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2. Towards an open grapevine information system

Author

Adam-Blondon, A-F, Alaux, M, Pommier, C, Cantu, D, Cheng, Z-M, Cramer, GR, Davies, C, Delrot, S, Deluc, L, Di Gaspero, G, Grimplet, J, Fennell, A, Londo, JP, Kersey, P, Mattivi, F, Naithani, S, Neveu, P, Nikolski, M, Pezzotti, M, Reisch, BI, Töpfer, R, Vivier, MA, Ware, D, and Quesneville, H

Subjects
Agricultural, Veterinary and Food Sciences, Horticultural Production, Networking and Information Technology R&D (NITRD), Generic health relevance, Horticultural production, Plant biology
Abstract

Viticulture, like other fields of agriculture, is currently facing important challenges that will be addressed only through sustained, dedicated and coordinated research. Although the methods used in biology have evolved tremendously in recent years and now involve the routine production of large data sets of varied nature, in many domains of study, including grapevine research, there is a need to improve the findability, accessibility, interoperability and reusability (FAIR-ness) of these data. Considering the heterogeneous nature of the data produced, the transnational nature of the scientific community and the experience gained elsewhere, we have formed an open working group, in the framework of the International Grapevine Genome Program (www.vitaceae.org), to construct a coordinated federation of information systems holding grapevine data distributed around the world, providing an integrated set of interfaces supporting advanced data modeling, rich semantic integration and the next generation of data mining tools. To achieve this goal, it will be critical to develop, implement and adopt appropriate standards for data annotation and formatting. The development of this system, the GrapeIS, linking genotypes to phenotypes, and scientific research to agronomical and oeneological data, should provide new insights into grape biology, and allow the development of new varieties to meet the challenges of biotic and abiotic stress, environmental change, and consumer demand.

Published
2016

4. An Arabidopsis gene regulatory network for secondary cell wall synthesis

Author

Taylor-Teeples, M, Lin, L, de Lucas, M, Turco, G, Toal, TW, Gaudinier, A, Young, NF, Trabucco, GM, Veling, MT, Lamothe, R, Handakumbura, PP, Xiong, G, Wang, C, Corwin, J, Tsoukalas, A, Zhang, L, Ware, D, Pauly, M, Kliebenstein, DJ, Dehesh, K, Tagkopoulos, I, Breton, G, Pruneda-Paz, JL, Ahnert, SE, Kay, SA, Hazen, SP, and Brady, SM

Subjects
Plant Biology, Biochemistry and Cell Biology, Bioinformatics and Computational Biology, Biological Sciences, Biotechnology, Genetics, 1.1 Normal biological development and functioning, Arabidopsis, Arabidopsis Proteins, Cell Wall, DNA, Plant, E2F Transcription Factors, Feedback, Gene Expression Regulation, Developmental, Gene Expression Regulation, Plant, Gene Regulatory Networks, Iron Deficiencies, Organ Specificity, Promoter Regions, Genetic, Reproducibility of Results, Salinity, Time Factors, Transcription Factors, Xylem, General Science & Technology
Abstract

The plant cell wall is an important factor for determining cell shape, function and response to the environment. Secondary cell walls, such as those found in xylem, are composed of cellulose, hemicelluloses and lignin and account for the bulk of plant biomass. The coordination between transcriptional regulation of synthesis for each polymer is complex and vital to cell function. A regulatory hierarchy of developmental switches has been proposed, although the full complement of regulators remains unknown. Here we present a protein-DNA network between Arabidopsis thaliana transcription factors and secondary cell wall metabolic genes with gene expression regulated by a series of feed-forward loops. This model allowed us to develop and validate new hypotheses about secondary wall gene regulation under abiotic stress. Distinct stresses are able to perturb targeted genes to potentially promote functional adaptation. These interactions will serve as a foundation for understanding the regulation of a complex, integral plant component.

Published
2015

18. Contemporary cesarean delivery practice in the United States

Author

Zhang, Jun, Troendle, James, Reddy, Uma M., Laughon, Katherine S., Branch, Ware D., Burkman, Ronald, Landy, Helain J., Hibbard, Judith U., Haberman, Shoshana, Ramirez, Mildred M., Bailit, Jennifer L., Hoffman, Matthew K., Gregory, Kimberly D., Gonzalez-Quintero, Victor H., Kominiarek, Michelle, Learman, Lee A., Hatjis, Christos G., and van Veldhuisen, Paul

Published
2010

19. Maternal and neonatal outcomes by labor onset type and gestational age

Author

Bailit, Jennifer L., Gregory, Kimberly D., Reddy, Uma M., Gonzalez-Quintero, Victor H., Hibbard, Judith U., Ramirez, Mildred M., Branch, Ware D., Burkman, Ronald, Haberman, Shoshana, Hatjis, Christos G., Hoffman, Matthew K., Kominiarek, Michelle, Landy, Helain J., Learman, Lee A., Troendle, James, Van Veldhuisen, Paul, Wilkins, Isabelle, Sun, Liping, and Zhang, Jun

Published
2010

20. Baghuk Mountain (Central Iran): high-resolution stratigraphy of a continuous Central Tethyan Permian–Triassic boundary section

Author

Korn, D., Leda, L., Heuer, F., Moradi Salimi, H., Farshid, E., Akbari, A., Schobben , Martin, Ghaderi, A., Struck, U., Gliwa, J., Ware, D., and Hairapetian, V.

Subjects
Fossil
Abstract

Permian–Triassic boundary sections at Baghuk Mountain (Central Iran) are investigated with respect to their lithological succession, biostratigraphy (particularly conodonts, nautiloids and ammonoids) as well as chemostratigraphy (carbon isotopes). The rock successions consist of the Late Permian Hambast Formation, the youngest Permian Baghuk Member (new name for the “Boundary Clay”) and the Early Triassic Claraia beds. Correlation of the data allows the establishment of a high-resolution stratigraphy based on conodonts with seven Changhsingian zones. Abundant ammonoids enable the separation of ammonoid assemblages with the successive Wuchiapingian genera Prototoceras, Pseudotoceras and Vedioceras, as well as the Changhsingian genera Shevyrevites, Paratirolites, Alibashites, Abichites and Arasella. Griesbachian and Dienerian ammonoids are usually poorly preserved. Nautiloids occur predominantly in the Wuchiapingian part of the section with two successive assemblages dominated by the Liroceratidae and Tainoceratidae, respectively. Numerous Early Triassic strata contain microbialites of various outer morphology and microstructure. The carbon isotope curve (δ13Ccarb) shows a continuous late Changhsingian negative excursion continuing across the Baghuk Member with the lightest values at the base of the Triassic.

Published
2021

24. 1036 Familial aggregation of stillbirth

Author

Page, Jessica M., primary, Workalemahu, Tsegaselassie, additional, Blue, Nathan R., additional, Fraser, Alison, additional, Varner, Michael W., additional, Branch, Ware D., additional, and Silver, Robert M., additional

Published
2021
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31. Bed Rest is an Analog to Study the Physiological Changes of Spaceflight and to Evaluate Countermeasures

Author

Pfannenstiel, P, Ottenbacher, M, Inniss, A, Ware, D, Anderson, K, Stranges, S, Keith, K, Cromwell, R, Neigut. J, and Powell, D

Subjects
Aerospace Medicine
Abstract

The UTMB/NASA Flight Analog Research Unit is an inpatient unit with a bionutrition kitchen and unique testing areas for studying subjects subjected to 6 degree head-down complete bed rest for prolonged periods as an analog for zero gravity. Bed rest allows study of physiological changes and performance of functional tasks representative of critical interplanetary mission operations and measures of the efficacy of countermeasures designed to protect against the resulting deleterious effects. METHODS/STUDY POPULATION: Subjects are healthy adults 24-55 years old; 60 75 in tall; body mass index 18.5-30; and bone mineral density normal by DXA scan. Over 100 subjects have been studied in 7 campaigns since 2004. The iRAT countermeasure combines high intensity interval aerobic exercises on alternating days with continuous aerobic exercise. Resistance exercise is performed 3 days per week. Subjects are tested on an integrated suite of functional and interdisciplinary physiological tests before and after 70 days of total bed rest. RESULTS/ANTICIPATED RESULTS: It is anticipated that post-bed rest functional performance will be predicted by a weighted combination of sensorimotor, cardiovascular and muscle physiological factors. Control subjects who do not participate in the exercise countermeasure will have significantly greater decreases in these parameters. DISCUSSION/SIGNIFICANCE OF IMPACT: Astronauts experience alterations in multiple physiological systems due to exposure to the microgravity, leading to disruption in the ability to perform functional tasks after reintroduction to a gravitational environment. Current flight exercise countermeasures are not fully protective of cardiovascular, muscle and bone health. There is a need to refine and optimize countermeasures to mitigate health risks associated with long-term space missions.

Published
2012

33. Current status of the multinational Arabidopsis community

Author

Parry, Geraint, Provart, Nicholas J., Brady, Siobhan M., Uzilday, Baris, Adams, K., Araújo, W., Aubourg, S., Baginsky, S., Bakker, E., Bärenfaller, K., Batley, J., Beale, M., Beilstein, M., Belkhadir, Y., Berardini, T., Bergelson, J., Blanco-Herrera, F., Brady, S., Braun, Hans-Peter, Briggs, S., Brownfield, L., Cardarelli, M., Castellanos-Uribe, M., Coruzzi, G., Dassanayake, M., Jaeger, G.D., Dilkes, B., Doherty, C., Ecker, J., Edger, P., Edwards, D., Kasmi, F.E., Eriksson, M., Exposito-Alonso, M., Falter-Braun, P., Fernie, A., Ferro, M., Fiehn, O., Friesner, J., Greenham, K., Guo, Y., Hamann, T., Hancock, A., Hauser, M.-T., Heazlewood, J., Ho, C.-H., Hõrak, H., Huala, E., Hwang, I., Iuchi, S., Jaiswal, P., Jakobson, L., Jiang, Y., Jiao, Y., Jones, A., Kadota, Y., Khurana, J., Kliebenstein, D., Knee, E., Kobayashi, M., Koch, M., Krouk, G., Larson, T., Last, R., Lepiniec, L., Li, S., Lurin, C., Lysak, M., Maere, S., Malinowski, R., Maumus, F., May, S., Mayer, K., Mendoza-Cozatl, D., Mendoza-Poudereux, I., Meyers, B., Micol, J.L., Millar, H., Mock, H.-P., Mukhtar, K., Mukhtar, S., Murcha, M., Nakagami, H., Nakamura, Y., Nicolov, L., Nikolau, B., Nowack, M., Nunes-Nesi, A., Palmgren, M., Parry, G., Patron, N., Peck, S., Pedmale, U., Perrot-Rechenmann, C., Pieruschka, R., Pío-Beltrán, J., Pires, J.C., Provart, N., Rajjou, L., Reiser, L., Reumann, S., Rhee, S., Rigas, S., Rolland, N., Romanowski, A., Santoni, V., Savaldi-Goldstein, S., Schmitz, R., Schulze, W., Seki, M., Shimizu, K.K., Slotkin, K., Small, I., Somers, D., Sozzani, R., Spillane, C., Srinivasan, R., Taylor, N., Tello-Ruiz, M.-K., Thelen, J., Tohge, T., Town, C., Toyoda, T., Uzilday, B., Peer, Y.V.D., Wijk, K., Gillhaussen, P.V., Walley, J., Ware, D., Weckwerth, W., Whitelegge, J., Wienkoop, S., Wright, C., Wrzaczek, M., Yamazaki, M., Yanovsky, M., Žárský, V., Zhong, X., Biological Systems Engineering, Organisms and Environment Research Division, Cardiff School of Biosciences, Cardiff University, University of Toronto, University of California [Davis] (UC Davis), University of California, 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), Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany, Department of Ecology and Evolution [Chicago], University of Chicago, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Rothamsted Research, Biotechnology and Biological Sciences Research Council (BBSRC), University of Arizona, Gregor Mendel Institute (GMI) - Vienna Biocenter (VBC), Austrian Academy of Sciences (OeAW), University of California (UC), Center for Genomics and Systems Biology, Department of Biology [New York], New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU)-New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU), Flanders Institute for Biotechnology, National Center for Atmospheric Research [Boulder] (NCAR), Max Planck Institute of Molecular Plant Physiology (MPI-MP), Max-Planck-Gesellschaft, Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut National de la Santé et de la Recherche Médicale (INSERM)-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)-Université Grenoble Alpes (UGA), Agricultural Sustainability Institute and Department of Neurobiology, Physiology, and Behavior, Norwegian University of Science and Technology (NTNU), University of Melbourne, King Abdullah University of Science and Technology (KAUST), University of Chinese Academy of Sciences [Beijing] (UCAS), The Sainsbury Laboratory [Norwich] (TSL), IBM Research – Tokyo, University Medical Center Groningen [Groningen] (UMCG), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre for Novel Agricultural Products, Department of Biology, University of York [York, UK], Biologie des Semences (LBS), Institut National de la Recherche Agronomique (INRA)-Institut National Agronomique Paris-Grignon (INA P-G), Sichuan University [Chengdu] (SCU), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Plant Systems Biology, Unité de Recherche Génomique Info (URGI), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Nottingham, UK (UON), Institute of Bioinformatics and System Biology (IBIS), Helmholtz Zentrum München = German Research Center for Environmental Health, Saint Mary's University [Halifax], Max Planck Institute for Plant Breeding Research (MPIPZ), National Institute of Genetics (NIG), University of Copenhagen = Københavns Universitet (UCPH), Division of Biology [La Jolla], University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC), Earlham Institute [Norwich], Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association, University of Missouri [Columbia] (Mizzou), University of Missouri System, Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Plant Biology, Carnegie Institution for Science, Dynamique du protéome et biogenèse du chloroplaste (ChloroGenesis), Physiologie cellulaire et végétale (LPCV), 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)-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), Plateforme de Spectrométrie de Masse Protéomique - Mass Spectrometry Proteomics Platform (MSPP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Plant Systems Biology, Institute of Physiology and Biotechnology of plants, RIKEN Center for Sustainable Resource Science [Yokohama] (RIKEN CSRS), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Unité de recherche Génétique et amélioration des plantes (GAP), Institut National de la Recherche Agronomique (INRA), Department of Biology, Duke University, Genetics and Biotechnology Lab, Plant & AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland [Galway] (NUI Galway), Universidade Federal de São Paulo, RIKEN Plant Science Center and RIKEN Bioinformatics and Systems Engineering Division, Cold Spring Harbor Laboratory (CSHL), University of Vienna [Vienna], University of California [Los Angeles] (UCLA), Department of Plant Molecular Biology, Université de Lausanne = University of Lausanne (UNIL), UKRI-BBSRC grant BB/M004376/1, HHMI Faculty Scholar Fellowship, Turkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) 118Z137, UK Research & Innovation (UKRI) Biotechnology and Biological Sciences Research Council (BBSRC) BB/M004376/1, Sainsbury Lab, Norwich Research Park, Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Helmholtz-Zentrum München (HZM), University of Copenhagen = Københavns Universitet (KU), University of California-University of California, Carnegie Institution for Science [Washington], Université de Lausanne (UNIL), Ege Üniversitesi, Organismal and Evolutionary Biology Research Programme, Plant Biology, Viikki Plant Science Centre (ViPS), Receptor-Ligand Signaling Group, University of Zurich, Parry, Geraint, Provart, Nicholas J, and Brady, Siobhan M

Subjects
0106 biological sciences, Arabidopsis thaliana, [SDV]Life Sciences [q-bio], White Paper, Genetics and Molecular Biology (miscellaneous), Plant Science, Biochemistry, 01 natural sciences, Dewey Decimal Classification::500 | Naturwissenschaften::580 | Pflanzen (Botanik), Research community, Arabidopsis, 1110 Plant Science, 0303 health sciences, Ecology, biology, 1184 Genetics, developmental biology, physiology, ddc:580, Multinational corporation, MAP, 590 Animals (Zoology), Life Sciences & Biomedicine, Arabidopsis research community, Evolution, Steering committee, Multinational Arabidopsis Steering Committee, Library science, 1301 Biochemistry, Genetics and Molecular Biology (miscellaneous), Biochemistry, Genetics and Molecular Biology (miscellaneous), Business and Economics, 10127 Institute of Evolutionary Biology and Environmental Studies, 03 medical and health sciences, Behavior and Systematics, Political science, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, MASC, roadmap, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, Plant Sciences, Botany, 15. Life on land, 11831 Plant biology, biology.organism_classification, White Papers, collaboration, 1105 Ecology, Evolution, Behavior and Systematics, QK1-989, Arabidopsis Thaliana, Collaboration, Research Network, Roadmap, 570 Life sciences, 1182 Biochemistry, cell and molecular biology, 2303 Ecology, 010606 plant biology & botany
Abstract

The multinational Arabidopsis research community is highly collaborative and over the past thirty years these activities have been documented by the Multinational Arabidopsis Steering Committee (MASC). Here, we (a) highlight recent research advances made with the reference plantArabidopsis thaliana; (b) provide summaries from recent reports submitted by MASC subcommittees, projects and resources associated with MASC and from MASC country representatives; and (c) initiate a call for ideas and foci for the "fourth decadal roadmap," which will advise and coordinate the global activities of the Arabidopsis research community., UKRI-BBSRC grant [BB/M004376/1]; HHMI Faculty Scholar Fellowship; Scientific and Technological Research Council of TurkeyTurkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [118Z137], UKRI-BBSRC grant, Grant/Award Number: BB/M004376/1; HHMI Faculty Scholar Fellowship; the Scientific and Technological Research Council of Turkey, Grant/Award Number: 118Z137

Published
2020
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44. The Kalkarindji Large Igneous Province, Australia: Petrogenesis of the oldest and most compositionally homogenous province of the Phanerozoic

Author

Ware, D. Bryant, Jourdan, F, Merle, Renaud, Chiaradia, Massimo, Hodges, Kyle, Ware, D. Bryant, Jourdan, F, Merle, Renaud, Chiaradia, Massimo, and Hodges, Kyle

Abstract

The Kalkarindji Large Igneous Province (LIP) is a Middle Cambrian (511 Ma) continental flood basalt (CFB) province located in northern and central–west Australia that has been linked to an extinction event at the Early–Middle Cambrian boundary. The extent of this LIP has been estimated at about 2·1 x 106 km2, with exposures in Western Australia, Northern Territory, Queensland and South Australia. Major and trace element datasets reveal geochemical characteristics typical for continental flood basalts (CFBs) including: tholeiitic affinity; an enrichment in incompatible elements, in particular, large-ion lithophile elements (LILE); enrichment of light rare earth elements (LREE) compared to heavy rare earth elements (HREE) relative to N-MORB; negative Nb and Ta anomalies in normalized extended element patterns. Here we present the first comprehensive geochemical investigation of the Kalkarindji CFB province. The Kalkarindji CFBs are geochemically homogeneous, low-Ti basaltic andesites, with a nearly complete lack of basalts as defined using a total-alkalis vs silica diagram. All of the rocks analysed for Sr, Nd, Pb isotopic ratios display enriched initial (t = 511 Ma) isotopic compositions (143Nd/144Ni = 0·511928–0·511981; 87Sr/86Sri = 0·70917–0·71029; 206Pb/204Pbi = 18·105–18·843; 207Pb/204Pbi = 15·726–15·805; 208Pb/204Pbi = 38·374–39·208). Crustal assimilation models are interpreted to suggest that the geochemical characteristics, as well as the homogenous composition across the entire province, cannot be explained by continental crust contamination. Therefore, the enriched isotopic ratios (particularly the extremely high 207Pb/204Pbi and elevated 208Pb/204Pbi for moderate 206Pb/204Pbi), coupled with relative depletions in Nb and Ta concentrations, indicate the involvement of an ancient enriched lithospheric-like component in the genesis of the Kalkarindji CFB. We propose a model in which the source region was affected by an enrichment event at around 2·5 Ga (possibl

Published
2018

45. An Early Triassic (Dienerian) microgastropod assemblage from the Salt Range, Pakistan and its implication for gastropod recovery from the end-Permian mass extinction

Author

Nützel, A, Ware, D, Bucher, H, Hautmann, M, Roohi, G, Ur-Rehman, K, Yaseen, A, Nützel, A, Ware, D, Bucher, H, Hautmann, M, Roohi, G, Ur-Rehman, K, and Yaseen, A

Abstract

A single limestone sample from the Early Triassic (late Dienerian) of the Salt Range in Pakistan has yielded numerous small gastropods (smaller 2 mm), few bivalves and abundant ammonoids. The limestone is interpreted as a tempestite. Many of the gastropods are extremely well-preserved including protoconch preservation and micro-ornaments. Five species of gastropods are present: (1) isolated larval shells representing a neritimorph taxon of the family Trachyspiridae, (2) early juvenile and larval specimens of the caenogastropod Strobeus pakistanensis, (3) the new caenogastropod species Coelostylina hydrobiformis Nützel & Ware, (4) the new heterobranch genus and species Eographis microlineata Nützel & Ware representing the earliest occurrence of the extant family Hyalogyrinidae (Valvatoidea), (5) the heterobranch Sinuarbullina sp., a genus which originates in the Early Triassic and has also been reported from China, Spitsbergen and the US. Three genera (trachyspirid, Strobeus and Coelostylina) represent survivors from the end-Permian mass extinction whereas Eographis and Sinuarbullina have their earliest known occurrence in the Early Triassic. Eographis is the first Early Triassic genus for which coaxial larval heterostrophy is shown. Together with the Devonian genus Palaeocarboninia and the Carboniferous genus Heteroaclisina, it witnesses a high age of Ectobranchia (living families Hyalogyrinidae, Valvatidae, Cornirostridae and Xylodisculidae). This supports the assumption that this group is the first extant offshoot of the Heterobranchia. The studied assemblage is strongly dominated by Strobeus pakistanensis. The small size of the gastropods reflects their ontogenetic stage (early juvenile and larval shells) as well as a small adult size in some of the species. Most of the present gastropods had planktotrophic larval development providing further evidence against the hypothesis that the end-Permian mass extinction event selected against larval planktotrophy. Failure

Published
2018

47. Antibodies to Phosphatidylserine/Prothrombin Complex in Antiphospholipid Syndrome: Analytical and Clinical Perspectives

Author

Lisa K, Peterson, Rohan, Willis, E Nigel, Harris, Ware D, Branch, and Anne E, Tebo

Subjects
Humans, Prothrombin, Phosphatidylserines, Antiphospholipid Syndrome, Antibodies, Biomarkers
Abstract

Antiphospholipid syndrome (APS) is an autoimmune disorder characterized by thrombosis and/or pregnancy-related morbidity accompanied by persistently positive antiphospholipid antibodies (aPL). Current laboratory criteria for APS classification recommend testing for lupus anticoagulant as well as IgG and IgM anticardiolipin, and beta-2 glycoprotein I (anti-β2GPI) antibodies. However, there appears to be a subset of patients with classical APS manifestations who test negative for the recommended criteria aPL tests. While acknowledging that such patients may have clinical features that are not of an autoimmune etiology, experts also speculate that these "seronegative" patients may test negative for relevant autoantibodies as a result of a lack of harmonization and/or standardization. Alternatively, they may have aPL that target other antigens involved in the pathogenesis of APS. In the latter, autoantibodies that recognize a phosphatidylserine/prothrombin (PS/PT) complex have been reported to be associated with APS and may have diagnostic relevance. This review highlights analytical and clinical attributes associated with PS/PT antibodies, taking into consideration the performance characteristics of criteria aPL tests in APS with specific recommendations for harmonization and standardization efforts.

Published
2016

49. Genetic structure and domestication history of the grape

Author

Myles, S, Boyko, A, Owens, C, Brown, P, Grassi, F, Aradhya, M, Prins, B, Reynolds, A, Chia, J, Ware, D, Bustamante, C, Buckler, E, Myles S, Boyko AR, Owens CL, Brown PJ, GRASSI, Fabrizio, Aradhya MK, Prins B, Reynolds A, Chia JM, Ware D, Bustamante CD, Buckler ES, Myles, S, Boyko, A, Owens, C, Brown, P, Grassi, F, Aradhya, M, Prins, B, Reynolds, A, Chia, J, Ware, D, Bustamante, C, Buckler, E, Myles S, Boyko AR, Owens CL, Brown PJ, GRASSI, Fabrizio, Aradhya MK, Prins B, Reynolds A, Chia JM, Ware D, Bustamante CD, and Buckler ES

Abstract

The grape is one of the earliest domesticated fruit crops and, since antiquity, it has been widely cultivated and prized for its fruit and wine. Here, we characterize genome-wide patterns of genetic variation in over 1,000 samples of the domesticated grape, Vitis vinifera subsp. vinifera, and its wild relative, V. vinifera subsp. sylvestris from the US Department of Agriculture grape germ-plasm collection. We find support for a Near East origin of vinifera and present evidence of introgression from local sylvestris as the grape moved into Europe. High levels of genetic diversity and rapid linkage disequilibrium (LD) decay have been maintained in vinifera, which is consistent with a weak domestication bottleneck followed by thousands of years of widespread vegetative propagation. The considerable genetic diversity within vinifera, however, is contained within a complex network of close pedigree relationships that has been generated by crosses among elite cultivars. We show that first-degree relationships are rare between wine and table grapes and among grapes from geographically distant regions. Our results suggest that although substantial genetic diversity has been maintained in the grape subsequent to domestication, there has been a limited exploration of this diversity. We propose that the adoption of vegetative propagation was a double-edged sword: Although it provided a benefit by ensuring true breeding cultivars, it also discouraged the generation of unique cultivars through crosses. The grape currently faces severe pathogen pressures, and the long-term sustainability of the grape and wine industries will rely on the exploitation of the grape's tremendous natural genetic diversity.

Published
2011

50. Paracentral acute middle maculopathy as a finding in patients with severe vision loss following phacoemulsification cataract surgery

Author

Creese, K, Ong, D, Sandhu, SS, Ware, D, Harper, CA, Al-Qureshi, SH, Wickremasinghe, SS, Creese, K, Ong, D, Sandhu, SS, Ware, D, Harper, CA, Al-Qureshi, SH, and Wickremasinghe, SS

Abstract

IMPORTANCE: Paracentral acute middle maculopathy (PAMM) diagnosed by spectral domain optical coherence tomography (SD-OCT) in patients with poor visual outcome post cataract surgery. BACKGROUND: Case series of severe vision loss due to PAMM after cataract surgery. DESIGN: Retrospective case series. PARTICIPANTS: Cases from five surgical centres in Victoria, Australia. METHODS: Retrospective analysis of cases with unexplained 'patch-off' vision loss post cataract surgery. All patients in our cohort had PAMM and presumed diagnosis of central or transient retinal artery occlusion. MAIN OUTCOME MEASURES: A review of the patient histories focusing on pre-operative ocular and systemic vascular risk factors, anaesthetic and operative factors. RESULTS: Ten cases were included. All patients had 6/72 Snellen visual acuity or worse noted on day one post surgery. Three patients had features of central retinal artery occlusion consisting of retinal pallor with a 'cherry red' macula but absent relative afferent pupillary defect. Seven had no features of retinal pallor or attenuation of retinal arterioles. On SD-OCT, all eyes had evident PAMM. Six patients had a history of cardiovascular disease or blood dyscrasia. CONCLUSIONS AND RELEVANCE: PAMM should be considered in patients with 'patch off' visual loss and absence of other fundal signs. We hypothesise that spasm or transient occlusion of central retinal artery leads to arterial hypoperfusion with subsequent ischaemia or infarction of the retina. Underlying arterial disease may have led to pre-existing hypoperfusion that may have been further compromised by raised intraocular pressure during the procedure itself or via raised orbital pressure from the anaesthesia.

Published
2017

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