRX revealed altered photosynthetic electron transfer and were affected in oxidative stress response underpinning a function of CRX in stress acclimation., Calcium and redox signalling have important roles in acclimation processes. Here, the authors characterise a protein from Chlamydomonas reinhardtii that can integrate calcium and redox-related signalling.
Published: 2016

28. Influence of H7N9 virus infection and associated treatment on human gut microbiota

Author: Lingjiao Wu, Ang Li, Yonghong Xiao, Jing Guo, Lanjuan Li, Jiawei Zhou, Lihua Guo, Weifeng Liang, Lin Liu, Jian Zuo, Yixin Zhu, Beiwen Zheng, S. Dusko Ehrlich, Nan Qin, Jian Yao, Ni Shujun, Zhejiang University, MetaGenoPolis, Institut National de la Recherche Agronomique (INRA), King‘s College London, National Program on Key Basic Research Project (2013CB531401), Natural Science Foundation of Zhejiang Province (NO. LR15H030002) Important National Science and Technology Project Research of Clinical Treatment for Emerging Severe Acute Respiratory Infectious Disease (2014ZX10004006), National Natural Science Foundation of China (NO. 81301475, 81301461, 31401144), Science Fund for Creative Research Groups of the National Natural Science Foundation of China (NO. 81121002), Important National Science and Technology Project-Research of Clinical treatment for Emerging severe acute respiratory infectious disease (2004ZX10004006), National Supporting Project (KJYJ-2013-01-05), the Technology Group Project for Infectious Disease Control of Zhejiang Province (2009R50041) and the China National Mega-projects for Infectious Diseases (2012ZX10004-210), and Metagenopolis grant ANR-11-DPBS-0001
Subjects: Adult, Male, medicine.drug_class, [SDV]Life Sciences [q-bio], Antibiotics, Enterococcus faecium, Influenza A Virus, H7N9 Subtype, Deep sequencing, Article, Microbiology, 03 medical and health sciences, Clostridium, Roseburia inulinivorans, Influenza, Human, medicine, Escherichia coli, Humans, 030304 developmental biology, Aged, Aged, 80 and over, 0303 health sciences, Multidisciplinary, biology, 030306 microbiology, High-Throughput Nucleotide Sequencing, Middle Aged, biology.organism_classification, Virology, 3. Good health, Gastrointestinal Microbiome, Metagenomics, Enterotype, Female, Bacteria
Abstract: Between March and June, 2013, forty H7N9 patients were hospitalized in our hospital. Next-generation sequencing technologies have been used to sequence the fecal DNA samples of the patient, the within sample diversity analysis, enterotyping, functional gene and metagenomic species analysis have been carried on both the patients and healthy controls. The influence of associated treatment in H7N9 infected patients is dramatic and was firstly revealed in species level due to deep sequencing technology. We found that most of the MetaGenomic Species (MGS) enriched in the control samples were Roseburia inulinivorans DSM 16841, butyrate producing bacterium SS3/4 and most of MGS enriched in the H7N9 patients were Clostridium sp. 7 2 43FAA and Enterococcus faecium. It was concluded that H7N9 viral infection and antibiotic administration have a significant effect on the microbiota community with decreased diversity and overgrowth of the bacteria such as Escherichia coli and Enterococcus faecium. Enterotype analysis showed that the communities were unstable. Treatment including antivirals, probiotics and antibiotics helps to improve the microbiota diversity and the abundance of beneficial bacteria in the gut.
Published: 2015

29. Environmental and socioeconomic correlates of extinction risk in endemic species

Author: Robin Pouteau, Caroline Brunel, Bernd Lenzner, Petr Pyšek, Franz Essl, Mark van Kleunen, Carsten Meyer, Jan Pergl, Hanno Seebens, Wayne Dawson, Holger Kreft, Marten Winter, Patrick Weigelt, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), Fonctionnement agroécologique et performances des systèmes de cultures horticoles (UPR HORTSYS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Durham University, University of Vienna [Vienna], Georg-August-University = Georg-August-Universität Göttingen, Leipzig University, Institute of Botany of the Czech Academy of Sciences (IB / CAS), Czech Academy of Sciences [Prague] (CAS), German Centre for Integrative Biodiversity Research (iDiv), Taizhou University, University of Konstanz, National Natural Science Foundation of China (grant no.31901176), Taizhou University (2018YQ001), BiodivERsA-Belmont Forum Project 'AlienScenarios' (I 4011-B32), CM acknowledges support by the Volkswagen Foundation through a Freigeist Fellowship., PP and JP were supported by EXPRO grant 19-28807X (Czech Science Foundation) and long-term research development project RVO 67985939 (Academy of Sciences of the Czech Republic)., HS acknowledges support by BiodivERsA/ BMBF project AlienScenarios (01LC1807A)., MvK acknowledges support by the German Research Foundation DFG (264740629)., Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Duke University [Durham], and University of Göttingen - Georg-August-Universität Göttingen
Subjects: 0106 biological sciences, anthropocene, Range (biology), [SDV.BID]Life Sciences [q-bio]/Biodiversity, anthropocene, biodiversity crisis, data limitation, global change, sixth mass extinction, 010603 evolutionary biology, 01 natural sciences, Invasive species, 03 medical and health sciences, ddc:570, IUCN Red List, biodiversity crisis, Taxonomic rank, Endemism, global change, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Invertebrate, sixth mass extinction, 0303 health sciences, Extinction, Ecology, data limitation, 15. Life on land, Geography, 13. Climate action, Threatened species
Abstract: Aim:Our current understanding of the causes of global extinction risk is mostly informed by the expert knowledge-based “threats classification scheme” of the IUCN Red List of Threatened Species. Studies based on this dataset came to different conclusions about the relative importance of threats to species, depending on which taxonomic groups and levels of extinction risk were considered, and which version of the database was used. A key reason may lie in data limitations as causes of threat are well known for charismatic and well-studied species, but not for the majority of species assessed. Here, we aim to fill current knowledge gaps about the importance of drivers of global extinction risks by focusing on endemic species.Location:Global.Methods:We examined country-level variation in the proportion of globally threatened and extinct endemic species (Index of Threat, IoT) with a range of spatially explicit information about anthropogenic pressures, mitigation measures and data limitations.Results:IoT coincided with several anthropogenic pressures, with substantial differences among kingdoms, life-forms, levels of extinction risk and geographic locations. IoT of plants, particularly tropical woody plants of moderate extinction risk, was higher in countries with higher GDP and more invasive species. Furthermore, IoT of animals, particularly tropical mammals and invertebrates of moderate extinction risk, was higher in countries with higher GDP and smaller roadless areas.Main conclusions:The extinction crisis for endemic species is associated with a complex network of potential drivers that need to be considered in concert in conservation policy and practice. Although our results require careful interpretation and remain sensitive to data limitations, we encourage similar studies at smaller scales to identify potential drivers of extinction risk at a higher resolution, particularly in regions where species assessments have been conducted consistently or on organisms with a uniform response time to pressures. published
Published: 2021

30. Sex differences in the factors associated with sleep duration in university students

Author: HongYi Shen, Hongru Chen, XiangYun Gai, Li Lu, Min Dong, Yuying Liu, Jie Gao, TianTian Zhang, Shou Liu, LiZhen Ye, ShengYan Jian, Bordeaux population health (BPH), Université de Bordeaux (UB)-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM), National Natural Science Foundation of China, and Public Health
Subjects: Male, China, Universities, Cross-sectional study, University student, education, Psychological intervention, Lifestyle behaviors, Physical exercise, Logistic regression, 03 medical and health sciences, 0302 clinical medicine, SDG 3 - Good Health and Well-being, Surveys and Questionnaires, Sex differences, Anxiety symptoms, Internet use, medicine, Humans, Duration (project management), Students, Sex Characteristics, Sleep duration, business.industry, 4. Education, Depressive symptoms, Sleep in non-human animals, Mental health, 030227 psychiatry, Psychiatry and Mental health, Clinical Psychology, Cross-Sectional Studies, Anxiety, Female, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, medicine.symptom, Sleep, business, 030217 neurology & neurosurgery, Demography
Abstract: Background Insufficient sleep duration among university students was commonly associated with many detrimental effects. University students experience substantial environmental and psychological changes. Female and male university students may differ in many spheres. However, most research on sleep duration of university students is based on an aggregate sample rather than digging the sex-specific profiles. The objective of this study is to examine potential sex differences in the correlates of sleep duration and explore the underlying mechanism of correlations. Methods This is a large-scale university-based mental health survey, which was conducted in university students in Qinghai Province in Northwest China in December 2019. A multi-stage logistic regression was separately fitted by sex to examine the factors associated with short sleep duration in university students. Results A total of 5,552 university students with an average sleep duration of 6.88 h (SD = 1.04) were included, among which 35.0% of the participants may currently be sleeping less than the optimal duration. Female students (6.84 h, SD = 1.00) slept shorter than males (6.94 h, SD = 1.09). The only parallel between sexes was that both female and male students with 3–5 times weekly breakfast were less likely to have short sleep duration. Adjusting for depressive symptoms in the following step eliminated the association between anxiety symptoms and short sleep duration in the model for female students. Female-specific associated factors with short sleep duration were age, grade, academic pressure, weekly physical exercise, depressive symptoms. Male-specific characteristics were current smoking tobacco cigarette, self-perceived health, duration of daily Internet use. Conclusion Characteristic profiles of sleep duration differed between female and male university students; only a few male-specific factors were identified. Psychological guidance and education courses as well as other interventions to improve university students’ sleep and related health should be designed and implemented based on sex differences.
Published: 2021

31. Enhanced alpha-ketoglutaric acid production in Yarrowia lipolytica WSH-Z06 by regulation of the pyruvate carboxylation pathway

Author: Guocheng Du, Catherine Madzak, Jian Chen, Jingwen Zhou, Xiaoxia Yin, Jiangnan University, Microbiologie et Génétique Moléculaire (MGM), Institut National de la Recherche Agronomique (INRA)-Institut National Agronomique Paris-Grignon (INA P-G)-Centre National de la Recherche Scientifique (CNRS), Major State Basic Research Development Program of China (973 Program) [2012CB7208022012CB720806], Key Program of National Natural Science Foundation of China [31130043], National Natural Science Foundation of China [31171638], Research Program of Sate Key Laboratory of Food Science and Technology, Jiangnan University [SKLF-TS-200901], Priority Academic Program Development of Jiangsu Higher Education Institutions, and 111 Project [111-2-06]
Subjects: Pyruvate decarboxylation, Yarrowia lipolytica, Saccharomyces cerevisiae Proteins, PROTEIN EXPRESSION, [SDV]Life Sciences [q-bio], Rhizopus oryzae, Yarrowia, Industrial fermentation, Saccharomyces cerevisiae, Applied Microbiology and Biotechnology, Organic acid production, Gene Expression Regulation, Enzymologic, CITRIC ACIDS, SACCHAROMYCES-CEREVISIAE, 03 medical and health sciences, chemistry.chemical_compound, alpha-Ketoglutaric acid, REDISTRIBUTION, Gene Expression Regulation, Fungal, Pyruvic Acid, ETHANOL, YEAST, Pyruvate Carboxylase, 030304 developmental biology, 0303 health sciences, biology, 030306 microbiology, CARBON FLUX, General Medicine, TORULOPSIS-GLABRATA, biology.organism_classification, Yeast, Up-Regulation, Pyruvate carboxylase, Pyruvate carboxylation, chemistry, Carboxylation, Biochemistry, Ketoglutaric Acids, SECRETION, OVEREXPRESSION, Metabolic engineering, Biotechnology
Abstract: International audience; In previous research, a thiamine-auxotrophic yeast for alpha-ketoglutaric acid (KGA) overproduction was screened in our laboratory and named Yarrowia lipolytica WSH-Z06 (CCTCC no. M207143). However, the high concentration of by-products (mainly pyruvate) limited its application on an industrial scale. To enhance KGA production and reduce pyruvate (PA) accumulation, the pyruvate carboxylation pathway was regulated. By overexpressing the pyruvate carboxylase genes ScPYC1 from Saccharomyces cerevisiae and RoPYC2 from Rhizopus oryzae in Y. lipolytica WSH-Z06, the yields of KGA in Y. lipolytica-ScPYC1 and Y. lipolytica-RoPYC2 increased by 24.5 and 35.3 %, and the yields of PA decreased by 51.9 and 69.8 % in shake flasks, respectively. These changes in the expression levels and activities of key intracellular enzymes showed that enhancing the pyruvate carboxylation pathway had successfully redistributed the carbon flux from PA to KGA. Finally, by controlling the pH in a 3-L fermenter, the maximum concentration of KGA in Y. lipolytica-RoPYC2 reached 62.5 g L-1 with an evident decrease in PA yield from 35.2 to 13.5 g L-1.
Published: 2012

32. Screening mutations of OTOF gene in Chinese patients with auditory neuropathy, including a familial case of temperature-sensitive auditory neuropathy

Author: Dominique Weil, Qing Yin Zheng, Dayong Wang, Cindy Benedict-Alderfer, Yu Bin Ji, Shao Qi Rao, Yichen Wang, Christine Petit, Yan Shen, Liang Zong, Ya Li Zhao, Qiu Ju Wang, Jian Qiang Li, Qiong Liu, Huanming Yang, Department of Otolaryngology/Head and Neck Surgery, Institute of Otolaryngology-Chinese PLA General Hospital, Beijing Genomics Institute [Shenzhen] (BGI), Collège de France - Chaire Génétique et physiologie cellulaire, Collège de France (CdF (institution)), Department of Biochemistry and Molecular Biology, Chinese Academy of Medical Sciences-Institute of Basic Medical Sciences-Peking Union Medical College, Department of Medical Statistics and Epidemiology, School of public health, The University of Hong Kong (HKU)-The University of Hong Kong (HKU), Chinese National Human Genome Centre, Department of Otolaryngology-HNS, Case Western Reserve University [Cleveland], This work was supported by grants from the National Natural Science Foundation of China, Key Project (No.30830104), the National Natural Science Foundation of China (Grant No.30672310&30771203), Beijing Nature Science Technology Major Project (7070002), the Chinese National 973 Project (GrantNo. 2007CB507400), the Chinese National Eleventh Five-years Scientific Program (Grant No. 2006BAI02B06 and No. 2007BAI18B12), the Natural Science Foundation of Guangdong Province Key Project (Grant No.4203003) and the Sun Yat-Sen University Start-up Fund (Grant No. 3171310)., BMC, Ed., and Chaire Génétique et physiologie cellulaire
Subjects: medicine.medical_specialty, lcsh:Internal medicine, lcsh:QH426-470, Hearing loss, Auditory neuropathy, Deafness, Audiology, Biology, [SDV.GEN.GH] Life Sciences [q-bio]/Genetics/Human genetics, medicine.disease_cause, 03 medical and health sciences, Familial case, Exon, Cricetulus, 0302 clinical medicine, Asian People, Cricetinae, Genetics, OTOF, medicine, Animals, Humans, Family, Genetics(clinical), Hearing Loss, lcsh:RC31-1245, Gene, Genetics (clinical), 030304 developmental biology, 0303 health sciences, Mutation, Base Sequence, Temperature, Membrane Proteins, Exons, medicine.disease, Human genetics, 3. Good health, lcsh:Genetics, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, medicine.symptom, 030217 neurology & neurosurgery, Research Article
Abstract: Background Mutations in OTOF gene, encoding otoferlin, cause DFNB9 deafness and non-syndromic auditory neuropathy (AN). The aim of this study is to identify OTOF mutations in Chinese patients with non-syndromic auditory neuropathy. Methods 73 unrelated Chinese Han patients with AN, including one case of temperature sensitive non-syndromic auditory neuropathy (TS-NSRAN) and 92 ethnicity-matched controls with normal hearing were screened. Forty-five pairs of PCR primers were designed to amplify all of the exons and their flanking regions of the OTOF gene. The PCR products were sequenced and analyzed for mutation identification. Results Five novel possibly pathogenic variants (c.1740delC, c.2975_2978delAG, c.1194T>A, c.1780G>A, c.4819C > T) were identified in the group of 73 AN patients, in which two novel mutant alleles (c.2975_2978delAG + c.4819C > T) were identified in one Chinese TS-NSRAN case. Besides, 10 non-pathogenic variants of the OTOF gene were found in AN patients and controls. Conclusions Screening revealed that mutations in the OTOF gene account for AN in 4 of 73(5.5%) sporadic AN patients, which shows a lower genetic load of that gene in contrast to the previous studies based on other populations. Notably, we found two novel mutant alleles related to temperature sensitive non-syndromic auditory neuropathy. This mutation screening study further confirms that the OTOF gene contributes to ANs and to TS-NSRAN.
Published: 2010

33. Genomic analyses provide insights into peach local adaptation and responses to climate change

Author: Wenwu Guo, Weichao Fang, Zhangjun Fei, Sanwen Huang, Changwen Chen, Pere Arús, Jiao Wang, Jian Guo, Liping Guan, Xinwei Wang, Junxiu Wang, Lirong Wang, Qi Wang, Ke Cao, Kuozhan Liu, Nan Li, Gengrui Zhu, Tiyu Ding, Yong Li, National Natural Science Foundation of China, National Science Foundation (US), Producció Vegetal, and Genòmica i Biotecnologia
Subjects: Prunus persica, 0303 health sciences, Candidate gene, Natural selection, Human evolutionary genetics, Research, Climate Change, Genomics, Biology, Adaptation, Physiological, Genome, 03 medical and health sciences, 0302 clinical medicine, Evolutionary biology, Genetics, Adaptation, Genome, Plant, 030217 neurology & neurosurgery, Genetics (clinical), Selection (genetic algorithm), 030304 developmental biology, Genetic association, Local adaptation
Abstract: The environment has constantly shaped plant genomes, but the genetic bases underlying how plants adapt to environmental influences remain largely unknown. We constructed a high-density genomic variation map of 263 geographically representative peach landraces and wild relatives. A combination of whole-genome selection scans and genome-wide environmental association studies (GWEAS) was performed to reveal the genomic bases of peach adaptation to diverse climates. A total of 2092 selective sweeps that underlie local adaptation to both mild and extreme climates were identified, including 339 sweeps conferring genomic pattern of adaptation to high altitudes. Using genome-wide environmental association studies (GWEAS), a total of 2755 genomic loci strongly associated with 51 specific environmental variables were detected. The molecular mechanism underlying adaptive evolution of high drought, strong UVB, cold hardiness, sugar content, flesh color, and bloom date were revealed. Finally, based on 30 yr of observation, a candidate gene associated with bloom date advance, representing peach responses to global warming, was identified. Collectively, our study provides insights into molecular bases of how environments have shaped peach genomes by natural selection and adds candidate genes for future studies on evolutionary genetics, adaptation to climate changes, and breeding., This work was supported by grants from the Agricultural Science and Technology Innovation Program (CAAS-ASTIP-2020-ZFRI01), the National Natural Science Foundation of China (31572094), the Crop Germplasm Resources Conservation Project (2016NWB041), and the U.S. National Science Foundation (IOS-1339287 and IOS-1855585).
Published: 2021

34. Modeling canopy photosynthesis and light interception partitioning among shoots in bi-axis and single-axis apple trees (Malus domestica Borkh.)

Author: Mingyu Han, Sayed Hussain, Evelyne Costes, Xiaolong Ma, Weiwei Yang, Dong Zhang, Doudou Ma, Jidong Shi, Northwest A and F University, Shihezi University, Shaanxi Huasheng (Group) Corp. Fruit Co., Abdul Wali Khan University, Architecture et Fonctionnement des Espèces Fruitières [AGAP] (AFEF), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), National Natural Science Foundation of China (NSFC) (31860527), Shaanxi province Key Research and Development Program (2017ZDXM-NY-511019, 2016KTZDNY01-04), China Apple Research System CARS-27, National Key R&D Program Projects 2018YFD1000200, and China Scholarship Council
Subjects: 0106 biological sciences, 0301 basic medicine, Canopy, Malus, Physiology, Vegetative reproduction, Plant Science, 01 natural sciences, Training system, 03 medical and health sciences, Vegetative shoot, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Fruiting shoot, STAR, Ecology, biology, Forestry, 15. Life on land, biology.organism_classification, 3D digitizing, Horticulture, 030104 developmental biology, Mutual shading, Shoot, Allometry, Shading, Interception, Orchard, Virtual orchard, 010606 plant biology & botany
Abstract: International audience; Key message Bi-axis training increased vegetative shoot light interception and modeled photosynthetic rate, and reduced fruiting shoot mutual shading and vegetative growth by optimizing canopy structure compared to single-axis in young apple trees. Improving light interception and distribution within canopy are constant objectives of training through manipulating tree architecture. A bi-axis training system with two primary scaffolds has been proposed to improve flowering and dry matter production in apple trees. In this study, 'Fuji' apple trees trained using a bi-axis or single-axis training system were compared. Twelve three-dimensional (3D) virtual apple trees were reconstructed by combining 3D digitizing and allometric relationships for three shoot types (vegetative long shoot, VL; fruiting shoot, FS; vegetative short shoot, VS), to evaluate canopy structure impacts on light interception. Light interception efficiency was evaluated by silhouette to total area ratio (STAR). The potential canopy photosynthetic rate was evaluated by the eco-physiological RATP model. The leaf area of VL in bi-axis trained trees was approximately 40% lower than that in single-axis trees. Lower leaf area and more uniform spatial distribution were noted in VL in bi-axis than in single-axis trees. This led to more even spatial light distribution and more shoots having higher STAR in bi-axis than in single-axis trees, regardless of the whole tree or shoot type. In the virtual orchard, bi-axis trees had a 25% and 10% STAR increase in VS and VL, respectively, but a similar STAR for FS compared to single-axis trees. Mutual shading between neighboring trees in the virtual orchard made of bi-axis trees was significantly lower than that with single-axis trees for FS. The modeled canopy net photosynthetic rate was 26% higher in bi-axis than in single-axis trees. With the increase in tree age, the projected leaf area increased, but the porosity of the canopy decreased, and mutual shading increased for the whole canopy and all shoot types, irrespective of training systems. These results indicated that manipulating scaffolds in apple trees can regulate canopy structure, light interception, and vegetative growth during the early developmental stages.
Published: 2021

35. Analysis of allelic variants of RhMLO genes in rose and functional studies on susceptibility to powdery mildew related to clade V homologs

Author: Peihong Fang, Xin Zhang, Xintong Liu, Juliane Geike, Deepika Lakwani, Helgard Kaufmann, Fabrice Foucher, Jérémy Clotault, Yuling Bai, Thomas Debener, Zhao Zhang, Marinus J. M. Smulders, Paul Arens, China Agricultural University (CAU), Wageningen University and Research [Wageningen] (WUR), Chinese Research Academy of Environmental Sciences, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-AGROCAMPUS OUEST, 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Leibniz Universität Hannover [Hannover] (LUH), Leibniz University Hannover, National Natural Science Foundation of China (NSFC) : 31501791, and China Scholarship Council : TKI TU, TU18142.
Subjects: 0106 biological sciences, Candidate gene, Plant disease resistance, Rosa, 01 natural sciences, Genome, Chromosomes, Plant, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Laboratorium voor Plantenveredeling, Ascomycota, Gene Expression Regulation, Plant, Genetics, Rosa chinensis, Gene family, Life Science, Gene, Alleles, Phylogeny, 030304 developmental biology, Disease Resistance, Plant Diseases, Plant Proteins, 2. Zero hunger, 0303 health sciences, biology, Chromosome Mapping, food and beverages, General Medicine, biology.organism_classification, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, Plant Breeding, Original Article, EPS, Agronomy and Crop Science, Powdery mildew, Podosphaera pannosa, 010606 plant biology & botany, Biotechnology
Abstract: Key messageRose has 19 MLO genes. Of these, RhMLO1 and RhMLO2 were shown to be required for powdery mildew infection, which suggests their potential as susceptibility targets towards disease resistance.AbstractPowdery mildew, caused byPodosphaera pannosa, is one of the most serious and widespread fungal diseases for roses, especially in greenhouse-grown cut roses. It has been shown that certainMLO genes are involved in powdery mildew susceptibility and that loss of function in these genes in various crops leads to broad-spectrum, long-lasting resistance against this fungal disease. For this reason, theseMLOgenes are called susceptibility genes. We carried out a genome-wide identification of theMLOgene family in theRosa chinensisgenome, and screened for allelic variants among 22 accessions from seven differentRosaspecies using re-sequencing and transcriptome data. We identified 19MLOgenes in rose, of which four are candidate genes for functional homologs in clade V, which is the clade containing all dicotMLOsusceptibility genes. We detected a total of 198 different allelic variants in the set ofRosaspecies and accessions, corresponding to 5–15 different alleles for each of the genes. Some diploidRosaspecies shared alleles with tetraploid rose cultivars, consistent with the notion that diploid species have contributed to the formation of tetraploid roses. Among the fourRhMLOgenes in clade V, we demonstrated using expression study, virus-induced gene silencing as well as transient RNAi silencing that two of them,RhMLO1andRhMLO2, are required for infection byP. pannosaand suggest their potential as susceptibility targets for powdery mildew resistance breeding in rose.
Published: 2021

36. A<scp>HY5‐COL3‐COL13</scp>regulatory chain for controlling hypocotyl elongation inArabidopsis

Author: Hongmei Chen, Shulan Sun, Qin Zhang, Yaqin Wang, Xiaojing Wang, Sujuan Gao, Bin Liu, Hong Long, Lili Ye, Jing Yan, National Natural Science Foundation of China, China Postdoctoral Science Foundation, and National Thousand Young Talents program of China
Subjects: 0106 biological sciences, 0301 basic medicine, Light, Physiology, education, Arabidopsis, Plant Science, Biology, Real-Time Polymerase Chain Reaction, 01 natural sciences, Hypocotyl, 03 medical and health sciences, RNA interference, Immunoprecipitation, Arabidopsis thaliana, Transcription factor, Arabidopsis Proteins, fungi, food and beverages, RNA, Promoter, biology.organism_classification, Cell biology, Basic-Leucine Zipper Transcription Factors, 030104 developmental biology, Photomorphogenesis, Transcription Factors, General, Carrier Proteins, 010606 plant biology & botany
Abstract: CONSTANS-LIKE (COL) family members are commonly implicated in light signal transduction during early photomorphogenesis. However, some of their functions remain unclear. Here, we propose a role for COL13 in hypocotyl elongation in Arabidopsis thaliana. We found that COL13 RNA accumulates at high levels in hypocotyls and that a disruption in the COL13 function via a T-DNA insertion or RNAi led to the formation of longer hypocotyls of Arabidopsis seedlings under red light. On the contrary, overexpression of COL13 resulted in the formation of shorter hypocotyls. Using various genetic, genomic, and biochemical assays, we proved that another COL protein, COL3, directly binds to the promoter of COL13, and the promoter region of COL3 was targeted by the transcription factor LONG HYPOCOTYL 5 (HY5), to form an HY5-COL3-COL13 regulatory chain for regulating hypocotyl elongation under red light. Additionally, further study demonstrated that COL13 interacts with COL3, and COL13 promotes the interaction between COL3 and CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1), suggesting a possible COP1-dependent COL3-COL13 feedback pathway. Our results provide new information regarding the gene network in mediating hypocotyl elongation., China International Postdoctoral grant, Grant/Award Number: 20170053; National Natural Science Foundation of China, Grant/Award Numbers: 31572161, 31672188; Youth Foundation of the National Natural Science Foundation of China, Grant/Award Number: 30900107
Published: 2020

37. miR-26a mediates LC-PUFA biosynthesis by targeting the Lxrα–Srebp1 pathway in the marine teleost Siganus canaliculatus

Author: Shuqi Wang, Xianda He, Douglas R. Tocher, Cuihong You, Cuiying Chen, Yuanyou Li, Mei Zhang, Yu Hu, Xiaobo Wen, Óscar Monroig, National Natural Science Foundation of China, National Key Research and Development Program (China), Natural Science Foundation of Guangdong Province, Monroig, Óscar, Tocher, Douglas R., Monroig, Óscar [0000-0001-8712-0440], and Tocher, Douglas R. [0000-0002-8603-9410]
Subjects: 0301 basic medicine, Lxrα, miR-26a, Srebp1, Biosynthesis, LC-PUFA, Biochemistry, 03 medical and health sciences, chemistry.chemical_compound, medicine, Liver X receptor, Molecular Biology, Regulation of gene expression, Gene knockdown, 030102 biochemistry & molecular biology, Fatty acid metabolism, Lipid metabolism, Cell Biology, Fatty acid, Gene regulation, Cell biology, Sterol regulatory element-binding protein, Siganus canaliculatus, 030104 developmental biology, medicine.anatomical_structure, chemistry, Hepatocyte, lipids (amino acids, peptides, and proteins), MicroRNA (miRNA)
Abstract: MicroRNAs have been recently shown to be important regulators of lipid metabolism. However, the mechanisms of microRNA-mediated regulation of long-chain polyunsaturated fatty acid (LC-PUFA) biosynthesis in vertebrates remain largely unknown. Herein, we for the first time addressed the role of miR-26a in LC-PUFA biosynthesis in the marine rabbitfish Siganus canaliculatus The results showed that miR-26a was significantly down-regulated in liver of rabbitfish reared in brackish water and in S. canaliculatus hepatocyte line (SCHL) incubated with the LC-PUFA precursor α-linolenic acid, suggesting that miR-26a may be involved in LC-PUFA biosynthesis because of its abundance being regulated by factors affecting LC-PUFA biosynthesis. Opposite patterns were observed in the expression of liver X receptor α (lxrα) and sterol regulatory element-binding protein-1 (srebp1), as well as the LC-PUFA biosynthesis-related genes (Δ4 fads2, Δ6Δ5 fads2, and elovl5) in SCHL cells incubated with α-linolenic acid. Luciferase reporter assays revealed rabbitfish lxrα as a target of miR-26a, and overexpression of miR-26a in SCHL cells markedly reduced protein levels of Lxrα, Srebp1, and Δ6Δ5 Fads2 induced by the agonist T0901317. Moreover, increasing endogenous Lxrα by knockdown of miR-26a facilitated Srebp1 activation and concomitant increased expression of genes involved in LC-PUFA biosynthesis and consequently promoted LC-PUFA biosynthesis both in vitro and in vivo These results indicate a critical role of miR-26a in regulating LC-PUFA biosynthesis through targeting the Lxrα-Srebp1 pathway and provide new insights into the regulatory network controlling LC-PUFA biosynthesis and accumulation in vertebrates., This work was financially supported by National Natural Science Foundation of China Grants 31873040 and 31702357, National Key R&D Program of China Grant 2018YFD0900400, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding Grant 2017B030314058, and The Shantou University (STU) Scientific Research Foundation for Talents Grant NTF19019.
Published: 2020

38. Can food processing produce hypoallergenic egg?

Author: Daniel Lozano-Ojalvo, Qianlu Xing, Xiaojuan Ma, Rui Liang, National Natural Science Foundation of China, and Guizhou Science and Technology Department
Subjects: Food industry, Food Handling, 030309 nutrition & dietetics, Eggs, Egg protein, Biology, medicine.disease_cause, 03 medical and health sciences, 0404 agricultural biotechnology, Allergen, medicine, Animals, Humans, Food science, Egg Hypersensitivity, 0303 health sciences, business.industry, Adverse food reaction, Egg Proteins, Hypoallergenic, 04 agricultural and veterinary sciences, Allergens, medicine.disease, 040401 food science, Egg allergy, embryonic structures, Food processing, business, Chickens, After treatment, Food Science
Abstract: Eggs and their derived products are common foods that can induce food allergic reaction, especially in children. The reported incidence of egg allergy is 1% to 2%, and its prevalence has rapidly increased in recent years. Currently, there is no approved treatment for it. The clinical guidance for this adverse food reaction is the complete elimination of egg (and their derived products) from diet, which is difficult due to the wide use of egg ingredients in food industry. Food processing methods can affect the conformational and/or linear epitopes of allergens and may change the allergenicity of egg. Thermal treatment and various other processing methods based on the enzymatic hydrolysis and irradiation have been found useful in reducing allergenicity of certain egg allergens. However, processed egg proteins can also show an increased allergenicity after treatment and the correct pattern to follow for the generation of hypoallergenic products remains unclear. This review explores the influence of processing methods on egg allergenicity and reports the best options for the generation of hypoallergenic egg products to date., This work was supported by the National Natural Science Foundation of China (No. 31660443); Young Talents Program of Zunyi Medical College (No. 18zy‐009); Guizhou Province Science and Technology Projects (No. 2019‐1348); and Guizhou Health and Family Planning Project (NO. D‐488).
Published: 2020

39. fat-1 transgenic zebrafish are protected from abnormal lipid deposition induced by high-vegetable oil feeding

Author: Shouxiang Sun, Filipe Castro, Xiaojuan Cao, Jian Gao, Óscar Monroig, National Natural Science Foundation of China, and Fundamental Research Funds for the Central Universities (China)
Subjects: Vegetable oil-feeding, medicine.medical_specialty, Fat-1, food.ingredient, Diet, High-Fat, Applied Microbiology and Biotechnology, Soybean oil, Mice, 03 medical and health sciences, food, Downregulation and upregulation, Internal medicine, Fatty Acids, Omega-3, medicine, Animals, Plant Oils, Zebrafish, Caenorhabditis elegans, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Lipid deposition, biology, 030306 microbiology, Chemistry, Wild type, food and beverages, Lipid metabolism, General Medicine, Lipid Metabolism, biology.organism_classification, Mice, Inbred C57BL, Endocrinology, Vegetable oil, Liver, Mitochondrial energy metabolism, lipids (amino acids, peptides, and proteins), Biotechnology, Polyunsaturated fatty acid
Abstract: High dietary concentration of vegetable oil, particularly those rich in n-6 polyunsaturated fatty acids (PUFAs), can induce negative physiological effects including excessive lipid deposition in teleost fish. Omega-3 desaturase (Fat-1) of Caenorhabditis elegans is able to convert n-6 PUFAs to n-3 PUFAs and thus induces a low n-6/n-3 PUFAs ratio alleviating lipid deposition. In this study, we investigated the effects of dietary n-6 PUFAs on lipid metabolism of fat-1 transgenic zebrafish (Tg:fat-1), to explore the role of fat-1 in fish lipid metabolism. We first generated Tg:fat-1 zebrafish and assayed the effects of a low-fat diet (LFD) and a high-fat diet (HFD) prepared from soybean oil. Wild type zebrafish (WT) fed with HFD (HFD-WT) exhibited increased obesity and lipid deposition, especially in the abdominal cavity and liver. These defects were absent from HFD-Tg:fat-1. For each diet group, Tg:fat-1 exhibited significantly decreased levels of almost all hepatic lipid classes compared with WT. Expression levels of lipid synthesis-related genes and lipid deposition-related genes were markedly lower in the liver of HFD-Tg:fat-1 compared with HFD-WT. In contrast, the steatolysis-related genes significantly upregulated in HFD-Tg:fat-1. Then expression profiles of mitochondrial energy metabolism-related genes and ATP contents in the livers from LFD-WT, LFD-Tg:fat-1, HFD-WT, and HFD-Tg:fat-1 were determined. Our findings suggest that fat-1 protects fish from abnormal lipid deposition induced by high-vegetable oil feeding, through endogenously converting n-6 PUFAs to n-3 PUFAs., This study was supported by the National Natural Science Foundation of China (31672660 and 31872579) and Fundamental Research Funds for the Central Universities (2662018PY034)
Published: 2020

40. Climate mediates continental scale patterns of stream microbial functional diversity

Author: Jizhong Zhou, Emilio O. Casamayor, Félix Picazo, Lijuan Ren, Jianjun Wang, Qinglong L. Wu, Annika Vilmi, Yongqin Liu, Janne Soininen, Juha Aalto, Ji Shen, National Natural Science Foundation of China, Chinese Academy of Sciences, Institute of Biotechnology (-2009), Department of Geosciences and Geography, Biosciences, and Helsinki Institute of Sustainability Science (HELSUS)
Subjects: DECOMPOSITION, 0106 biological sciences, Microbiology (medical), China, Microbial functional genes, Climate, Biodiversity, Beta diversity, Climate change, Elevational gradients, Biology, 010603 evolutionary biology, 01 natural sciences, Microbiology, Freshwater ecosystem, lcsh:Microbial ecology, 03 medical and health sciences, Rivers, REGRESSION, WATER, Ecosystem, 14. Life underwater, BETA-DIVERSITY, Macroecology, TEMPERATURE, 1172 Environmental sciences, 030304 developmental biology, 0303 health sciences, Norway, Ecology, Research, SPECIES RICHNESS, 15. Life on land, COMMUNITY, Stream biofilm, Spain, 13. Climate action, lcsh:QR100-130, BIODIVERSITY, Alpha diversity, Species richness, SOIL CARBON, human activities
Abstract: [Background]: Understanding the large-scale patterns of microbial functional diversity is essential for anticipating climate change impacts on ecosystems worldwide. However, studies of functional biogeography remain scarce for microorganisms, especially in freshwater ecosystems. Here we study 15,289 functional genes of stream biofilm microbes along three elevational gradients in Norway, Spain and China., [Results]: We find that alpha diversity declines towards high elevations and assemblage composition shows increasing turnover with greater elevational distances. These elevational patterns are highly consistent across mountains, kingdoms and functional categories and exhibit the strongest trends in China due to its largest environmental gradients. Across mountains, functional gene assemblages differ in alpha diversity and composition between the mountains in Europe and Asia. Climate, such as mean temperature of the warmest quarter or mean precipitation of the coldest quarter, is the best predictor of alpha diversity and assemblage composition at both mountain and continental scales, with local non-climatic predictors gaining more importance at mountain scale. Under future climate, we project substantial variations in alpha diversity and assemblage composition across the Eurasian river network, primarily occurring in northern and central regions, respectively., [Conclusions]: We conclude that climate controls microbial functional gene diversity in streams at large spatial scales; therefore, the underlying ecosystem processes are highly sensitive to climate variations, especially at high latitudes. This biogeographical framework for microbial functional diversity serves as a baseline to anticipate ecosystem responses and biogeochemical feedback to ongoing climate change., The study was supported by National Natural Science Foundation of China (91851117), the Program of Global Change and Mitigation (2017YFA0605200), CAS Key Research Program of Frontier Sciences (QYZDB-SSW-DQC043), CAS Strategic Pilot Science and Technology (XDA20050101), and National Natural Science Foundation of China (41571058, 41871048). AV was supported by the Chinese Academy of Sciences President’s International Fellowship Initiative (2018PS0007). EOC was supported by grant BRIDGES CGL2015-69043-P (Spanish Office for Science-MINECO-ERDF).
Published: 2020

41. The miR-15/16 Cluster Is Involved in the Regulation of Vertebrate LC-PUFA Biosynthesis by Targeting pparγ as Demonostrated in Rabbitfish Siganus canaliculatus

Author: Yang Liu, Yuanyou Li, Hongyu Ma, Junjun Sun, Shuqi Wang, Cuiying Chen, Óscar Monroig, Cuihong You, Douglas R. Tocher, National Key Research and Development Program (China), National Natural Science Foundation of China, Natural Science Foundation of Guangdong Province, Agriculture Research System of China, Monroig, Óscar, and Monroig, Óscar [0000-0001-8712-0440]
Subjects: Fish Proteins, 0106 biological sciences, 0301 basic medicine, FADS2, Rabbitfish Siganus canaliculatus, 01 natural sciences, Applied Microbiology and Biotechnology, Cell Line, 03 medical and health sciences, chemistry.chemical_compound, Biosynthesis, 010608 biotechnology, microRNA, Animals, RNA, Messenger, Receptor, Gene knockdown, Messenger RNA, Binding Sites, biology, Fishes, Peroxisome, LC-PUFA biosynthesis, biology.organism_classification, Cell biology, PPAR gamma, MicroRNAs, 030104 developmental biology, Gene Expression Regulation, chemistry, pparγ, Fatty Acids, Unsaturated, Hepatocytes, miR-15/16 cluste, Rabbitfish
Abstract: Post-transcriptional regulatory mechanisms play important roles in the regulation of long-chain (≥ C20) polyunsaturated fatty acid (LC-PUFA) biosynthesis. Here, we address a potentially important role of the miR-15/16 cluster in the regulation of LC-PUFA biosynthesis in rabbitfish Siganus canaliculatus. In rabbitfish, miR-15 and miR-16 were both highly responsive to fatty acids affecting LC-PUFA biosynthesis and displayed a similar expression pattern in a range of rabbitfish tissues. A common potential binding site for miR-15 and miR-16 was predicted in the 3′UTR of peroxisome proliferator-activated receptor gamma (pparγ), an inhibitor of LC-PUFA biosynthesis in rabbitfish, and luciferase reporter assays revealed that pparγ was a potential target of miR-15/16 cluster. In vitro individual or co-overexpression of miR-15 and miR-16 in rabbitfish hepatocyte line (SCHL) inhibited both mRNA and protein levels of Pparγ, and increased the mRNA levels of Δ6Δ5 fads2, Δ4 fads2, and elovl5, key enzymes of LC-PUFA biosynthesis. Inhibition of pparγ was more pronounced with co-overexpression of miR-15 and miR-16 than with individual overexpression in SCHL. Knockdown of miR-15/16 cluster gave opposite results, and increased mRNA levels of LC-PUFA biosynthesis enzymes were observed after knockdown of pparγ. Furthermore, miR-15/16 cluster overexpression significantly increased the contents of 22:6n-3, 20:4n-6 and total LC-PUFA in SCHL with higher 18:4n-3/18:3n-3 and 22:6n-3/22:5n-3 ratio. These suggested that miR-15 and miR-16 as a miRNA cluster together enhanced LC-PUFA biosynthesis by targeting pparγ in rabbitfish. This is the first report of the participation of miR-15/16 cluster in LC-PUFA biosynthesis in vertebrates., This work was financially supported by the National Key R&D Program of China (2018YFD0900400), National Natural Science Foundation of China (No. 31873040 & No. 31702357), Natural Science Foundation of Guangdong Province (2018A030313910), China Agriculture Research System (CARS-47), Innovation and Strong School Projects in Guangdong Province (2016KTSCX037), STU Scientific Research Foundation for Talents (NTF19019), Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding (2017B030314058), and Natural Science Foundation of Guangdong Province (2020A1515011252).
Published: 2020

42. Risk for Transportation of Coronavirus Disease from Wuhan to Other Cities in China

Author: Zhanwei Du, Xianwen Wang, Benjamin J. Cowling, Xiaoke Xu, Simon Cauchemez, Lin Wang, Lauren Ancel Meyers, University of Texas at Austin [Austin], Institut Pasteur [Paris] (IP), Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Dalian Minzu University, Dalian University of Technology, The University of Hong Kong (HKU), Santa Fe Institute, We acknowledge the financial support from National Institutes of Health (grant no. U01 GM087719), the Investissement d’Avenir program, the Laboratoire d’Excellence Integrative Biology of Emerging Infectious Diseases program (grant no. ANR-10-LABX-62-IBEID), European Union V.E.O project, the Open Fund of Key Laboratory of Urban Land Resources Monitoring and Simulation, Ministry of Land and Resources (grant no. KF-2019-04-034), and the National Natural Science Foundation of China (grant no. 61773091)., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), Institut Pasteur [Paris], Wang, Lin [0000-0002-5371-2138], and Apollo - University of Cambridge Repository
Subjects: Risk for Transportation of 2019 Novel Coronavirus Disease from Wuhan to Other Cities in China, MESH: Coronavirus Infections, Epidemiology, coronavirus, lcsh:Medicine, Transportation, medicine.disease_cause, MESH: Risk Assessment, Disease Outbreaks, law.invention, 0302 clinical medicine, law, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], Pandemic, MESH: COVID-19, 030212 general & internal medicine, MESH: Disease Outbreaks, Socioeconomics, Coronavirus, MESH: China, 3. Good health, Geography, Infectious Diseases, MESH: Stochastic Processes, 2019-nCoV, Quarantine, MESH: Betacoronavirus, Coronavirus Infections, Risk assessment, MESH: Quarantine, severe acute respiratory syndrome coronavirus 2, Wuhan, MESH: Forecasting, Microbiology (medical), China, MESH: Pandemics, Coronavirus disease 2019 (COVID-19), Pneumonia, Viral, 030231 tropical medicine, Risk Assessment, lcsh:Infectious and parasitic diseases, 2019 novel coronavirus disease, Betacoronavirus, 03 medical and health sciences, Research Letter, medicine, MESH: Cities, Humans, lcsh:RC109-216, viruses, MESH: SARS-CoV-2, Cities, Pandemics, Stochastic Processes, Models, Statistical, MESH: Humans, outbreak, SARS-CoV-2, MESH: Transportation, lcsh:R, importation, Outbreak, COVID-19, Metropolitan area, MESH: Pneumonia, Viral, MESH: Models, Statistical, Forecasting
Abstract: International audience; On January 23, 2020, China quarantined Wuhan to contain coronavirus disease (COVID-19). We estimated the probability of transportation of COVID-19 from Wuhan to 369 other cities in China before the quarantine. Expected COVID-19 risk is >50% in 130 (95% CI 89-190) cities and >99% in the 4 largest metropolitan areas.
Published: 2020
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43. Environmental remodeling of human gut microbiota and antibiotic resistome in livestock farms

Author: Z. L. Zeng, Ting Huang, Yu-Feng Zhou, Zhiwei Fang, Qiu Long Yan, Bing Hu Fang, You-Zhi Tang, You Jun Feng, Ke Cheng, Manish Boolchandani, Hong-Xia Jiang, Yong Xue Sun, Xian Bo Deng, Liang Li, Rong Min Zhang, Jing Xia, Jian Sun, Yang Yu, Xin Lei Lian, José L. Martínez, Alaric W. D’Souza, Ya Hong Liu, Gautam Dantas, Liang Xing Fang, Shenghui Li, Xiao-Ping Liao, National Key Research and Development Program (China), Ministry of Education of the People's Republic of China, Natural Science Foundation of Guangdong Province, National Natural Science Foundation of China, George Washington University, and National Institutes of Health (US)
Subjects: Adult, Male, 0301 basic medicine, Farms, Swine, Science, 030106 microbiology, General Physics and Astronomy, Zoology, Drug resistance, Biology, Gut flora, Antimicrobial resistance, Article, General Biochemistry, Genetics and Molecular Biology, Microbial ecology, Young Adult, 03 medical and health sciences, Antibiotic resistance, Occupational Exposure, Drug Resistance, Bacterial, Animals, Humans, Microbiome, Students, lcsh:Science, Schools, Veterinary, Multidisciplinary, Bacteria, Gastrointestinal Microbiome, Probabilistic data networks, fungi, General Chemistry, biology.organism_classification, Anti-Bacterial Agents, Resistome, Gastrointestinal Tract, 030104 developmental biology, Metagenomics, lcsh:Q
Abstract: © The Author(s) 2020., Anthropogenic environments have been implicated in enrichment and exchange of antibiotic resistance genes and bacteria. Here we study the impact of confined and controlled swine farm environments on temporal changes in the gut microbiome and resistome of veterinary students with occupational exposure for 3 months. By analyzing 16S rRNA and whole metagenome shotgun sequencing data in tandem with culture-based methods, we show that farm exposure shapes the gut microbiome of students, resulting in enrichment of potentially pathogenic taxa and antimicrobial resistance genes. Comparison of students’ gut microbiomes and resistomes to farm workers’ and environmental samples revealed extensive sharing of resistance genes and bacteria following exposure and after three months of their visit. Notably, antibiotic resistance genes were found in similar genetic contexts in student samples and farm environmental samples. Dynamic Bayesian network modeling predicted that the observed changes partially reverse over a 4-6 month period. Our results indicate that acute changes in a human’s living environment can persistently shape their gut microbiota and antibiotic resistome., This work was jointly supported by the National Key Research and Development Program of China (2016YFD0501300 to Y.-H.L.), the Program for Changjiang Scholars and Innovative Research Team in University of Ministry of Education of China (IRT_17R39 to Y.-H.L.), the Foundation for Innovation and Strengthening School Project of Guangdong (2016KCXTD010 to Y.-H.L.), the National Natural Science Foundation of China (31730097 to Y.-H.L.), the 111 Project (D20008 to J.S., X.-P.L., and Y.-H.L.), the Institutional Program Unifying Population and Laboratory-Based Sciences Burroughs Wellcome Fund grant to Washington University (supporting A.W.D.), and the National Institutes of Health (NIH) Director’s New Innovator Award (to G.D.).
Published: 2020

44. Comparative analysis of Lactobacillus gasseri from Chinese subjects reveals a new species-level taxa

Author: Hao Zhang, R. Paul Ross, Bo Yang, Xingya Zhou, Jianxin Zhao, Wei Chen, Catherine Stanton, National Natural Science Foundation of China, Fundamental Research Funds for the Central Universities, National Firs-Class Discipline Program of Food Science and Technology, Jiangsu Province 'Collaborative Innovation Center for Food Safety and Quality Control', JUSRP11733, and JUFSTR20180102
Subjects: Adult, DNA, Bacterial, Genotype, lcsh:QH426-470, lcsh:Biotechnology, Gut flora, Lactobacillus gasseri, Genome, law.invention, Feces, 03 medical and health sciences, Probiotic, Asian People, Bacterial Proteins, Bacteriocins, law, RNA, Ribosomal, 16S, lcsh:TP248.13-248.65, Genetics, Humans, Phylogeny, 030304 developmental biology, Human feces, 0303 health sciences, Genetic diversity, biology, Phylogenetic tree, 030306 microbiology, Probiotics, Pan/core-genome, Infant, Genomics, biology.organism_classification, Lactobacillus paragasseri, lcsh:Genetics, ANI, CRISPR-Cas Systems, Genome, Bacterial, Research Article, Biotechnology
Abstract: Background Lactobacillus gasseri as a probiotic has history of safe consumption is prevalent in infants and adults gut microbiota to maintain gut homeostasis. Results In this study, to explore the genomic diversity and mine potential probiotic characteristics of L. gasseri, 92 strains of L. gasseri were isolated from Chinese human feces and identified based on 16 s rDNA sequencing, after draft genomes sequencing, further average nucleotide identity (ANI) value and phylogenetic analysis reclassified them as L. paragasseri (n = 79) and L. gasseri (n = 13), respectively. Their pan/core-genomes were determined, revealing that L. paragasseri had an open pan-genome. Comparative analysis was carried out to identify genetic features, and the results indicated that 39 strains of L. paragasseri harboured Type II-A CRISPR-Cas system while 12 strains of L. gasseri contained Type I-E and II-A CRISPR-Cas systems. Bacteriocin operons and the number of carbohydrate-active enzymes were significantly different between the two species. Conclusions This is the first time to study pan/core-genome of L. gasseri and L. paragasseri, and compare their genetic diversity, and all the results provided better understating on genetics of the two species.
Published: 2020

45. A strong mitigation scenario maintains climate neutrality of northern peatlands

Author: Qiu, Chunjing, Ciais, Philippe, Zhu, Dan, Guenet, Bertrand, Chang, Jinfeng, Chaudhary, Nitin, Kleinen, Thomas, Li, Xinyu, Müller, Jurek, Xi, Yi, Zhang, Wenxin, Ballantyne, Ashley, Brewer, Simon, Brovkin, Victor, Charman, Dan, Gustafson, Adrian, Gallego-Sala, Angela, Gasser, Thomas, Holden, Joseph, Joos, Fortunat, Kwon, Min Jung, Lauerwald, Ronny, Miller, Paul, Peng, Shushi, Page, Susan, Smith, Benjamin, Stocker, Benjamin, Sannel, A. Britta K., Salmon, Elodie, Schurgers, Guy, Shurpali, Narasinha, Wårlind, David, Westermann, Sebastian, Kwon, Min, Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), 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), Mathématiques et Informatique Appliquées (MIA Paris-Saclay), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Sino-French Institute for Earth System Science, College of Urban and Environmental Sciences, Peking University [Beijing], Laboratoire de géologie de l'ENS (LGENS), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Département des Géosciences - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Ecologie fonctionnelle et écotoxicologie des agroécosystèmes (ECOSYS), European Research Council, ERC: SyG-2013-610028 IMBALANCE-P, Agence Nationale de la Recherche, ANR, This work was supported by the European Research Council Synergy grant (SyG-2013-610028 IMBALANCE-P) and the French State Aid managed by the ANR under the ?Investissements d'avenir? programme (ANR-16-CONV-0003_Cland). ORCHIDEE-PEAT performed simulations using HPC resources from GENCI-TGCC (2020-A0070106328). A.V.G.-S. was funded by the Natural Environment Research Council (NERC standard grant no. NE/I012915/1 and no. NE/S001166/1). W.Z. acknowledges funding from the Swedish Research Council FORMAS 2016-01201 and Swedish National Space Agency 209/19. N.C. acknowledges funding by the Nunataryuk (EU grant agreement no. 773421) and the Swedish Research Council FORMAS (contract no. 2019-01151). LPJ-GUESS_dyn simulations were performed on the supercomputing facilities at the University of Oslo, Norway, and on the Aurora and Tetralith resources of the Swedish National Infrastructure for Computing (SNIC) at the Lund University Centre for Scientific and Technical Computing (Lunarc), project no. 2021/2-61 and no. 2021/2-28, and Link?ping University, project no. snic2020/5-563. A.G. P.A.M. W.Z. B.S. D.W. and N.C. acknowledge support from the strategic research areas Modeling the Regional and Global Earth System (MERGE) and Biodiversity and Ecosystem Services in a Changing Climate (BECC) at Lund University. P.A.M. and D.W. received financial support from the H2020 CRESCENDO project (grant agreement no. 641816). LPJ-GUESS simulations were enabled by resources provided by the Swedish National Infrastructure for Computing (SNIC) at LUNARC partially funded by the Swedish Research Council through grant agreement no. 2018-05973. J.M. and F.J. acknowledge financial support by the Swiss National Science Foundation (no. 200020_172476 and no. 200020_200511) and funding from the European Union's Horizon 2020 research and innovation program under grant agreement no. 820989 (project COMFORT) and no. 821003 (project 4C). The work reflects only the authors views, the European Commission and their executive agency are not responsible for any use that may be made of the information the work contains. B.G. received funding from the European Union's Horizon 2020 research and innovation program under grant agreement no. 641816 (CRESCENDO) and no. 821003 (4C project). B.D.S was funded by the Swiss National Science Foundation grant no. PCEFP2_181115. T.K. acknowledges support from the German Federal Ministry for Education and Research (BMBF) through the PalMod programme (grant no. 01LP1507B and no. 01LP1921A). LPJ-MPI experiments were performed at the German Climate Computing Centre (DKRZ), using resources from the Max Planck Institute for Meteorology. N.J.S. acknowledges financial support from Academy of Finland (no. 296887 and no. 334422) and the Finnish Ministry of Agriculture and Forestry (no. VN/28562/2020). J.C. acknowledged support from the Fundamental Research Funds for the Central Universities (no. 2021QNA6005). D.Z. acknowledges funding from the National Natural Science Foundation of China (grant no. 42101090 and no. 41988101). W.Z and G.S. acknowledge support from the Danish National Research Foundation (DNRF100). C.Q. P.C. D.Z. and B.G. designed the research, C.Q. and P.C. drafted the manuscript, J.C. prepared the climate forcing for ORCHIDEE-PEAT and computed estimates of global and Northern Hemisphere CO2 emissions from ISIMIP2b terrestrial biosphere models, C.Q. N.C. T.K. X.Y.L. J.M. Y.X. and W.Z. performed model simulations, A.V.G.-S. and S.C.B. provided estimates for future peat carbon sink from Gallego-Sala et al.15, all authors contributed to the interpretation of the results and draft revision., ANR-16-CONV-0003,CLAND,CLAND : Changement climatique et usage des terres(2016), European Project: 641816,H2020,H2020-SC5-2014-two-stage,CRESCENDO(2015), ICOS-ATC (ICOS-ATC), 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), Modélisation des Surfaces et Interfaces Continentales (MOSAIC), Key Laboratory of Plant-Soil Interactions - College of Resources and Environmental Sciences (PSI), China Agricultural University (CAU), Department of Geosciences [Oslo], Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO), Department of Physical Geography and Ecosystem Science [Lund], Lund University [Lund], Max Planck Institute for Meteorology (MPI-M), Max-Planck-Gesellschaft, Climate and Environmental Physics [Bern] (CEP), Physikalisches Institut [Bern], Universität Bern [Bern] (UNIBE)-Universität Bern [Bern] (UNIBE), Oeschger Centre for Climate Change Research (OCCR), University of Bern, Center for Permafrost (CENPERM), Department of Geosciences and Natural Resource Management [Copenhagen] (IGN), Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Department of Ecosystem and Conservation Sciences, University of Montana, University of Utah, College of Life and Environmental Sciences [Exeter], University of Exeter, International Institute for Applied Systems Analysis [Laxenburg] (IIASA), School of Geography [Leeds], University of Leeds, University of Leicester, Hawkesbury Institute for the Environment [Richmond] (HIE), Western Sydney University, Department of Environmental Systems Science [ETH Zürich] (D-USYS), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Department of Physical Geography [Stockholm], Stockholm University, Laboratoire de Physique et Chimie de l'Environnement et de l'Espace (LPC2E), Observatoire des Sciences de l'Univers en région Centre (OSUC), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Centre National d’Études Spatiales [Paris] (CNES), and Natural Resources Institute Finland (LUKE)
Subjects: [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 0303 health sciences, 010504 meteorology & atmospheric sciences, 530 Physics, methane, [SDE.MCG]Environmental Sciences/Global Changes, carbon dioxide, carbon-cycle feedback, 15. Life on land, 01 natural sciences, 03 medical and health sciences, long-term climate change, 13. Climate action, [SDU.STU.CL]Sciences of the Universe [physics]/Earth Sciences/Climatology, land surface models, Earth and Planetary Sciences (miscellaneous), peatland, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, 030304 developmental biology, 0105 earth and related environmental sciences, General Environmental Science, permafrost
Abstract: Northern peatlands store 300–600 Pg C, of which approximately half are underlain by permafrost. Climate warming and, in some regions, soil drying from enhanced evaporation are progressively threatening this large carbon stock. Here, we assess future CO2 and CH4 fluxes from northern peatlands using five land surface models that explicitly include representation of peatland processes. Under Representative Concentration Pathways (RCP) 2.6, northern peatlands are projected to remain a net sink of CO2 and climate neutral for the next three centuries. A shift to a net CO2 source and a substantial increase in CH4 emissions are projected under RCP8.5, which could exacerbate global warming by 0.21°C (range, 0.09–0.49°C) by the year 2300. The true warming impact of peatlands might be higher owing to processes not simulated by the models and direct anthropogenic disturbance. Our study highlights the importance of understanding how future warming might trigger high carbon losses from northern peatlands.
Published: 2022

46. Temperature thresholds drive the global distribution of soil fungal decomposers

Author: Feng, Youzhi, Zhang, Jianwei, Berdugo, Miguel, Guirado, Emilio, Guerra, Carlos A., Egidi, Eleonora, Wang, Juntao, Singh, Brajesh K., Delgado‐Baquerizo, Manuel, National Natural Science Foundation of China, Chinese Academy of Sciences, Ministerio de Ciencia e Innovación (España), Feng, Youzhi [0000-0002-8519-841X], Guerra, Carlos A. [0000-0003-4917-2105], Singh, Brajesh K. [0000-0003-4413-4185], Delgado-Baquerizo, Manuel [0000-0002-6499-576X], Wang, Jun-Tao [0000-0002-1822-2176], Universidad de Alicante. Instituto Multidisciplinar para el Estudio del Medio 'Ramón Margalef', Feng, Youzhi, Guerra, Carlos A., Singh, Brajesh K., Delgado-Baquerizo, Manuel, Wang, Jun-Tao, and Berdugo, Miguel
Subjects: 0303 health sciences, Global and Planetary Change, Soil decomposition, 010504 meteorology & atmospheric sciences, Ecology, Temperature, Biodiversity, Ecología, 15. Life on land, 01 natural sciences, Carbon, Carbon Cycle, Soil, 03 medical and health sciences, Biogeography, 13. Climate action, Fungal decomposers, Environmental Chemistry, Global change, Ecosystem, Soil Microbiology, 030304 developmental biology, 0105 earth and related environmental sciences, General Environmental Science
Abstract: 11 páginas.-- 4 fig.- referncias.- Additional supporting information may be found in the online version of the article at the publisher’s website http://dx.doi.org/10.1111/gcb.16096, Unraveling the biogeographic pattern of soil fungal decomposers along temperature gradients – in a smooth linearity or an abrupt jump – can help us connect the global carbon cycle to global warming. Through a standardized global field survey, we identify the existence of temperature thresholds that control the global distribution of soil fungal decomposers, leading to abrupt reductions in their proportion (i.e. the relative abundance in fungal community) immediately after crossing particular air and soil temperature thresholds. For example, small increases over the mean annual temperature threshold of ~9ºC result in abrupt reductions in their proportion, paralleling a similar temperature threshold for soil carbon content. We further find that the proportion of soil fungal decomposers is more sensitive to temperature increases under arid conditions. Given the positive correlation between the global distributions of fungal decomposers and soil heterotrophic respiration, the reported temperature-driven abrupt reductions in fungal decomposers could further suppress their driven soil decomposition processes and reduce carbon fluxes from soils to the atmosphere with implications for climate change feedback. This work not only advances the current knowledge on the global distribution of soil fungal decomposers, but also highlights that small changes in temperature around certain thresholds can lead to potential unexpected consequences in global carbon cycling under projected climate change, Y.Z.F. is supported by National Natural Science Foundation of China (42177297), the Strategic Priority Research Program of the Chinese Academy of Sciences (Grant No. XDA28010302) and the Youth Innovation Promotion Association, CAS (Member No. 2014271). M.D-B. was supported by a Ramón y Cajal grant (RYC2018-025483-I), a project from the Spanish Ministry of Science and Innovation (PID2020-115813RA-I00), and a project PAIDI 2020 from the Junta de Andalucía (P20_00879). E.G. is supported by the European Research Council (ERC Grant agreement 647038 [BIODESERT]). B.K.S. lab on microbial diversity work is supported by Australian Research Council (DP170104634). We also thank Melissa Martin for revising the English of the manuscript.
Published: 2022

47. Podocytes maintain high basal levels of autophagy independent of mtor signaling

Author: Bjoern Hartleben, Wei Liang, Shuya Liu, Kosuke Yamahara, Ketan Patel, Kathrin Thedieck, Tillmann Bork, Olivia Lenoir, Philipp Lee, Christoph Schell, Tobias B. Huber, Zhejia Tian, Pierre-Louise Tharaux, Department of Medicine IV [Freiburg, Germany] (Faculty of Medicine), University of Freiburg [Freiburg], Division of Nephrology [Wuhan, China], Wuhan University [China]-Renmin Hospital [Wuhan, China], Department of Medicine [Otsu, Japan], Shiga University of Medical Science, Department of Medicine [Hamburg, Germany], Universitaetsklinikum Hamburg-Eppendorf = University Medical Center Hamburg-Eppendorf [Hamburg] (UKE), Center for Molecular Biosciences Innsbruck [Innsbruck, Austria] (Institute of Biochemistry), University of Innsbruck, University Medical Center Groningen [Groningen] (UMCG), University of Oldenburg, Hannover Medical School [Hannover] (MHH), Freiburg Institute for Advanced Studies [Freiburg, Germany], Albert-Ludwigs-Universität Freiburg, School of Biological Sciences [Reading], University of Reading (UOR), Paris-Centre de Recherche Cardiovasculaire (PARCC - UMR-S U970), Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service de néphrologie [Hôpital Européen Georges Pompidou - APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), This work was supported by the German Research Foundation [CRC1140, CRC1192], European Foundation for the Study of Diabetes (EFSD), German Research Foundation Heisenberg Program [HU1016/ 5-1], German Research Foundation Heisenberg Program [HU1016/8-2], EC | European Research Council (ERC), H2020-IMI2 BEAt-DKD [115974], BMBF-STOP-FSGS [01GM1518C], Excellence Initiative of the German Federal and State Governments BIOSS, FRIAS Freiburg Institute of Advanced Studies, Alexander von Humboldt Foundation, German Research Foundation [CRC992], National Natural Science Foundation of China (NSFC) [81470912], Berta Ottenstein Program, Else Kroener Fresenius Foundation NAKSYS, BMBF GlioPATH [01ZX1402B], BMBF MAPTor-NET [031A426B], German Research Foundation [TH 1358/3-1], MESI-STRAT [754688], Uehara Memorial Foundation, German TS Foundation, Stichting TSC Fonds (calls 2015 and 2017), PoLiMeR Innovative Training Network (Marie SklodowskaCurie grant agreement No. 812616, Rosalind-Franklin Fellowship of the Universitiy of Groningen., Tharaux, Pierre-Louis, Leopold Franzens Universität Innsbruck - University of Innsbruck, and Center for Liver, Digestive and Metabolic Diseases (CLDM)
Subjects: AMPK, 0301 basic medicine, podocyte, Research Paper - Basic Science, PROTEIN, glomerulus, Podocyte, ACTIVATION, LC3, PHOSPHORYLATION, ULK1, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, CELL-LINE, biology, Podocytes, TOR Serine-Threonine Kinases, MTOR, Raptor, Cell biology, medicine.anatomical_structure, signaling, Signal Transduction, Research Article, autophagy, kidney, Mice, Transgenic, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Mechanistic Target of Rapamycin Complex 1, DIABETIC-NEPHROPATHY, Nephrin, 03 medical and health sciences, medicine, Animals, Humans, Protein kinase A, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, Molecular Biology, Mechanistic target of rapamycin, PI3K/AKT/mTOR pathway, Sirolimus, 030102 biochemistry & molecular biology, rapamycin, RPTOR, Autophagy, KIDNEY-DISEASE, Cell Biology, Tsc1, 030104 developmental biology, MAMMALIAN TARGET, biology.protein, Podocin, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract: International audience; While constant basal levels of macroautophagy/autophagy are a prerequisite to preserve long-lived podocytes at the filtration barrier, MTOR regulates at the same time podocyte size and compensatory hypertrophy. Since MTOR is known to generally suppress autophagy, the apparently independent regulation of these two key pathways of glomerular maintenance remained puzzling. We now report that long-term genetic manipulation of MTOR activity does in fact not influence high basal levels of autophagy in podocytes either in vitro or in vivo. Instead we present data showing that autophagy in podocytes is mainly controlled by AMP-activated protein kinase (AMPK) and ULK1 (unc-51 like kinase 1). Pharmacological inhibition of MTOR further shows that the uncoupling of MTOR activity and autophagy is time dependent. Together, our data reveal a novel and unexpected cell-specific mechanism, which permits concurrent MTOR activity as well as high basal autophagy rates in podocytes. Thus, these data indicate manipulation of the AMPK-ULK1 axis rather than inhibition of MTOR as a promising therapeutic intervention to enhance autophagy and preserve podocyte homeostasis in glomerular diseases.Abbreviations: AICAR: 5-aminoimidazole-4-carboxamide ribonucleotide; AMPK: AMP-activated protein kinase; ATG: autophagy related; BW: body weight; Cq: chloroquine; ER: endoplasmic reticulum; ESRD: end stage renal disease; FACS: fluorescence activated cell sorting; GFP: green fluorescent protein; i.p.: intra peritoneal; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MTOR: mechanistic target of rapamycin kinase; NPHS1: nephrosis 1, nephrin; NPHS2: nephrosis 2, podocin; PLA: proximity-ligation assay; PRKAA: 5'-AMP-activated protein kinase catalytic subunit alpha; RPTOR/RAPTOR: regulatory associated protein of MTOR, complex 1; RFP: red fluorescent protein; TSC1: tuberous sclerosis 1; ULK1: unc-51 like kinase 1.
Published: 2019

48. Effects of transglutaminase pre-crosslinking on salt-induced gelation of soy protein isolate emulsion

Author: Shutao Liu, Kaiyun Luo, Benu Adhikari, Xufeng Wang, Jie Chen, Song Miao, National Natural Science Foundation of China, National High-Tech Research and Development Program of China, NSFC, 31271946, 2013AA102200, and NSFC, 31471583
Subjects: Pre-crosslinking, Tissue transglutaminase, G protein, Salt, Salt (chemistry), Hydrophobic effect, 03 medical and health sciences, 0404 agricultural biotechnology, 0302 clinical medicine, Rheology, Soy protein isolate, Soy protein, chemistry.chemical_classification, integumentary system, biology, Emulsion gel, 04 agricultural and veterinary sciences, Dynamic mechanical analysis, Transglutaminase, 040401 food science, chemistry, Emulsion, 030221 ophthalmology & optometry, Biophysics, biology.protein, Food Science
Abstract: peer-reviewed The salt-induced gelation behavior of soy protein isolate (SPI) emulsions was markedly influenced by microbial transglutaminase (TGase) pre-crosslinking. Rheological data showed that when SPI emulsions were incubated with TGase at low concentrations (1 and 3 U/g protein) at 50 °C for 30 min prior to gelation, no change in storage modulus (G′), but enhanced resistance to deformation of the gels was observed. Extensive crosslinking by TGase (5 U/g protein) resulted in severe decreases in gel firmness and fracture properties (yielding stress and strain), likely due to the impairment of hydrophobic bonds and the formation of coarse networks. The water-holding capacity of the gels was significantly enhanced by increased concentrations of TGase. Interactive force analysis indicated that non-covalent interactions and disulfide bonds are the primary forces involved in CaSO4-induced SPI emulsion gel, but TGase treatment may limit hydrophobic interactions within the gel network. These results are of great potential value for the application of TGase in the food industry.
Published: 2019

49. Ordered subsets Non-Local means constrained reconstruction for sparse view cone beam CT system

Author: Limin Luo, Yining Hu, Lizhe Xie, Wang Zheng, Centre de Recherche en Information Biomédicale sino-français (CRIBS), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Southeast University [Jiangsu]-Institut National de la Santé et de la Recherche Médicale (INSERM), Southeast University [Jiangsu], Nanjing Medical University, 81530060, National Natural Science Foundation of China, BK20180670, Basic Research Program of Jiangsu Province, JSKLOD-KF-1708, Open Project from Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, K93-9-2014-10C, Key Laboratory of Computer Network and Information Integration (), and Université de Rennes (UR)-Southeast University [Jiangsu]-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: Time Factors, Computer science, Computation, ComputingMethodologies_IMAGEPROCESSINGANDCOMPUTERVISION, Biomedical Engineering, Biophysics, General Physics and Astronomy, Iterative reconstruction, Signal-To-Noise Ratio, 030218 nuclear medicine & medical imaging, 03 medical and health sciences, CUDA, 0302 clinical medicine, Image Processing, Computer-Assisted, Humans, Radiology, Nuclear Medicine and imaging, Cone beam CT, Tomography, Phantoms, Imaging, 3D reconstruction, X-Ray Microtomography, Cone-Beam Computed Tomography, Non-local means, Sparse view, Low dose, Kernel (image processing), 030220 oncology & carcinogenesis, Image reconstruction, [SDV.IB]Life Sciences [q-bio]/Bioengineering, Algorithm, Algorithms, Ordered subsets
Abstract: International audience; Sparse-view sampling scans reduce the patient's radiation dose by reducing the total exposure duration. CT reconstructions under such scan mode are often accompanied by severe artifacts due to the high ill-posedness of the problem. In this paper, we use a Non-Local means kernel as a regularization constraint to reconstruct image volumes from sparse-angle sampled cone-beam CT scans. To overcome the huge computational cost of the 3D reconstruction, we propose a sequential update scheme relying on ordered subsets in the image domain. It is shown through experiments on simulated and real data and comparisons with other methods that the proposed approach is robust enough to deal with the number of views reduced up to 1/10. When coupled with a CUDA parallel computing technique, the computation speed of the iterative reconstruction is greatly improved.
Published: 2019

50. Multiplex CRISPR/Cas9 editing of the long‐chain acyl‐CoA synthetase family in the diatom Phaeodactylum tricornutum reveals that mitochondrial ptACSL3 is involved in the synthesis of storage lipids

Author: Xiahui Hao, Wenchao Chen, Alberto Amato, Juliette Jouhet, Eric Maréchal, Daniel Moog, Hanhua Hu, Hu Jin, Lingjie You, Fenghong Huang, Mark Moosburner, Andrew E. Allen, Yangmin Gong, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences Ministry of Agriculture, Key Laboratory of Biology and Genetic Improvement of Oil Crops, LIPID, Physiologie cellulaire et végétale (LPCV), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), Laboratory for Cell Biology, Philipps-University Marburg, Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Scripps Institution of Oceanography (SIO), University of California [San Diego] (UC San Diego), University of California-University of California, J. Craig Venter Institute [La Jolla, USA] (JCVI), National Natural Science Foundation of China (41776175 and 31961133008), Agricultural Science and Technology Innovation Project of Chinese Academy of Agricultural Sciences (CAAS-ASTIP-2013-OCRI), 2021 CEA-CAS bilateral program, Institut Carnot 3BCAR, Grants from the United States Department of Energy Genomics Science program, US National Science Foundation, NSF-MCB-1818390, Gordon and Betty Moore Foundation GBMF3828, ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010), ANR-11-BTBR-0008,OCEANOMICS,Biotechnologies et bioressources pour la valorisation des écosystèmes marins planctoniques(2011), ANR-15-IDEX-0002,UGA,IDEX UGA(2015), Scripps Institution of Oceanography (SIO - UC San Diego), and University of California (UC)-University of California (UC)
Subjects: 0106 biological sciences, Diatoms, 0303 health sciences, Physiology, Fatty Acids, Multiplexed CRISPR/Cas9, Plant Science, Fatty acid, Long-chain acyl-CoA synthetase, 01 natural sciences, Phaeodactylum tricornutum, Triacylglycerol, Mitochondria, 03 medical and health sciences, Coenzyme A Ligases, Coenzyme A, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, CRISPR-Cas Systems, 030304 developmental biology, 010606 plant biology & botany
Abstract: International audience; Long-chain acyl-CoA synthetases (LACSs) play diverse and fundamentally important roles in lipid metabolism. While their functions have been well-established in bacteria, yeast and plants, the mechanisms by which LACS isozymes regulate lipid metabolism in unicellular oil-producing microalgae, including the diatom Phaeodactylum tricornutum, remain largely unknown. In P. tricornutum, a family of five genes (ptACSL1~5) encodes LACS activities. We generated single lacs knockout/knockdown mutants using multiplexed CRISPR/Cas9 method, and determined their substrate specificities towards different fatty acids (FAs) and subcellular localizations. ptACSL3 is localized in the mitochondria and its disruption led to compromised growth and reduced triacylglycerol (TAG) content when cells were bubbled with air. The ptACSL3 mutants showed altered FA profiles in two galactoglycerolipids and phosphatidylcholine (PC) with significantly reduced distribution of 16:0 and 16:1. ptACSL5 is localized in the peroxisome and its knockdown resulted in reduced growth rate and altered molecular species of PC and TAG, indicating a role in controlling the composition of acyl-CoAs for lipid synthesis. Our work demonstrates the potential of generating gene knockout mutants with the mutation of large fragment deletion using multiplexed CRISPR/Cas9 and provides insight into the functions of LACS isozymes in lipid metabolism in the oleaginous microalgae.
Published: 2021

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