Search

Your search keyword '"Medina Monica"' showing total 336 results
Start Over Author "Medina Monica"
336 results on '"Medina Monica"'

1. A new algorithm DEtectS critical Congenital Heart Disease at different altitudes: ANDES-CHD study

Author

Bravo-Jaimes, Katia, Vasquez-Loarte, Tania, Rojas-Camayo, Jose, Medina, Monica, Mejia, Christian R., Zapata-Galarza, Henry, Berrocal, Marilia, Orozco, Jeanette, Lozano, Daniel, Santivañez, Maryuri, Sangay, Carlos, Rosales, William, Mamani, Leddy, Macedo, Nelly, Coronado, Joel, Huaman, Gian, Marquez, Rafael, Li, Zhuo, Masood, Kiran M., Alejos, Juan, Reardon, Leigh, and Lin, Jeannette

Published
2024
Full Text
View/download PDF

3. Expansion of the global RNA virome reveals diverse clades of bacteriophages

Author

Neri, Uri, Wolf, Yuri I, Roux, Simon, Camargo, Antonio Pedro, Lee, Benjamin, Kazlauskas, Darius, Chen, I Min, Ivanova, Natalia, Allen, Lisa Zeigler, Paez-Espino, David, Bryant, Donald A, Bhaya, Devaki, Consortium, RNA Virus Discovery, Narrowe, Adrienne B, Probst, Alexander J, Sczyrba, Alexander, Kohler, Annegret, Séguin, Armand, Shade, Ashley, Campbell, Barbara J, Lindahl, Björn D, Reese, Brandi Kiel, Roque, Breanna M, DeRito, Chris, Averill, Colin, Cullen, Daniel, Beck, David AC, Walsh, David A, Ward, David M, Wu, Dongying, Eloe-Fadrosh, Emiley, Brodie, Eoin L, Young, Erica B, Lilleskov, Erik A, Castillo, Federico J, Martin, Francis M, LeCleir, Gary R, Attwood, Graeme T, Cadillo-Quiroz, Hinsby, Simon, Holly M, Hewson, Ian, Grigoriev, Igor V, Tiedje, James M, Jansson, Janet K, Lee, Janey, VanderGheynst, Jean S, Dangl, Jeff, Bowman, Jeff S, Blanchard, Jeffrey L, Bowen, Jennifer L, Xu, Jiangbing, Banfield, Jillian F, Deming, Jody W, Kostka, Joel E, Gladden, John M, Rapp, Josephine Z, Sharpe, Joshua, McMahon, Katherine D, Treseder, Kathleen K, Bidle, Kay D, Wrighton, Kelly C, Thamatrakoln, Kimberlee, Nusslein, Klaus, Meredith, Laura K, Ramirez, Lucia, Buee, Marc, Huntemann, Marcel, Kalyuzhnaya, Marina G, Waldrop, Mark P, Sullivan, Matthew B, Schrenk, Matthew O, Hess, Matthias, Vega, Michael A, O’Malley, Michelle A, Medina, Monica, Gilbert, Naomi E, Delherbe, Nathalie, Mason, Olivia U, Dijkstra, Paul, Chuckran, Peter F, Baldrian, Petr, Constant, Philippe, Stepanauskas, Ramunas, Daly, Rebecca A, Lamendella, Regina, Gruninger, Robert J, McKay, Robert M, Hylander, Samuel, Lebeis, Sarah L, Esser, Sarah P, Acinas, Silvia G, Wilhelm, Steven S, Singer, Steven W, Tringe, Susannah S, Woyke, Tanja, Reddy, TBK, Bell, Terrence H, Mock, Thomas, McAllister, Tim, and Thiel, Vera

Subjects
Microbiology, Biological Sciences, Bioinformatics and Computational Biology, Genetics, Infectious Diseases, Biotechnology, Microbiome, Infection, Bacteriophages, DNA-Directed RNA Polymerases, Genome, Viral, Phylogeny, RNA, RNA Viruses, RNA-Dependent RNA Polymerase, Virome, RNA Virus Discovery Consortium, Bactriophage, Functional protein annotation, Metatranscriptomics, RNA Virus, RNA dependent RNA polymerase, Viral Ecology, Virus, Virus - Host prediction, viral phylogeny, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences
Abstract

High-throughput RNA sequencing offers broad opportunities to explore the Earth RNA virome. Mining 5,150 diverse metatranscriptomes uncovered >2.5 million RNA virus contigs. Analysis of >330,000 RNA-dependent RNA polymerases (RdRPs) shows that this expansion corresponds to a 5-fold increase of the known RNA virus diversity. Gene content analysis revealed multiple protein domains previously not found in RNA viruses and implicated in virus-host interactions. Extended RdRP phylogeny supports the monophyly of the five established phyla and reveals two putative additional bacteriophage phyla and numerous putative additional classes and orders. The dramatically expanded phylum Lenarviricota, consisting of bacterial and related eukaryotic viruses, now accounts for a third of the RNA virome. Identification of CRISPR spacer matches and bacteriolytic proteins suggests that subsets of picobirnaviruses and partitiviruses, previously associated with eukaryotes, infect prokaryotic hosts.

Published
2022

4. Thousands of small, novel genes predicted in global phage genomes

Author

Fremin, Brayon J, Bhatt, Ami S, Kyrpides, Nikos C, Consortium, Global Phage Small Open Reading Frame, Sengupta, Aditi, Sczyrba, Alexander, da Silva, Aline Maria, Buchan, Alison, Gaudin, Amelie, Brune, Andreas, Hirsch, Ann M, Neumann, Anthony, Shade, Ashley, Visel, Axel, Campbell, Barbara, Baker, Brett, Hedlund, Brian P, Crump, Byron C, Currie, Cameron, Kelly, Charlene, Craft, Chris, Hazard, Christina, Francis, Christopher, Schadt, Christopher W, Averill, Colin, Mobilian, Courtney, Buckley, Dan, Hunt, Dana, Noguera, Daniel, Beck, David, Valentine, David L, Walsh, David, Sumner, Dawn, Lymperopoulou, Despoina, Bhaya, Devaki, Bryant, Donald A, Morrison, Elise, Brodie, Eoin, Young, Erica, Lilleskov, Erik, Högfors-Rönnholm, Eva, Chen, Feng, Stewart, Frank, Nicol, Graeme W, Teeling, Hanno, Beller, Harry R, Dionisi, Hebe, Liao, Hui-Ling, Beman, J Michael, Stegen, James, Tiedje, James, Jansson, Janet, VanderGheynst, Jean, Norton, Jeanette, Dangl, Jeff, Blanchard, Jeffrey, Bowen, Jennifer, Macalady, Jennifer, Pett-Ridge, Jennifer, Rich, Jeremy, Payet, Jérôme P, Gladden, John D, Raff, Jonathan D, Klassen, Jonathan L, Tarn, Jonathan, Neufeld, Josh, Gravuer, Kelly, Hofmockel, Kirsten, Chen, Ko-Hsuan, Konstantinidis, Konstantinos, DeAngelis, Kristen M, Partida-Martinez, Laila P, Meredith, Laura, Chistoserdova, Ludmila, Moran, Mary Ann, Scarborough, Matthew, Schrenk, Matthew, Sullivan, Matthew, David, Maude, O'Malley, Michelle A, Medina, Monica, Habteselassie, Mussie, Ward, Nicholas D, Pietrasiak, Nicole, Mason, Olivia U, Sorensen, Patrick O, de los Santos, Paulina Estrada, Baldrian, Petr, McKay, R Michael, Simister, Rachel, Stepanauskas, Ramunas, Neumann, Rebecca, Malmstrom, Rex, Cavicchioli, Ricardo, Kelly, Robert, Hatzenpichler, Roland, Stocker, Roman, Cattolico, Rose Ann, Ziels, Ryan, and Vilgalys, Rytas

Subjects
Microbiology, Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, 2.1 Biological and endogenous factors, Generic health relevance, Bacteriophages, Genome, Viral, Genomics, Microbiota, Phylogeny, Global Phage Small Open Reading Frame (GP-SmORF) Consortium, CP: Microbiology, MetaRibo-Seq, comparative genomics, gene families, microbiome, phage, sORFs, small genes, Biochemistry and Cell Biology, Medical Physiology, Biological sciences
Abstract

Small genes (40,000 small-gene families in ∼2.3 million phage genome contigs. We find that small genes in phage genomes are approximately 3-fold more prevalent than in host prokaryotic genomes. Our approach enriches for small genes that are translated in microbiomes, suggesting the small genes identified are coding. More than 9,000 families encode potentially secreted or transmembrane proteins, more than 5,000 families encode predicted anti-CRISPR proteins, and more than 500 families encode predicted antimicrobial proteins. By combining homology and genomic-neighborhood analyses, we reveal substantial novelty and diversity within phage biology, including small phage genes found in multiple host phyla, small genes encoding proteins that play essential roles in host infection, and small genes that share genomic neighborhoods and whose encoded proteins may share related functions.

Published
2022

5. Evolutionary insights into scleractinian corals using comparative genomic hybridizations

Author

Aranda Manuel, DeSalvo Michael K, Bayer Till, Medina Monica, and Voolstra Christian R

Subjects
Coral reefs, Comparative genomic hybridization (CGH), Microarray, Mitochondria, Evolution, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Coral reefs belong to the most ecologically and economically important ecosystems on our planet. Yet, they are under steady decline worldwide due to rising sea surface temperatures, disease, and pollution. Understanding the molecular impact of these stressors on different coral species is imperative in order to predict how coral populations will respond to this continued disturbance. The use of molecular tools such as microarrays has provided deep insight into the molecular stress response of corals. Here, we have performed comparative genomic hybridizations (CGH) with different coral species to an Acropora palmata microarray platform containing 13,546 cDNA clones in order to identify potentially rapidly evolving genes and to determine the suitability of existing microarray platforms for use in gene expression studies (via heterologous hybridization). Results Our results showed that the current microarray platform for A. palmata is able to provide biological relevant information for a wide variety of coral species covering both the complex clade as well the robust clade. Analysis of the fraction of highly diverged genes showed a significantly higher amount of genes without annotation corroborating previous findings that point towards a higher rate of divergence for taxonomically restricted genes. Among the genes with annotation, we found many mitochondrial genes to be highly diverged in M. faveolata when compared to A. palmata, while the majority of nuclear encoded genes maintained an average divergence rate. Conclusions The use of present microarray platforms for transcriptional analyses in different coral species will greatly enhance the understanding of the molecular basis of stress and health and highlight evolutionary differences between scleractinian coral species. On a genomic basis, we show that cDNA arrays can be used to identify patterns of divergence. Mitochondrion-encoded genes seem to have diverged faster than nuclear encoded genes in robust corals. Accordingly, this needs to be taken into account when using mitochondrial markers for scleractinian phylogenies.

Published
2012
Full Text
View/download PDF

6. A community perspective on the concept of marine holobionts: state-of-the-art, challenges, and future directions

Author

Dittami, Simon, Arboleda, Enrique, Auguet, Jean-Christophe, Bigalke, Arite, Briand, Enora, Cárdenas, Paco, Cardini, Ulisse, Decelle, Johan, Engelen, Ashwin, Eveillard, Damien, Gachon, Claire, Griffiths, Sarah, Harder, Tilmann, Kayal, Ehsan, Kazamia, Elena, Lallier, François, Medina, Mónica, Marzinelli, Ezequiel, Morganti, Teresa, Pons, Laura, Prado, Soizic, Valverde, José Pintado, Saha, Mahasweta, Selosse, Marc-Andre, Skillings, Derek, Stock, Willem, Sunagawa, Shinichi, Toulza, Eve, Vorobev, Alexey, Leblanc, Catherine, and Not, Fabrice

Subjects
Quantitative Biology - Populations and Evolution
Abstract

Host-microbe interactions play crucial roles in marine ecosystems, but we still have very little understanding of the mechanisms that govern these relationships, the evolutionary processes that shape them, and their ecological consequences. The holobiont concept is a renewed paradigm in biology that can help describe and understand these complex systems. It posits that a host and its associated microbiota, living together in a long-lasting relationship, form the holobiont, and have to be studied together, as a coherent biological and functional unit, in order to understand the biology, ecology and evolution of the organisms. Here we discuss critical concepts and opportunities in marine holobiont research and identify key challenges in the field. We highlight the potential economic, sociological, and environmental impacts of the holobiont concept in marine biological, evolutionary, and environmental sciences with comparisons to terrestrial science whenever appropriate. A deeper understanding of such complex systems, however, will require further technological and conceptual advances. The most significant challenge will be to bridge functional research on simple and tractable model systems and global approaches. This will require scientists to work together as an (inter)active community in order to address, for instance, ecological and evolutionary questions and the roles of holobionts in biogeochemical cycles., Comment: PeerJ Preprints, Computer Science Preprints., 2019

Published
2019
Full Text
View/download PDF

11. The Power of Community School Councils in Urban Schools

Author

Medina, Monica A., Grim, Jim, Cosby, Gayle, and Brodnax, Rita

Abstract

Demand for school reform, particularly urban schools labeled as "failing," requires a community engagement strategy centered on intermingled social problems: poverty, racial isolation and discrimination, cultural clashes, socio-economic inequalities, and funding disparities. While school administrators are challenged to turn schools around with limited time and resources quickly, their efforts are not a silver bullet. Engaging community requires committed partnerships that support schools to advance quality learning. Community school councils, an organizing strategy, focus on addressing potential threats and enhancing strengths for student success. This case study describes the participatory action structure of community school councils in an urban public high school, a middle school, and three elementary schools. The theoretical framework of the study is based on Bryk's five essential elements of school improvement and their interplay that predicts school improvement or stagnation in the long term (Bryk et al., 2010) and more recent findings that community schools demonstrate an evidence-based strategy for equitable school improvement. This study is relevant to school communities with comparable demographics interested in a comprehensive strategy that expands the traditional educational mission to address social/emotional and health needs of children and families by engaging the broader community to support student learning, strengthening families and school communities.

Published
2020
Full Text
View/download PDF

12. Venous thromboembolism in pancreatic neuroendocrine neoplasm: a cohort study

Author

Gervaso, Lorenzo, primary, Laffi, Alice, additional, Gaeta, Aurora, additional, Gandini, Sara, additional, Boldrini, Laura, additional, Meneses-Medina, Monica Isabel, additional, Rubino, Manila, additional, Benini, Lavinia, additional, Borghesani, Michele, additional, Algeri, Laura, additional, Curigliano, Giuseppe, additional, Spada, Francesca, additional, Cella, Chiara Alessandra, additional, and Fazio, Nicola, additional

Published
2024
Full Text
View/download PDF

16. Corrigendum: Whole genome analysis of a schistosomiasis-transmitting freshwater snail.

Author

Adema, Coen, Hillier, LaDeana, Jones, Catherine, Loker, Eric, Knight, Matty, Minx, Patrick, Oliveira, Guilherme, Raghavan, Nithya, Shedlock, Andrew, do Amaral, Laurence, Arican-Goktas, Halime, Assis, Juliana, Baba, Elio, Baron, Olga, Bayne, Christopher, Bickham-Wright, Utibe, Biggar, Kyle, Blouin, Michael, Bonning, Bryony, Botka, Chris, Bridger, Joanna, Buckley, Katherine, Buddenborg, Sarah, Lima Caldeira, Roberta, Carleton, Julia, Carvalho, Omar, Castillo, Maria, Chalmers, Iain, Christensens, Mikkel, Clifton, Sandra, Cosseau, Celine, Coustau, Christine, Cripps, Richard, Cuesta-Astroz, Yesid, Cummins, Scott, Di Stefano, Leon, Dinguirard, Nathalie, Duval, David, Emrich, Scott, Feschotte, Cédric, Feyereisen, Rene, FitzGerald, Peter, Fronick, Catrina, Fulton, Lucinda, Galinier, Richard, Gava, Sandra, Geusz, Michael, Geyer, Kathrin, Giraldo-Calderón, Gloria, de Souza Gomes, Matheus, Gordy, Michelle, Gourbal, Benjamin, Grunau, Christoph, Hanington, Patrick, Hoffmann, Karl, Hughes, Daniel, Humphries, Judith, Jackson, Daniel, Jannotti-Passos, Liana, de Jesus Jeremias, Wander, Jobling, Susan, Kamel, Bishoy, Kapusta, Aurélie, Kaur, Satwant, Koene, Joris, Kohn, Andrea, Lawson, Dan, Lawton, Scott, Liang, Di, Limpanont, Yanin, Liu, Sijun, Lockyer, Anne, Lovato, Ty, Ludolf, Fernanda, Magrini, Vince, McManus, Donald, Medina, Monica, Misra, Milind, Mitta, Guillaume, Mkoji, Gerald, Montague, Michael, Montelongo, Cesar, Moroz, Leonid, Munoz-Torres, Monica, Niazi, Umar, Noble, Leslie, Oliveira, Francislon, Pais, Fabiano, Papenfuss, Anthony, Peace, Rob, Pena, Janeth, Pila, Emmanuel, Quelais, Titouan, Raney, Brian, Rast, Jonathan, Rollinson, David, Rosse, Izinara, Rotgans, Bronwyn, Routledge, Edwin, and Ryan, Kathryn

Abstract

This corrects the article DOI: 10.1038/ncomms15451.

Published
2017

17. Whole genome analysis of a schistosomiasis-transmitting freshwater snail.

Author

Adema, Coen M, Hillier, LaDeana W, Jones, Catherine S, Loker, Eric S, Knight, Matty, Minx, Patrick, Oliveira, Guilherme, Raghavan, Nithya, Shedlock, Andrew, do Amaral, Laurence Rodrigues, Arican-Goktas, Halime D, Assis, Juliana G, Baba, Elio Hideo, Baron, Olga L, Bayne, Christopher J, Bickham-Wright, Utibe, Biggar, Kyle K, Blouin, Michael, Bonning, Bryony C, Botka, Chris, Bridger, Joanna M, Buckley, Katherine M, Buddenborg, Sarah K, Lima Caldeira, Roberta, Carleton, Julia, Carvalho, Omar S, Castillo, Maria G, Chalmers, Iain W, Christensens, Mikkel, Clifton, Sandra, Cosseau, Celine, Coustau, Christine, Cripps, Richard M, Cuesta-Astroz, Yesid, Cummins, Scott F, di Stephano, Leon, Dinguirard, Nathalie, Duval, David, Emrich, Scott, Feschotte, Cédric, Feyereisen, Rene, FitzGerald, Peter, Fronick, Catrina, Fulton, Lucinda, Galinier, Richard, Gava, Sandra G, Geusz, Michael, Geyer, Kathrin K, Giraldo-Calderón, Gloria I, de Souza Gomes, Matheus, Gordy, Michelle A, Gourbal, Benjamin, Grunau, Christoph, Hanington, Patrick C, Hoffmann, Karl F, Hughes, Daniel, Humphries, Judith, Jackson, Daniel J, Jannotti-Passos, Liana K, de Jesus Jeremias, Wander, Jobling, Susan, Kamel, Bishoy, Kapusta, Aurélie, Kaur, Satwant, Koene, Joris M, Kohn, Andrea B, Lawson, Dan, Lawton, Scott P, Liang, Di, Limpanont, Yanin, Liu, Sijun, Lockyer, Anne E, Lovato, TyAnna L, Ludolf, Fernanda, Magrini, Vince, McManus, Donald P, Medina, Monica, Misra, Milind, Mitta, Guillaume, Mkoji, Gerald M, Montague, Michael J, Montelongo, Cesar, Moroz, Leonid L, Munoz-Torres, Monica C, Niazi, Umar, Noble, Leslie R, Oliveira, Francislon S, Pais, Fabiano S, Papenfuss, Anthony T, Peace, Rob, Pena, Janeth J, Pila, Emmanuel A, Quelais, Titouan, Raney, Brian J, Rast, Jonathan P, Rollinson, David, Rosse, Izinara C, Rotgans, Bronwyn, Routledge, Edwin J, and Ryan, Kathryn M

Subjects
Animals, Schistosoma mansoni, Biomphalaria, Schistosomiasis mansoni, Proteome, DNA Transposable Elements, Pheromones, Sequence Analysis, DNA, Animal Communication, Fresh Water, Evolution, Molecular, Gene Expression Regulation, Genome, Host-Parasite Interactions, Stress, Physiological, Evolution, Molecular, Sequence Analysis, DNA, Stress, Physiological
Abstract

Biomphalaria snails are instrumental in transmission of the human blood fluke Schistosoma mansoni. With the World Health Organization's goal to eliminate schistosomiasis as a global health problem by 2025, there is now renewed emphasis on snail control. Here, we characterize the genome of Biomphalaria glabrata, a lophotrochozoan protostome, and provide timely and important information on snail biology. We describe aspects of phero-perception, stress responses, immune function and regulation of gene expression that support the persistence of B. glabrata in the field and may define this species as a suitable snail host for S. mansoni. We identify several potential targets for developing novel control measures aimed at reducing snail-mediated transmission of schistosomiasis.

Published
2017

18. Community Engagement through Partnerships: Lessons Learned from a Decade of Full-Service Community School Implementation

Author

Medina, Monica A., Cosby, Gayle, and Grim, Jim

Abstract

Improving performance in an environment often tested by intermingled social problems, including poverty, racial isolation, cultural clashes between teachers and students, and school funding disparities requires authentic, committed family, school, and community partnerships. Using Bryk's (2010) model for effective and improving schools, our study describes challenges and achievements experienced over a decade of implementing the full-service community school (FSCS) reform in two neighborhoods in Indianapolis, Indiana. We also share lessons about funding, collaborative structures and processes, and organizational responses to change. The study has broad implications for both FSCSs and urban schools with comparable demographics that are working to build effective partnerships to address social problems in lasting ways.

Published
2019
Full Text
View/download PDF

19. Comparative genomics explains the evolutionary success of reef-forming corals.

Author

Bhattacharya, Debashish, Agrawal, Shobhit, Aranda, Manuel, Baumgarten, Sebastian, Belcaid, Mahdi, Drake, Jeana L, Erwin, Douglas, Foret, Sylvian, Gates, Ruth D, Gruber, David F, Kamel, Bishoy, Lesser, Michael P, Levy, Oren, Liew, Yi Jin, MacManes, Matthew, Mass, Tali, Medina, Monica, Mehr, Shaadi, Meyer, Eli, Price, Dana C, Putnam, Hollie M, Qiu, Huan, Shinzato, Chuya, Shoguchi, Eiichi, Stokes, Alexander J, Tambutté, Sylvie, Tchernov, Dan, Voolstra, Christian R, Wagner, Nicole, Walker, Charles W, Weber, Andreas Pm, Weis, Virginia, Zelzion, Ehud, Zoccola, Didier, and Falkowski, Paul G

Subjects
Animals, Anthozoa, Calcium Carbonate, Reactive Nitrogen Species, Reactive Oxygen Species, Genomics, Temperature, Adaptation, Physiological, Phylogeny, Symbiosis, Photosynthesis, Gene Transfer, Horizontal, Calcification, Physiologic, Genome, Hydrogen-Ion Concentration, Light, Metabolic Networks and Pathways, Stress, Physiological, Biological Evolution, Coral Reefs, biomineralization, corals, ecology, evolutionary biology, genomics, horizontal gene transfer, stress response, symbiosis, Adaptation, Physiological, Gene Transfer, Horizontal, Calcification, Physiologic, Stress, Biochemistry and Cell Biology
Abstract

Transcriptome and genome data from twenty stony coral species and a selection of reference bilaterians were studied to elucidate coral evolutionary history. We identified genes that encode the proteins responsible for the precipitation and aggregation of the aragonite skeleton on which the organisms live, and revealed a network of environmental sensors that coordinate responses of the host animals to temperature, light, and pH. Furthermore, we describe a variety of stress-related pathways, including apoptotic pathways that allow the host animals to detoxify reactive oxygen and nitrogen species that are generated by their intracellular photosynthetic symbionts, and determine the fate of corals under environmental stress. Some of these genes arose through horizontal gene transfer and comprise at least 0.2% of the animal gene inventory. Our analysis elucidates the evolutionary strategies that have allowed symbiotic corals to adapt and thrive for hundreds of millions of years.

Published
2016

21. Functional Characterization of Cnidarian HCN Channels Points to an Early Evolution of Ih.

Author

Baker, Emma C, Layden, Michael J, van Rossum, Damian B, Kamel, Bishoy, Medina, Monica, Simpson, Eboni, and Jegla, Timothy

Subjects
Animals, Cnidaria, Ion Channels, Cloning, Molecular, Phylogeny, Ion Channel Gating, Amino Acid Sequence, Sequence Homology, Amino Acid, Molecular Sequence Data, Cloning, Molecular, Sequence Homology, Amino Acid, General Science & Technology
Abstract

HCN channels play a unique role in bilaterian physiology as the only hyperpolarization-gated cation channels. Their voltage-gating is regulated by cyclic nucleotides and phosphatidylinositol 4,5-bisphosphate (PIP2). Activation of HCN channels provides the depolarizing current in response to hyperpolarization that is critical for intrinsic rhythmicity in neurons and the sinoatrial node. Additionally, HCN channels regulate dendritic excitability in a wide variety of neurons. Little is known about the early functional evolution of HCN channels, but the presence of HCN sequences in basal metazoan phyla and choanoflagellates, a protozoan sister group to the metazoans, indicate that the gene family predates metazoan emergence. We functionally characterized two HCN channel orthologs from Nematostella vectensis (Cnidaria, Anthozoa) to determine which properties of HCN channels were established prior to the emergence of bilaterians. We find Nematostella HCN channels share all the major functional features of bilaterian HCNs, including reversed voltage-dependence, activation by cAMP and PIP2, and block by extracellular Cs+. Thus bilaterian-like HCN channels were already present in the common parahoxozoan ancestor of bilaterians and cnidarians, at a time when the functional diversity of voltage-gated K+ channels was rapidly expanding. NvHCN1 and NvHCN2 are expressed broadly in planulae and in both the endoderm and ectoderm of juvenile polyps.

Published
2015

26. Empowering 21st Century Biology

Author

Robinson, Gene E., Banks, Jody A., Padilla, Dianna K., Burggren, Warren W., Cohen, C. Sarah, Delwiche, Charles F., Funk, Vicki, Hoekstra, Hopi E., Jarvis, Erich D., Johnson, Loretta, Martindale, Mark Q., del Rio, Carlos Martinez, Medina, Monica, Salt, David E., Sinha, Saurabh, Specht, Chelsea, Strange, Kevin, Strassmann, Joan E., Swalla, Billie J., and Tomanek, Lars

Published
2010
Full Text
View/download PDF

28. 'On Fire' or 'Lacking the Spark': Four Types of Self-Directed Critical Thinking of Preservice Teachers

Author

Medina, Monica A. and Shaver, Erik James

Abstract

Understanding the critical thought process of preservice teachers in an urban teaching environment is essential for the establishment of a social justice oriented teacher education curriculum. Utilizing artifacts taken from a preservice teacher education program, specifically monthly critically reflective teaching journals, four distinct thinking patterns emerged from this qualitative study. Student thought processes fell into one of four developmental categories of critical thinking: already critically oriented, improving criticality throughout the semester, starting critical and then falling off, and wholly uncritical thought. Findings from this study can help continue to inform gaps in literature regarding the ability to engage preservice teachers with issues of race, power, poverty and inequity inherent in society that all influence public schooling, especially within urban areas.

Published
2017

31. SARS-CoV-2 Infection Rate in Patients With Cancer and Health Care Workers in a Chemoradiotherapy Unit During the Pandemic: A Prospective Cohort in Mexico

Author

Meneses-Medina, Monica Isabel, Hernandez-Felix, Jorge Humberto, Anaya-Sánchez, Luis Guillermo, Valenzuela-Vidales, Ana Karen, Rosas-Camargo, Vanessa, Martos-Armendariz, Edgar Omar, Torres-Valdiviezo, Lucero Itzel, Cedro-Tanda, Alberto, Noguez-Ramos, Alejandro, Herrera-Montalvo, Luis Alonso, Hidalgo-Miranda, Alfredo, Valdez-Echeverria, Raymundo David, Galindo-Fraga, Arturo, and Huitzil-Meléndez, Fidel David

Published
2021
Full Text
View/download PDF

36. Phytophthora Genome Sequences Uncover Evolutionary Origins and Mechanisms of Pathogenesis

Author

Tyler, Brett M., Tripathy, Sucheta, Zhang, Xuemin, Dehal, Paramvir, Jiang, Rays H. Y., Aerts, Andrea, Arredondo, Felipe D., Baxter, Laura, Bensasson, Douda, Beynon, JIm L., Chapman, Jarrod, Damasceno, Cynthia M. B., Dorrance, Anne E., Dou, Daolong, Dickerman, Allan W., Dubchak, Inna L., Garbelotto, Matteo, Gijzen, Mark, Gordon, Stuart G., Govers, Francine, Grunwald, NIklaus J., Huang, Wayne, Ivors, Kelly L., Jones, Richard W., Kamoun, Sophien, Krampis, Konstantinos, Lamour, Kurt H., Lee, Mi-Kyung, McDonald, W. Hayes, Medina, Monica, Meijer, Harold J. G., Nordberg, Erik K., Maclean, Donald J., Ospina-Giraldo, Manuel D., Morris, Paul F., Phuntumart, Vipaporn, Putnam, Nicholas J., Rash, Sam, Rose, Jocelyn K. C., Sakihama, Yasuko, Salamov, Asaf A., Savidor, Alon, Scheuring, Chantel F., Smith, Brian M., Sobral, Bruno W. S., Terry, Astrid, Torto-Alalibo, Trudy A., Win, Joe, Xu, Zhanyou, Zhang, Hongbin, Grigoriev, Igor V., Rokhsar, Daniel S., and Boore, Jeffrey L.

Abstract

Draft genome sequences have been determined for the soybean pathogen Phytophthora sojae and the sudden oak death pathogen Phytophthora ramorum. Oömycetes such as these Phytophthora species share the kingdom Stramenopila with photosynthetic algae such as diatoms, and the presence of many Phytophthora genes of probable phototroph origin supports a photosynthetic ancestry for the stramenopiles. Comparison of the two species' genomes reveals a rapid expansion and diversification of many protein families associated with plant infection such as hydrolases, ABC transporters, protein toxins, proteinase inhibitors, and, in particular, a superfamily of 700 proteins with similarity to known oömycete avirulence genes.

Published
2006

37. Naked Stony Corals: Skeleton Loss in Scleractinia

Author

Medina, Monica, Collins, Allen G., Takaoka, Tori L., Kuehl, Jennifer, and Boore, Jeffrey L.

Subjects
Basic biological sciences, Coral Scleractinia Corallimorpharia Mitochondrial Evolution Phylogeny Aragonite
Published
2005

38. Complete Mitochondrial Genome Sequences for Four Bryozoan Species

Author

Takaoka, Tori L., Helfenbein, Kevin G., Boore, Jeffrey L., and Medina, Monica

Subjects
Mitochondrial Genomes
Abstract

Based on shared morphological characteristics, bryozoans have traditionally been grouped with phoronids and brachiopods to form the Lophophorata, a superphylum within the deuterostomes. However, molecular comparisons (mainly from 18S phylogenies) have challenged this placement suggesting that bryozoans are protostomes of the lophotrochozoan clade. There are enough lophotrochozoan genomes now available in the databases for comparative genomic analysis. Thus, to further test this phylogenetic hypothesis we sequenced complete mitochondrial genomes for the ectoprocts: Bugula sp., Flustrellidra sp., Membranipora sp. and Electra sp. These mitochondrial genomes are relatively small (approximately 14 kb) when compared to other metazoans, and the gene arrangements are very divergent among them as well as when compared to other lophotrochozoan taxa. We will be presenting the results from both gene order comparisons and protein encoding genes for phylogenetic reconstruction to test for the monophyly of bryozoans and lophophorates within the Lophotrochozoa.

Published
2005

39. Sequencing and comparing whole mitochondrial genomes of animals

Author

Boore, Jeffrey L., Macey, J. Robert, and Medina, Monica

Subjects
Basic biological sciences, mitochondrial genome DNA phylogenetics
Abstract

Comparing complete animal mitochondrial genome sequences is becoming increasingly common for phylogenetic reconstruction and as a model for genome evolution. Not only are they much more informative than shorter sequences of individual genes for inferring evolutionary relatedness, but these data also provide sets of genome-level characters, such as the relative arrangements of genes, that can be especially powerful. We describe here the protocols commonly used for physically isolating mtDNA, for amplifying these by PCR or RCA, for cloning, sequencing, assembly, validation, and gene annotation, and for comparing both sequences and gene arrangements. On several topics, we offer general observations based on our experiences to date with determining and comparing complete mtDNA sequences.

Published
2005

41. Phylogeny of the sea hares in the aplysia clade based on mitochondrial DNA sequence data

Author

Medina, Monica, Collins, Timothy, and Walsh, Patrick J.

Subjects
Basic biological sciences, Aplysia mitochondrial phylogeny
Abstract

Sea hare species within the Aplysia clade are distributed worldwide. Their phylogenetic and biogeographic relationships are, however, still poorly known. New molecular evidence is presented from a portion of the mitochondrial cytochrome oxidase c subunit 1 gene (cox1) that improves our understanding of the phylogeny of the group. Based on these data a preliminary discussion of the present distribution of sea hares in a biogeographic context is put forward. Our findings are consistent with only some aspects of the current taxonomy and nomenclatural changes are proposed. The first, is the use of a rank free classification for the different Aplysia clades and subclades as opposed to previously used genus and subgenus affiliations. The second, is the suggestion that Aplysia brasiliana (Rang, 1828) is a junior synonym of Aplysia fasciata (Poiret, 1789). The third, is the elimination of Neaplysia since its only member is confirmed to be part of the large Varria clade.

Published
2004

42. Complete sequences of the highly rearranged molluscan mitochondrial genomes of the scaphopod graptacme eborea and the bivalve mytilus edulis

Author

Boore, Jeffrey L., Medina, Monica, and Rosenberg, Lewis A.

Abstract

We have determined the complete sequence of the mitochondrial genome of the scaphopod mollusk Graptacme eborea (Conrad, 1846) (14,492 nts) and completed the sequence of the mitochondrial genome of the bivalve mollusk Mytilus edulis Linnaeus, 1758 (16,740 nts). (The name Graptacme eborea is a revision of the species formerly known as Dentalium eboreum.) G. eborea mtDNA contains the 37 genes that are typically found and has the genes divided about evenly between the two strands, but M. edulis contains an extra trnM and is missing atp8, and has all genes on the same strand. Each has a highly rearranged gene order relative to each other and to all other studied mtDNAs. G. eborea mtDNA has almost no strand skew, but the coding strand of M. edulis mtDNA is very rich in G and T. This is reflected in differential codon usage patterns and even in amino acid compositions. G. eborea mtDNA has fewer non-coding nucleotides than any other mtDNA studied to date, with the largest non-coding region being only 24 nt long. Phylogenetic analysis using 2,420 aligned amino acid positions of concatenated proteins weakly supports an association of the scaphopod with gastropods to the exclusion of Bivalvia, Cephalopoda, and Polyplacophora, but is generally unable to convincingly resolve the relationships among major groups of the Lophotrochozoa, in contrast to the good resolution seen for several other major metazoan groups.

Published
2004

44. A communal catalogue reveals Earths multiscale microbial diversity

Author

Thompson, Luke R., Sanders, Jon G., McDonald, Daniel, Amir, Amnon, Ladau, Joshua, Locey, Kenneth J., Prill, Robert J., Tripathi, Anupriya, Gibbons, Sean M., Ackermann, Gail, Navas-Molina, Jose A., Janssen, Stefan, Kopylova, Evguenia, Vzquez-Baeza, Yoshiki, Gonzlez, Antonio, Morton, James T., Mirarab, Siavash, Zech Xu, Zhenjiang, Jiang, Lingjing, Haroon, Mohamed F., Kanbar, Jad, Zhu, Qiyun, Jin Song, Se, Kosciolek, Tomasz, Bokulich, Nicholas A., Lefler, Joshua, Brislawn, Colin J., Humphrey, Gregory, Owens, Sarah M., Hampton-Marcell, Jarrad, Berg-Lyons, Donna, McKenzie, Valerie, Fierer, Noah, Fuhrman, Jed A., Clauset, Aaron, Stevens, Rick L., Shade, Ashley, Pollard, Katherine S., Goodwin, Kelly D., Jansson, Janet K., Gilbert, Jack A., Knight, Rob, Rivera, Jose L. Agosto, Al-Moosawi, Lisa, Alverdy, John, Amato, Katherine R., Andras, Jason, Angenent, Largus T., Antonopoulos, Dionysios A., Apprill, Amy, Armitage, David, Ballantine, Kate, Barta, Jiri, Baum, Julia K., Berry, Allison, Bhatnagar, Ashish, Bhatnagar, Monica, Biddle, Jennifer F., Bittner, Lucie, Boldgiv, Bazartseren, Bottos, Eric, Boyer, Donal M., Braun, Josephine, Brazelton, William, Brearley, Francis Q., Campbell, Alexandra H., Caporaso, J. Gregory, Cardona, Cesar, Carroll, JoLynn, Cary, S. Craig, Casper, Brenda B., Charles, Trevor C., Chu, Haiyan, Claar, Danielle C., Clark, Robert G., Clayton, Jonathan B., Clemente, Jose C., Cochran, Alyssa, Coleman, Maureen L., Collins, Gavin, Colwell, Rita R., Contreras, Monica, Crary, Benjamin B., Creer, Simon, Cristol, Daniel A., Crump, Byron C., Cui, Duoying, Daly, Sarah E., Davalos, Liliana, Dawson, Russell D., Defazio, Jennifer, Delsuc, Frederic, Dionisi, Hebe M., Dominguez-Bello, Maria Gloria, Dowell, Robin, Dubinsky, Eric A., Dunn, Peter O., Ercolini, Danilo, Espinoza, Robert E., Ezenwa, Vanessa, Fenner, Nathalie, Findlay, Helen S., Fleming, Irma D., Fogliano, Vincenzo, Forsman, Anna, Freeman, Chris, Friedman, Elliot S., Galindo, Giancarlo, Garcia, Liza, Garcia-Amado, Maria Alexandra, Garshelis, David, Gasser, Robin B., Gerdts, Gunnar, Gibson, Molly K., Gifford, Isaac, Gill, Ryan T., Giray, Tugrul, Gittel, Antje, Golyshin, Peter, Gong, Donglai, Grossart, Hans-Peter, Guyton, Kristina, Haig, Sarah-Jane, Hale, Vanessa, Hall, Ross Stephen, Hallam, Steven J., Handley, Kim M., Hasan, Nur A., Haydon, Shane R., Hickman, Jonathan E., Hidalgo, Glida, Hofmockel, Kirsten S., Hooker, Jeff, Hulth, Stefan, Hultman, Jenni, Hyde, Embriette, Ibanez-Alamo, Juan Diego, Jastrow, Julie D., Jex, Aaron R., Johnson, L. Scott, Johnston, Eric R., Joseph, Stephen, Jurburg, Stephanie D., Jurelevicius, Diogo, Karlsson, Anders, Karlsson, Roger, Kauppinen, Seth, Kellogg, Colleen T. E., Kennedy, Suzanne J., Kerkhof, Lee J., King, Gary M., Kling, George W., Koehler, Anson V., Krezalek, Monika, Kueneman, Jordan, Lamendella, Regina, Landon, Emily M., Lane-deGraaf, Kelly, LaRoche, Julie, Larsen, Peter, Laverock, Bonnie, Lax, Simon, Lentino, Miguel, Levin, Iris I., Liancourt, Pierre, Liang, Wenju, Linz, Alexandra M., Lipson, David A., Liu, Yongqin, Lladser, Manuel E., Lozada, Mariana, Spirito, Catherine M., MacCormack, Walter P., MacRae-Crerar, Aurora, Magris, Magda, Martin-Platero, Antonio M., Martin-Vivaldi, Manuel, Martinez, L. Margarita, Martinez-Bueno, Manuel, Marzinelli, Ezequiel M., Mason, Olivia U., Mayer, Gregory D., McDevitt-Irwin, Jamie M., McDonald, James E., McGuire, Krista L., McMahon, Katherine D., McMinds, Ryan, Medina, Monica, Mendelson, Joseph R., Metcalf, Jessica L., Meyer, Folker, Michelangeli, Fabian, Miller, Kim, Mills, David A., Minich, Jeremiah, Mocali, Stefano, Moitinho-Silva, Lucas, Moore, Anni, Morgan-Kiss, Rachael M., Munroe, Paul, Myrold, David, Neufeld, Josh D., Ni, Yingying, Nicol, Graeme W., Nielsen, Shaun, Nissimov, Jozef I., Niu, Kefeng, Nolan, Matthew J., Noyce, Karen, OBrien, Sarah L., Okamoto, Noriko, Orlando, Ludovic, Castellano, Yadira Ortiz, Osuolale, Olayinka, Oswald, Wyatt, Parnell, Jacob, Peralta-Sanchez, Juan M., Petraitis, Peter, Pfister, Catherine, Pilon-Smits, Elizabeth, Piombino, Paola, Pointing, Stephen B., Pollock, F. Joseph, Potter, Caitlin, Prithiviraj, Bharath, Quince, Christopher, Rani, Asha, Ranjan, Ravi, Rao, Subramanya, Rees, Andrew P., Richardson, Miles, Riebesell, Ulf, Robinson, Carol, Rockne, Karl J., Rodriguezl, Selena Marie, Rohwer, Forest, Roundstone, Wayne, Safran, Rebecca J., Sangwan, Naseer, Sanz, Virginia, Schrenk, Matthew, Schrenzel, Mark D., Scott, Nicole M., Seger, Rita L., Seguin-Orlando, Andaine, Seldin, Lucy, Seyler, Lauren M., Shakhsheer, Baddr, Sheets, Gabriela M., Shen, Congcong, Shi, Yu, Shin, Hakdong, Shogan, Benjamin D., Shutler, Dave, Siegel, Jeffrey, Simmons, Steve, Sjoling, Sara, Smith, Daniel P., Soler, Juan J., Sperling, Martin, Steinberg, Peter D., Stephens, Brent, Stevens, Melita A., Taghavi, Safiyh, Tai, Vera, Tait, Karen, Tan, Chia L., Tas, Neslihan, Taylor, D. Lee, Thomas, Torsten, Timling, Ina, Turner, Benjamin L., Urich, Tim, Ursell, Luke K., van der Lelie, Daniel, Van Treuren, William, van Zwieten, Lukas, Vargas-Robles, Daniela, Thurber, Rebecca Vega, Vitaglione, Paola, Walker, Donald A., Walters, William A., Wang, Shi, Wang, Tao, Weaver, Tom, Webster, Nicole S., Wehrle, Beck, Weisenhorn, Pamela, Weiss, Sophie, Werner, Jeffrey J., West, Kristin, Whitehead, Andrew, Whitehead, Susan R., Whittingham, Linda A., Willerslev, Eske, Williams, Allison E., Wood, Stephen A., Woodhams, Douglas C., Yang, Yeqin, Zaneveld, Jesse, Zarraonaindia, Iratxe, Zhang, Qikun, and Zhao, Hongxia

Subjects
Biological diversity -- Observations -- Environmental aspects, Microbial colonies -- Environmental aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Our growing awareness of the microbial worlds importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earths microbial diversity., Author(s): Luke R. Thompson [1, 2, 3]; Jon G. Sanders [1]; Daniel McDonald [1]; Amnon Amir [1]; Joshua Ladau [4]; Kenneth J. Locey [5]; Robert J. Prill [6]; Anupriya Tripathi [...]

Published
2017
Full Text
View/download PDF

46. PP.07 Preliminary Results of a Western Mexican Cohort of Metastatic NSCLC and frequency of ALK, EGFR and PD-L1

Author

de Jesús Mora Pineda, Mauricio, primary, Moreno Jaramillo, Gabriela Alhelí, additional, de Jesús Preciado Durán, María, additional, Contreras, Betsabé Haro, additional, Alcaraz Wong, Aldo Antonio, additional, Alvarado Rodriguez, Linda Alejandra, additional, Meneses Medina, Monica Isabel, additional, Hernandez-Felix, Jorge H., additional, Barron, Feliciano Barron, additional, and Ramírez, Ignacio Mariscal, additional

Published
2023
Full Text
View/download PDF

47. Unraveling the functional dark matter through global metagenomics

Author

Pavlopoulos, Georgios A., Baltoumas, Fotis A., Liu, Sirui, Selvitopi, Oguz, Camargo, Antonio Pedro, Nayfach, Stephen, Azad, Ariful, Roux, Simon, Call, Lee, Ivanova, Natalia N., Chen, I. Min, Paez-Espino, David, Karatzas, Evangelos, Acinas, Silvia G., Ahlgren, Nathan, Attwood, Graeme, Baldrian, Petr, Berry, Timothy, Bhatnagar, Jennifer M., Bhaya, Devaki, Bidle, Kay D., Blanchard, Jeffrey L., Boyd, Eric S., Bowen, Jennifer L., Bowman, Jeff, Brawley, Susan H., Brodie, Eoin L., Brune, Andreas, Bryant, Donald A., Buchan, Alison, Cadillo-Quiroz, Hinsby, Campbell, Barbara J., Cavicchioli, Ricardo, Chuckran, Peter F., Coleman, Maureen, Crowe, Sean, Colman, Daniel R., Currie, Cameron R., Dangl, Jeff, Delherbe, Nathalie, Denef, Vincent J., Dijkstra, Paul, Distel, Daniel D., Eloe-Fadrosh, Emiley, Fisher, Kirsten, Francis, Christopher, Garoutte, Aaron, Gaudin, Amelie, Gerwick, Lena, Godoy-Vitorino, Filipa, Guerra, Peter, Guo, Jiarong, Habteselassie, Mussie Y., Hallam, Steven J., Hatzenpichler, Roland, Hentschel, Ute, Hess, Matthias, Hirsch, Ann M., Hug, Laura A., Hultman, Jenni, Hunt, Dana E., Huntemann, Marcel, Inskeep, William P., James, Timothy Y., Jansson, Janet, Johnston, Eric R., Kalyuzhnaya, Marina, Kelly, Charlene N., Kelly, Robert M., Klassen, Jonathan L., Nüsslein, Klaus, Kostka, Joel E., Lindow, Steven, Lilleskov, Erik, Lynes, Mackenzie, Mackelprang, Rachel, Martin, Francis M., Mason, Olivia U., McKay, R. Michael, McMahon, Katherine, Mead, David A., Medina, Monica, Meredith, Laura K., Mock, Thomas, Mohn, William W., Moran, Mary Ann, Murray, Alison, Neufeld, Josh D., Neumann, Rebecca, Norton, Jeanette M., Partida-Martinez, Laila P., Pietrasiak, Nicole, Pelletier, Dale, Reddy, T. B. K., Reese, Brandi Kiel, Reichart, Nicholas J., Reiss, Rebecca, Saito, Mak A., Schachtman, Daniel P., Seshadri, Rekha, Shade, Ashley, Sherman, David, Simister, Rachel, Simon, Holly, Stegen, James, Stepanauskas, Ramunas, Sullivan, Matthew, Sumner, Dawn Y., Teeling, Hanno, Thamatrakoln, Kimberlee, Treseder, Kathleen, Tringe, Susannah, Vaishampayan, Parag, Valentine, David L., Waldo, Nicholas B., Waldrop, Mark P., Walsh, David A., Ward, David M., Wilkins, Michael, Whitman, Thea, Woolet, Jamie, Woyke, Tanja, Iliopoulos, Ioannis, Konstantinidis, Konstantinos, Tiedje, James M., Pett-Ridge, Jennifer, Baker, David, Visel, Axel, Ouzounis, Christos A., Ovchinnikov, Sergey, Buluç, Aydin, Kyrpides, Nikos C., Pavlopoulos, Georgios A., Baltoumas, Fotis A., Liu, Sirui, Selvitopi, Oguz, Camargo, Antonio Pedro, Nayfach, Stephen, Azad, Ariful, Roux, Simon, Call, Lee, Ivanova, Natalia N., Chen, I. Min, Paez-Espino, David, Karatzas, Evangelos, Acinas, Silvia G., Ahlgren, Nathan, Attwood, Graeme, Baldrian, Petr, Berry, Timothy, Bhatnagar, Jennifer M., Bhaya, Devaki, Bidle, Kay D., Blanchard, Jeffrey L., Boyd, Eric S., Bowen, Jennifer L., Bowman, Jeff, Brawley, Susan H., Brodie, Eoin L., Brune, Andreas, Bryant, Donald A., Buchan, Alison, Cadillo-Quiroz, Hinsby, Campbell, Barbara J., Cavicchioli, Ricardo, Chuckran, Peter F., Coleman, Maureen, Crowe, Sean, Colman, Daniel R., Currie, Cameron R., Dangl, Jeff, Delherbe, Nathalie, Denef, Vincent J., Dijkstra, Paul, Distel, Daniel D., Eloe-Fadrosh, Emiley, Fisher, Kirsten, Francis, Christopher, Garoutte, Aaron, Gaudin, Amelie, Gerwick, Lena, Godoy-Vitorino, Filipa, Guerra, Peter, Guo, Jiarong, Habteselassie, Mussie Y., Hallam, Steven J., Hatzenpichler, Roland, Hentschel, Ute, Hess, Matthias, Hirsch, Ann M., Hug, Laura A., Hultman, Jenni, Hunt, Dana E., Huntemann, Marcel, Inskeep, William P., James, Timothy Y., Jansson, Janet, Johnston, Eric R., Kalyuzhnaya, Marina, Kelly, Charlene N., Kelly, Robert M., Klassen, Jonathan L., Nüsslein, Klaus, Kostka, Joel E., Lindow, Steven, Lilleskov, Erik, Lynes, Mackenzie, Mackelprang, Rachel, Martin, Francis M., Mason, Olivia U., McKay, R. Michael, McMahon, Katherine, Mead, David A., Medina, Monica, Meredith, Laura K., Mock, Thomas, Mohn, William W., Moran, Mary Ann, Murray, Alison, Neufeld, Josh D., Neumann, Rebecca, Norton, Jeanette M., Partida-Martinez, Laila P., Pietrasiak, Nicole, Pelletier, Dale, Reddy, T. B. K., Reese, Brandi Kiel, Reichart, Nicholas J., Reiss, Rebecca, Saito, Mak A., Schachtman, Daniel P., Seshadri, Rekha, Shade, Ashley, Sherman, David, Simister, Rachel, Simon, Holly, Stegen, James, Stepanauskas, Ramunas, Sullivan, Matthew, Sumner, Dawn Y., Teeling, Hanno, Thamatrakoln, Kimberlee, Treseder, Kathleen, Tringe, Susannah, Vaishampayan, Parag, Valentine, David L., Waldo, Nicholas B., Waldrop, Mark P., Walsh, David A., Ward, David M., Wilkins, Michael, Whitman, Thea, Woolet, Jamie, Woyke, Tanja, Iliopoulos, Ioannis, Konstantinidis, Konstantinos, Tiedje, James M., Pett-Ridge, Jennifer, Baker, David, Visel, Axel, Ouzounis, Christos A., Ovchinnikov, Sergey, Buluç, Aydin, and Kyrpides, Nikos C.

Abstract

Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities1,2. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyse 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 reference genomes or the Pfam database3. Using massively parallel graph-based clustering, we group these proteins into 106,198 novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical and gene neighbourhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matter.

Published
2023
Full Text
View/download PDF

48. La Pandemia: el sentir de los estudiantes de educación superior

Author

Lozano Medina, Monica

Abstract

The objective of this study is to show the feelings of undergraduate students during the health contingency. A qualitative study was carried out, through the narrative of 35 students. The main results show that they faced various feelings and challenges in their learning throughout almost two years of confinement., El objetivo de este estudio es mostrar el sentir de los estudiantes de licenciatura durante la contingencia sanitaria. Se realizó un estudio cualitativo a través de la narrativa de 35 estudiantes. Los principales resultados muestran que éstos se enfrentaron a diversos sentimientos y retos en su aprendizaje a lo largo de casi dos años de confinamiento.

Published
2023

49. SF016/#728 Role of thoracoscopy in patients with epithelial ovarian cancer and stage IVA in a developing country

Author

Lalinde, Juan, primary, Calderon, Pedro, additional, Medina, Monica, additional, Suescun, Oscar, additional, Almeciga, Adriana, additional, Santana, Diana, additional, Vieira, Santiago, additional, Acosta, Jesus, additional, Salazar, Catherin, additional, Ruiz, Franco, additional, Viveros, David, additional, Alvarado, Fernando, additional, Buitrago, Miguel, additional, and Rueda, Santiago, additional

Published
2022
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results