Resultados de búsqueda - "bioinformatics"

Ancient Human Mitogenome of the Beagle Channel (Tierra del Fuego): An Argentine Collaborative Project por Arencibia, Valeria, Muñoz Hidalgo, Marianne Graziel, Crespo, Cristian, Maldonado, Lucas, Lichtenstein, Gabriel, Kamenetzky, Laura, Vera, Pablo Alfredo, Zangrando, Atilio F., Tessone, Augusto, Avena, Sergio, Lia, Veronica Viviana, Puebla, Andrea Fabiana, Dejean, Cristina

“…To obtain an ancient mitogenome in Argentina, several institutions collaborated to apply massively parallel sequencing and bioinformatic methodologies on an enriched ancient DNA library of an individual from the Beagle Channel (dated 1504 ± 46 years BP), a region of particular interest for this line of inquiry. …”
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Dataset of the first transcriptome assembly of the tree crop “yerba mate” (Ilex paraguariensis) and systematic characterization of protein coding genes por Aguilera, Patricia Mabel, Debat, Humberto Julio, Grabiele, Mauro

“…-Hil.) by NGS and de novo transcriptome assembly” (Debat et al., 2014) [1]. By means of a bioinformatic approach involving extensive NGS data analyses, we provide a resource encompassing the full transcriptome assembly of yerba mate, the first available reference for the Ilex L. genus. …”
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The glycosylphosphatidylinositol-anchored protein repertoire of Babesia bovis and its significance for erythrocyte invasion por Rodriguez, Anabel Elisa, Florin-Christensen, Mónica, Flores, Daniela, Echaide, Ignacio Eduardo, Suarez, Carlos Esteban, Schnittger, Leonhard

“…In addition, the repertoire of GPI-anchored proteins of B. bovis was predicted with high fidelity by searching its genome with available web-based bioinformatic tools. Altogether 17 GPI-anchored proteins were identified, 5 of which represent the already characterized variable merozoite surface antigens (VMSAs). …”
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GPI- Anchored Proteomes and Their Biochemical Pathway in Alveolates: Evolutionary Insights and Heterologous Expression in Tetrahymena Thermophila por Puca, Gervasio, Montes, Maria G., Orlowski, Juan, Tomazic, Mariela Luján, Gonzalez Maglio, Daniel H., de la Fuente, Carolina, Florin-Christensen, Mónica, Schnittger, Leonhard, Nusblat, Alejandro D.

“…To complement the bioinformatic analyses, we expressed the apicomplexan GPI-anchored antigen GPI4 from Babesia bovis in Tetrahymena thermophila. …”
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New allelic variants found in key rice salt-tolerance genes: an association study por Negrão, Sónia, Cecília Almadanim, M., Pires, Inês S., Abreu, Isabel A., Maroco, João, Courtois, Brigitte, Gregorio, Glenn B., McNally, Kenneth L., Margarida Oliveira, M.

“…We further evaluated the putative consequences of these SNPs at the protein level using bioinformatic tools. Amongst the five nonsynonymous SNPs significantly associated with salt‐stress traits, we found a T67K mutation that may cause the destabilization of one transmembrane domain in OsHKT1;5, and a P140A alteration that significantly increases the probability of OsHKT1;5 phosphorylation. …”
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Identification of the maize gravitropism gene lazy plant1 by a transposon-tagging genome resequencing strategy por Howard, Thomas P., Hayward, Andrew P, Tordillos, Anthony, Fragoso, Christopher A., Moreno, Maria A, Tohme, Joseph M., Kausch, Albert P, Mottinger, John P, Dellaporta, Stephen L.

“…The la1 gene is required for the negatively gravitropic response of shoots and mutant plants lack the ability to sense gravity. Using bioinformatic and fluorescence microscopy approaches, we show that the la1 gene encodes a cell membrane and nuclear localized protein. …”
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Role of calcium in the defense response induced by brassinosteroids in strawberry plants por Furio, Ramiro Nicolás, Martinez Zamora, Martin Gustavo, Salazar, Sergio Miguel, Coll, Yamilet, Perato, Silvia Marisa, Martos, Gustavo Gabriel, Díaz Ricci, Juan Carlos

“…By comparing Fragaria vesca and Fragaria ananassa genome sequences 28 nucleotide sequences coding for calcium-sensing proteins called CMLs were predicted. Bioinformatic analyses of the sequences revealed that all of them contained the characteristic EF-hand motif of Ca2+ binding, and regulatory cis-elements related to stress. qPCR studies showed that both BB16 and EP24 cause the upregulation of selected CMLs genes e.g. …”
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Molecular engineering improves antigen quality and enables integrated manufacturing of a trivalent subunit vaccine candidate for rotavirus por Dalvie, Neil C., Brady, Joseph R., Crowell, Laura E., Tracey, Mary Kate, Biedermann, Andrew M., Kaur, Kawaljit, Hickey, John M., Kristensen II, D. Lee, Bonnyman, Alexandra D., Rodriguez-Aponte, Sergio A., Whittaker, Charles A., Bok, Marina, Vega, Celina Guadalupe, Mukhopadhyay, Tarit K., Joshi, Sangeeta B., Volkin, David B., Parreño, Gladys, Love, Kerry R., Love, J. Christopher

“…Results: We describe a holistic approach for the molecular design of recombinant protein antigens—considering both their manufacturability and antigenicity—informed by bioinformatic analyses such as RNA-seq, ribosome profiling, and sequence-based prediction tools. …”
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New validated eucalyptus SSR markers located in candidate genes involved in growth and plant development por Acuña, Cintia Vanesa, Rivas, Juan Gabriel, Aguirre, Natalia Cristina, Villalba, Pamela Victoria, Martinez, Maria Carolina, Garcia, Martin Nahuel, Hopp, Horacio Esteban, Marcucci Poltri, Susana Noemi

“…Materials and methods: In total, 134 SSR in 129 candidate genes (CG-SSR) involved in plant development were selected and physically mapped to the E. grandis reference genome by bioinformatic tools. Experimental validation and polymorphism analysis were performed on 48 individuals from E. grandis and interspecific hybrids (E. grandis x E. camaldulensis; E. grandis x E. tereticornis), E. globulus, E. maidenii, E. dunnii and E. benthamii. …”
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Annotation and overview of the Pseudomonas savastanoi pv. savastanoi NCPPB 3335 draft genome reveals the virulence gene complement of a tumour-inducing pathogen of woody hosts por Rodriguez-Palenzuela, Pablo, Matas, Isabel M., Murillo, Jesús, Lopez-Solanilla, Emilia, Bardaji, Leire, Perez-Martinez, Isabel, Rodriguez-Moskera, Martin E., Penyalver, Ramón, López, María M., Quesada, Jose M., Biehl, Bryan S., Perna, Nicole T., Glasner, Jeremy D., Cabot, Eric L., Neeno-Eckwall, Eric, Ramos, Cayo

“…Pseudomonas savastanoi pv. savastanoi is a tumour-inducing pathogen of Olea europaea L. causing oliveknot disease. Bioinformatic analysis of the draftgenome sequence of strain NCPPB 3335, whichencodes 5232 predicted coding genes on a totallength of 5856 998 bp and a 57.12% G + C, revealed alarge degree of conservation with Pseudomonassyringae pv. phaseolicola 1448A and P. syringae pv.tabaci 11528. …”
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The Challenge of Environmental Samples for PCR Detection of Phytopathogenic Bacteria: A Case Study of Citrus Huanglongbing Disease por Morán, Félix, Barbé, Silvia, Bastin, Saskia, Navarro-Herrero, Inmaculada, Bertolini, Edson, López, María M., Hernández-Suárez, Estrella, Urbaneja, Alberto, Tena, Alejandro, Siverio, Felipe, Marco-Noales, Ester

“…Liberibacter’ species associated with HLB. The bioinformatic analysis of the sequences obtained with these primers revealed that all these amplifications came from the presence of other prokaryotic organisms in the samples. …”
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Design of an in-silico workflow to trace the spread of zoonotic bacteria using NGS data por Janssens, Adrien

“…In this work, we will discuss how bioinformatic tools, and in particular SNV calling and tree-building softwares, can be used to create a single-command, easy to use, fast-processing workflow using genomic sequencing data to analyze trace of bacteria from different locations and times; and how these results can be interpreted and exploited. …”
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Bacterias entomopatógenas en el control biológico de insectos por Grijalba Bernal, Erika Paola, Hurst, Mark, Ibarra, Jorge E., Jurat Fuentes, Juan Luis, Jackson, Trevor

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Highly syntenic and yet divergent: a tale of two Theilerias por Weir, W., Sunter, J., Chaussepied, M., Skilton, Robert A., Tait, A., Villiers, Etienne P. de, Bishop, Richard P., Shiels, B., Langsley, G.

“…The published genomic sequences of the two major host-transforming Theileria species of cattle represent a rich resource of information that has allowed novel bioinformatic and experimental studies into these important apicomplexan parasites. …”
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Deep assessment of genomic diversity in cassava for herbicide tolerance and starch biosynthesis por Duitama, Jorge, Kafuri, Lina, Tello, Daniel, Leiva Sandoval, Ana Maria, Hofinger, Bernhard, Datta, Sneha, Lentini, Zaida, Aranzales Rondón, Ericson, Till, Bradley, Ceballos, H.

“…Results of twelve bioinformatic pipelines for variant detection in pooled samples were compared to ensure the quality of the variant calling process. …”
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Identification of novel vaccine candidates against cryptosporidiosis of neonatal bovines by reverse vaccinology por Tomazic, Mariela Luján, Rodriguez, Anabel Elisa, Lombardelli Joaquín Andrés, Poklepovich Caride, Tomás Javier, Garro, Carlos Javier, Galarza, Roxana Ivon, Tiranti, Karina, Florin-Christensen, Mónica, Schnittger, Leonhard

“…A reverse vaccinology approach was employed to (i) identify the GPI-anchored proteome of C. parvum using available web-based bioinformatic tools and (ii) characterize previously unrecognized novel vaccine antigens. …”
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Loquat (Eriobotrya japonica) is a New Natural Host of Apple Stem Pitting Virus por Morán, Félix, Canales, Celia, Olmos, Antonio, Ruiz-García, Ana B.

“…A nearly complete genome of 9303 nts (ASPV-SL61) reconstructed bioinformatically shows the typical genomic structure of this viral species and a highest nucleotide identity (85.9%) with the Chinese ASPV isolate YLX from pear. …”
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Detection and diversity of maize yellow mosaic virus infecting maize in Nigeria por Yahaya, A., Dangora, D.B., Alabi, O.J., Zongoma, A.M., Kumar, P. Lava

“…A subset of amplified DNA fragments was cloned, Sanger-sequenced, and the obtained sequences were bioinformatically analyzed along with corresponding sequences from GenBank. …”
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Evaluation of genetic variability in four Nigerian locally-adapted chicken populations using major histocompatibility complex-linked LEI0258 microsatellite marker por Oladejo, O.A., Oseni, S.O., Kyallo, Martina M., Domelevo Entfellner, Jean-Baka, Tor, N.E., Tiambo, Christian K., Pelle, Roger

“…Blood samples were randomly collected from 50 mature birds in each population and DNA was extracted and subsequently subjected to PCR, Sanger sequencing, and bioinformatic analysis. There were two variable numbers of tandem repeats (VNTRs), with 90% of the alleles containing only one R13 and varying numbers of the R12 motifs that ranged from 1 to 19. …”
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Identification and evaluation of new Mycobacterium bovis antigens in the in vitro interferon gamma release assay for bovine tuberculosis diagnosis por Eirin, Maria Emilia, Macías, Analía, Magnano, Gabriel, Morsella, Claudia Graciela, Mendez, Laura Luján, Blanco, Federico Carlos, Bianco, María Veronica, Severina, Walter, Alito, Alicia Elsa, Pando, Maria de los Angeles, Singh, Mahavir G., Spallek, Ralph, Paolicchi, Fernando, Bigi, Fabiana, Cataldi, Angel Adrian

“…Our data confirm the feacibility to implement bioinformatic screening tools and suggest Mb2845c as a potential diagnostic antigen to be tested in protein cocktails to evaluate their contribution to bTB diagnosis.…”
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