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504. Genetic tool development in marine protists: emerging model organisms for experimental cell biology

Author

Faktorová, Drahomíra, Nisbet, R Ellen R, Fernández Robledo, José A, Casacuberta, Elena, Sudek, Lisa, Allen, Andrew E, Ares, Manuel, Aresté, Cristina, Balestreri, Cecilia, Barbrook, Adrian C, Beardslee, Patrick, Bender, Sara, Booth, David S, Bouget, François-Yves, Bowler, Chris, Breglia, Susana A, Brownlee, Colin, Burger, Gertraud, Cerutti, Heriberto, Cesaroni, Rachele, Chiurillo, Miguel A, Clemente, Thomas, Coles, Duncan B, Collier, Jackie L, Cooney, Elizabeth C, Coyne, Kathryn, Docampo, Roberto, Dupont, Christopher L, Edgcomb, Virginia, Einarsson, Elin, Elustondo, Pía A, Federici, Fernan, Freire-Beneitez, Veronica, Freyria, Nastasia J, Fukuda, Kodai, García, Paulo A, Girguis, Peter R, Gomaa, Fatma, Gornik, Sebastian G, Guo, Jian, Hampl, Vladimír, Hanawa, Yutaka, Haro-Contreras, Esteban R, Hehenberger, Elisabeth, Highfield, Andrea, Hirakawa, Yoshihisa, Hopes, Amanda, Howe, Christopher J, Hu, Ian, Ibañez, Jorge, Irwin, Nicholas AT, Ishii, Yuu, Janowicz, Natalia Ewa, Jones, Adam C, Kachale, Ambar, Fujimura-Kamada, Konomi, Kaur, Binnypreet, Kaye, Jonathan Z, Kazana, Eleanna, Keeling, Patrick J, King, Nicole, Klobutcher, Lawrence A, Lander, Noelia, Lassadi, Imen, Li, Zhuhong, Lin, Senjie, Lozano, Jean-Claude, Luan, Fulei, Maruyama, Shinichiro, Matute, Tamara, Miceli, Cristina, Minagawa, Jun, Moosburner, Mark, Najle, Sebastián R, Nanjappa, Deepak, Nimmo, Isabel C, Noble, Luke, Novák Vanclová, Anna MG, Nowacki, Mariusz, Nuñez, Isaac, Pain, Arnab, Piersanti, Angela, Pucciarelli, Sandra, Pyrih, Jan, Rest, Joshua S, Rius, Mariana, Robertson, Deborah, Ruaud, Albane, Ruiz-Trillo, Iñaki, Sigg, Monika A, Silver, Pamela A, Slamovits, Claudio H, Jason Smith, G, Sprecher, Brittany N, Stern, Rowena, Swart, Estienne C, Tsaousis, Anastasios D, Tsypin, Lev, Turkewitz, Aaron, Turnšek, Jernej, Valach, Matus, Vergé, Valérie, Von Dassow, Peter, Von Der Haar, Tobias, Waller, Ross F, Wang, Lu, Wen, Xiaoxue, Wheeler, Glen, Woods, April, Zhang, Huan, Mock, Thomas, Worden, Alexandra Z, and Lukeš, Julius

Subjects
Transformation, Genetic, Species Specificity, Green Fluorescent Proteins, Eukaryota, Marine Biology, 14. Life underwater, Biodiversity, DNA, Environment, Models, Biological, Ecosystem
Abstract

Diverse microbial ecosystems underpin life in the sea. Among these microbes are many unicellular eukaryotes that span the diversity of the eukaryotic tree of life. However, genetic tractability has been limited to a few species, which do not represent eukaryotic diversity or environmentally relevant taxa. Here, we report on the development of genetic tools in a range of protists primarily from marine environments. We present evidence for foreign DNA delivery and expression in 13 species never before transformed and for advancement of tools for eight other species, as well as potential reasons for why transformation of yet another 17 species tested was not achieved. Our resource in genetic manipulation will provide insights into the ancestral eukaryotic lifeforms, general eukaryote cell biology, protein diversification and the evolution of cellular pathways.

507. Genetic tool development in marine protists: emerging model organisms for experimental cell biology

Author

Faktorová, Drahomíra, Nisbet, R. Ellen R., Fernández Robledo, José A., Casacuberta, Elena, Sudek, Lisa, Allen, Andrew E., Ares, Manuel, Aresté, Cristina, Balestreri, Cecilia, Barbrook, Adrian C., Beardslee, Patrick, Bender, Sara, Booth, David S., Bouget, François-Yves, Bowler, Chris, Breglia, Susana A., Brownlee, Colin, Burger, Gertraud, Cerutti, Heriberto, Cesaroni, Rachele, Chiurillo, Miguel A., Clemente, Thomas, Coles, Duncan B., Collier, Jackie L., Cooney, Elizabeth C., Coyne, Kathryn, Docampo, Roberto, Dupont, Christopher L., Edgcomb, Virginia, Einarsson, Elin, Elustondo, Pía A., Federici, Fernan, Freire-Beneitez, Veronica, Freyria, Nastasia J., Fukuda, Kodai, García, Paulo A., Girguis, Peter R., Gomaa, Fatma, Gornik, Sebastian G., Guo, Jian, Hampl, Vladimír, Hanawa, Yutaka, Haro-Contreras, Esteban R., Hehenberger, Elisabeth, Highfield, Andrea, Hirakawa, Yoshihisa, Hopes, Amanda, Howe, Christopher J., Hu, Ian, Ibañez, Jorge, Irwin, Nicholas A. T., Ishii, Yuu, Janowicz, Natalia Ewa, Jones, Adam C., Kachale, Ambar, Fujimura-Kamada, Konomi, Kaur, Binnypreet, Kaye, Jonathan Z., Kazana, Eleanna, Keeling, Patrick J., King, Nicole, Klobutcher, Lawrence A., Lander, Noelia, Lassadi, Imen, Li, Zhuhong, Lin, Senjie, Lozano, Jean-Claude, Luan, Fulei, Maruyama, Shinichiro, Matute, Tamara, Miceli, Cristina, Minagawa, Jun, Moosburner, Mark, Najle, Sebastián R., Nanjappa, Deepak, Nimmo, Isabel C., Noble, Luke, Novák Vanclová, Anna M. G., Nowacki, Mariusz, Nuñez, Isaac, Pain, Arnab, Piersanti, Angela, Pucciarelli, Sandra, Pyrih, Jan, Rest, Joshua S., Rius, Mariana, Robertson, Deborah, Ruaud, Albane, Ruiz-Trillo, Iñaki, Sigg, Monika A., Silver, Pamela A., Slamovits, Claudio H., Jason Smith, G., Sprecher, Brittany N., Stern, Rowena, Swart, Estienne C., Tsaousis, Anastasios D., Tsypin, Lev, Turkewitz, Aaron, Turnšek, Jernej, Valach, Matus, Vergé, Valérie, Von Dassow, Peter, Von Der Haar, Tobias, Waller, Ross F., Wang, Lu, Wen, Xiaoxue, Wheeler, Glen, Woods, April, Zhang, Huan, Mock, Thomas, Worden, Alexandra Z., and Lukeš, Julius

Subjects
Resource, 631/1647/767/722, 14. Life underwater, 631/337
Abstract

Diverse microbial ecosystems underpin life in the sea. Among these microbes are many unicellular eukaryotes that span the diversity of the eukaryotic tree of life. However, genetic tractability has been limited to a few species, which do not represent eukaryotic diversity or environmentally relevant taxa. Here, we report on the development of genetic tools in a range of protists primarily from marine environments. We present evidence for foreign DNA delivery and expression in 13 species never before transformed and for advancement of tools for eight other species, as well as potential reasons for why transformation of yet another 17 species tested was not achieved. Our resource in genetic manipulation will provide insights into the ancestral eukaryotic lifeforms, general eukaryote cell biology, protein diversification and the evolution of cellular pathways.

510. The characterization of twenty sequenced human genomes

Author

Julie Hoover-Fong, Nara Sobreira, Elizabeth K. Ruzzo, Erin L. Heinzen, Jacques Fellay, Anna C. Need, Barton F. Haynes, Linda K. Hong, Kimberly Pelak, Jessica M. Maia, Jason Smith, Mingfu Zhu, Samuel P. Dickson, Alexander McKenzie, Dongliang Ge, Kevin V. Shianna, Katharina A. Lornsen, David Goldstein, James J. Goedert, Curtis Gumbs, Joshua D. Milner, Abanish Singh, Ruth Ottman, Elizabeth T. Cirulli, and C. Ryan Campbell

Subjects
Cancer Research, DNA Copy Number Variations, Genotype, lcsh:QH426-470, Sequence analysis, Population, Genomics, Biology, Hemophilia A, Polymorphism, Single Nucleotide, Genome, DNA sequencing, Gene Knockout Techniques, Open Reading Frames, 03 medical and health sciences, 0302 clinical medicine, INDEL Mutation, Gene Duplication, Databases, Genetic, Genetics, Humans, Genetics and Genomics/Genomics, education, Molecular Biology, Gene, Genetics (clinical), Ecology, Evolution, Behavior and Systematics, Oligonucleotide Array Sequence Analysis, 030304 developmental biology, 0604 Genetics, 0303 health sciences, education.field_of_study, Factor VIII, Polymorphism, Genetic, Base Sequence, Genome, Human, Exons, Sequence Analysis, DNA, Human genetics, Genetics and Genomics/Genome Projects, lcsh:Genetics, Genetics, Population, Case-Control Studies, Human genome, 030217 neurology & neurosurgery, Research Article, Developmental Biology
Abstract

We present the analysis of twenty human genomes to evaluate the prospects for identifying rare functional variants that contribute to a phenotype of interest. We sequenced at high coverage ten “case” genomes from individuals with severe hemophilia A and ten “control” genomes. We summarize the number of genetic variants emerging from a study of this magnitude, and provide a proof of concept for the identification of rare and highly-penetrant functional variants by confirming that the cause of hemophilia A is easily recognizable in this data set. We also show that the number of novel single nucleotide variants (SNVs) discovered per genome seems to stabilize at about 144,000 new variants per genome, after the first 15 individuals have been sequenced. Finally, we find that, on average, each genome carries 165 homozygous protein-truncating or stop loss variants in genes representing a diverse set of pathways., Author Summary We report here the nearly complete genomic sequence of 20 different individuals, determined using “next-generation” sequencing technologies. We use these data to characterize the type of genetic variation carried by humans in a sample of this size, which is to our knowledge the largest set of unrelated genomic sequences that have been reported. We summarize different categories of variation in each genome, and in total across all 20 of the genomes, finding a surprising number of variants predicted to reduce or remove the proteins encoded by many different genes. This work provides important fundamental information about the scope of human genetic variation, and suggests ways to further explore the relationship between these genetic variants and human disease.

512. Population trends among Jamaican reef corals

Author

James Porter, G. Jason Smith, Joseph E. Neigel, J. D. Woodley, Dorinda G. Dallmeyer, and James F. Battey

Subjects
geography, education.field_of_study, Multidisciplinary, geography.geographical_feature_category, Ecology, Coral, fungi, Population, technology, industry, and agriculture, Species diversity, Storm, Rainforest, biochemical phenomena, metabolism, and nutrition, Fishery, Ecosystem, education, Reef, Bay, geographic locations
Abstract

Disturbance has been cited as a potentially important agent in structuring ecological communities by modifying the effects of competition1–5. Catastrophic disturbance has also been proposed as a factor promoting the coexistence of competing species in highly diverse tropical ecosystems such as rain forests and coral reefs2,6–11. Here we describe patterns of recruitment and mortality among reef corals over 4 yr at several depths on the reefs of Discovery Bay, Jamaica, which were struck by Hurricane Alien on 6 August 198012. Photographic quadrats monitored since 1976 on a shallow water reef showed a negative correlation between coral abundance and mortality which was not offset by compensatory patterns of recruitment. This slow trend in the disproportionate reduction of rarer, competitively inferior species was reversed by Hurricane Alien, with storm-induced mortality being greatest in the most abundant species. On deeper reef stations, undisturbed by the storm, slower rates of colony loss were compensated for by commensurate rates of colony recruitment. Thus, patterns of differential mortality and recruitment contribute to the maintenance of high species diversity in this tropical marine ecosystem.

Published
1981
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513. Voices of the Young

Author

Jason Smith

Subjects
Work (electrical), Pedagogy, Sociology, Permission, Education
Abstract

Published with the permission of the author who wrote the piece in 1984 at the age of 12. He was an eighth grader at Central Junior High School in Oklahoma City, Oklahoma, under the guidance of his English teacher, Marjorie Masopust. No changes have been made in the original work.

Published
1985
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516. LETTERS TO THE EDITOR.

Author

Dula, James, Brown, James, Gatewood Jr., Rico, and Jason-Smith, Carletta

Subjects
LETTERS to the editor, PERIODICAL awards, LEGAL status of ex-convicts
Abstract

Several letters to the editor are presented including one on the appreciation for the John H. Sengstacke Award for Excellence received by the periodical "The Washington Informer," one on a story about the band Maze featuring its member Frankie Beverly in the June 24, 2010 issue, and one in response to the article about disciplinary action against ex-offenders in the U.S. by Benjamin Koconis in the June 24, 2010 issue.

Published
2010

517. Rare synchronous caecal and sigmoid volvulus: management of two cases.

Author

Muhammad, Butt, Alice, Lee, Rabiya, Aseem, and Jason, Smith

Subjects
*LARGE intestine, *BOWEL obstructions, *CECUM, *COLON cancer, *DIVERTICULITIS, *SIGMOID volvulus
Abstract

Colonic volvulus is one of leading causes of large bowel obstruction following colorectal cancer and diverticulitis, accounting for 5% of cases. Sigmoid volvulus is most common (75%) followed by volvulus of the caecum (15%), transverse colon (3%) and splenic flexure (2%). Synchronous volvulus of the caecum and sigmoid is very rare, with six reported cases in the literature to the best of our knowledge. We report two cases within 6 months. The key learning points include that classical radiological signs of both caecal and sigmoid volvulus may not be present, and that prompt, definitive management is necessary to prevent recurrence and morbidity. [ABSTRACT FROM AUTHOR]

Published
2021
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518. Considerations in Harmful Algal Bloom Research and Monitoring: Perspectives From a Consensus-Building Workshop and Technology Testing

Author

Beth A. Stauffer, Holly A. Bowers, Earle Buckley, Timothy W. Davis, Thomas H. Johengen, Raphael Kudela, Margaret A. McManus, Heidi Purcell, G. Jason Smith, Andrea Vander Woude, and Mario N. Tamburri

Subjects
harmful algal blooms, toxins, ocean observing, environmental technology, rapid detection, ecological forecasting, Science, General. Including nature conservation, geographical distribution, QH1-199.5
Abstract

Recurrent blooms of harmful algae and cyanobacteria (HABs) plague many coastal and inland waters throughout the United States and have significant socioeconomic impacts to the adjacent communities. Notable HAB events in recent years continue to underscore the many remaining gaps in knowledge and increased needs for technological advances leading to early detection. This review summarizes the main research and management priorities that can be addressed through ocean observation-based approaches and technological solutions for harmful algal blooms, provides an update to the state of the technology to detect HAB events based on recent activities of the Alliance for Coastal Technologies (ACT), offers considerations for ensuring data quality, and highlights both ongoing challenges and opportunities for solutions in integrating HAB-focused technologies in research and management. Specifically, technological advances are discussed for remote sensing (both multispectral satellite and hyperspectral); deployable in situ detection of HAB species on fixed or mobile platforms (based on bulk or taxa-specific biomass, images, or molecular approaches); and field-based and/or rapid quantitative detection of HAB toxins (via molecular and analytical chemistry methods). Suggestions for addressing challenges to continued development and adoption of new technologies are summarized, based on a consensus-building workshop hosted by ACT, including dealing with the uncertainties in investment for HAB research, monitoring, and management. Challenges associated with choosing appropriate technologies for a given ecosystem and/or management concern are also addressed, and examples of programs that are leveraging and combining complementary approaches are highlighted.

Published
2019
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519. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing.

Author

Patrick J Keeling, Fabien Burki, Heather M Wilcox, Bassem Allam, Eric E Allen, Linda A Amaral-Zettler, E Virginia Armbrust, John M Archibald, Arvind K Bharti, Callum J Bell, Bank Beszteri, Kay D Bidle, Connor T Cameron, Lisa Campbell, David A Caron, Rose Ann Cattolico, Jackie L Collier, Kathryn Coyne, Simon K Davy, Phillipe Deschamps, Sonya T Dyhrman, Bente Edvardsen, Ruth D Gates, Christopher J Gobler, Spencer J Greenwood, Stephanie M Guida, Jennifer L Jacobi, Kjetill S Jakobsen, Erick R James, Bethany Jenkins, Uwe John, Matthew D Johnson, Andrew R Juhl, Anja Kamp, Laura A Katz, Ronald Kiene, Alexander Kudryavtsev, Brian S Leander, Senjie Lin, Connie Lovejoy, Denis Lynn, Adrian Marchetti, George McManus, Aurora M Nedelcu, Susanne Menden-Deuer, Cristina Miceli, Thomas Mock, Marina Montresor, Mary Ann Moran, Shauna Murray, Govind Nadathur, Satoshi Nagai, Peter B Ngam, Brian Palenik, Jan Pawlowski, Giulio Petroni, Gwenael Piganeau, Matthew C Posewitz, Karin Rengefors, Giovanna Romano, Mary E Rumpho, Tatiana Rynearson, Kelly B Schilling, Declan C Schroeder, Alastair G B Simpson, Claudio H Slamovits, David R Smith, G Jason Smith, Sarah R Smith, Heidi M Sosik, Peter Stief, Edward Theriot, Scott N Twary, Pooja E Umale, Daniel Vaulot, Boris Wawrik, Glen L Wheeler, William H Wilson, Yan Xu, Adriana Zingone, and Alexandra Z Worden

Subjects
Biology (General), QH301-705.5
Published
2014
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521. Integration of the Duke Activity Status Index into preoperative risk evaluation: a multicentre prospective cohort study.

Author

Wijeysundera DN, Beattie WS, Hillis GS, Abbott TEF, Shulman MA, Ackland GL, Mazer CD, Myles PS, Pearse RM, Cuthbertson BH, Myles PS, Shulman MA, Wallace S, Farrington C, Thompson B, Ellis M, Borg B, Kerridge RK, Douglas J, Brannan J, Pretto J, Godsall MG, Beauchamp N, Allen S, Kennedy A, Wright E, Malherbe J, Ismail H, Riedel B, Melville A, Sivakumar H, Murmane A, Kenchington K, Kirabiyik Y, Gurunathan U, Stonell C, Brunello K, Steele K, Tronstad O, Masel P, Dent A, Smith E, Bodger A, Abolfathi M, Sivalingam P, Hall A, Painter TW, Macklin S, Elliott A, Carrera AM, Terblanche NCS, Pitt S, Samuels J, Wilde C, Leslie K, MacCormick A, Bramley D, Southcott AM, Grant J, Taylor H, Bates S, Towns M, Tippett A, Marshall F, Mazer CD, Kunasingam J, Yagnik A, Crescini C, Yagnik S, McCartney CJL, Choi S, Somascanthan P, Flores K, Wijeysundera DN, Beattie WS, Karkouti K, Clarke HA, Jerath A, McCluskey SA, Wasowicz M, Granton JT, Day L, Pazmino-Canizares J, Oh P, Belliard R, Lee L, Dobson K, Chan V, Brull R, Ami N, Stanbrook M, Hagen K, Campbell D, Short T, Van Der Westhuizen J, Higgie K, Lindsay H, Jang R, Wong C, Mcallister D, Ali M, Kumar J, Waymouth E, Kim C, Dimech J, Lorimer M, Tai J, Miller R, Sara R, Collingwood A, Olliff S, Gabriel S, Houston H, Dalley P, Hurford S, Hunt A, Andrews L, Navarra L, Jason-Smith A, Thompson H, McMillan N, Back G, Croal BL, Lum M, Martin D, James S, Filipe H, Pinto M, Kynaston S, Pearse RM, Abbott TEF, Phull M, Beilstein C, Bodger P, Everingham K, Hu Y, Niebrzegowska E, Corriea C, Creary T, Januszewska M, Ahmad T, Whalley J, Haslop R, McNeil J, Brown A, MacDonald N, Pakats M, Greaves K, Jhanji S, Raobaikady R, Black E, Rooms M, Lawrence H, Koutra M, Pirie K, Gertsman M, Jack S, Celinski M, Levett D, Edwards M, Salmon K, Bolger C, Loughney L, Seaward L, Collins H, Tyrell B, Tantony N, Golder K, Ackland GL, Stephens RCM, Gallego-Paredes L, Reyes A, Gutierrez Del Arroyo A, Raj A, and Lifford R

Subjects
Adult, Aged, Biomarkers blood, Female, Health Status, Humans, Male, Middle Aged, Myocardial Infarction etiology, Myocardial Infarction mortality, Natriuretic Peptide, Brain blood, Peptide Fragments blood, Postoperative Complications mortality, Prognosis, Prospective Studies, Risk Assessment, Risk Factors, Self Report, Surveys and Questionnaires, Exercise Tolerance physiology, Health Status Indicators, Preoperative Care methods
Abstract

Background: The Duke Activity Status Index (DASI) questionnaire might help incorporate self-reported functional capacity into preoperative risk assessment. Nonetheless, prognostically important thresholds in DASI scores remain unclear. We conducted a nested cohort analysis of the Measurement of Exercise Tolerance before Surgery (METS) study to characterise the association of preoperative DASI scores with postoperative death or complications., Methods: The analysis included 1546 participants (≥40 yr of age) at an elevated cardiac risk who had inpatient noncardiac surgery. The primary outcome was 30-day death or myocardial injury. The secondary outcomes were 30-day death or myocardial infarction, in-hospital moderate-to-severe complications, and 1 yr death or new disability. Multivariable logistic regression modelling was used to characterise the adjusted association of preoperative DASI scores with outcomes., Results: The DASI score had non-linear associations with outcomes. Self-reported functional capacity better than a DASI score of 34 was associated with reduced odds of 30-day death or myocardial injury (odds ratio: 0.97 per 1 point increase above 34; 95% confidence interval [CI]: 0.96-0.99) and 1 yr death or new disability (odds ratio: 0.96 per 1 point increase above 34; 95% CI: 0.92-0.99). Self-reported functional capacity worse than a DASI score of 34 was associated with increased odds of 30-day death or myocardial infarction (odds ratio: 1.05 per 1 point decrease below 34; 95% CI: 1.00-1.09), and moderate-to-severe complications (odds ratio: 1.03 per 1 point decrease below 34; 95% CI: 1.01-1.05)., Conclusions: A DASI score of 34 represents a threshold for identifying patients at risk for myocardial injury, myocardial infarction, moderate-to-severe complications, and new disability., (Copyright © 2019 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Published
2020
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