Search Results - "Proteomics"

Laser Microdissection: A High-Precision Approach to Isolate Specific Cell Types from Any Plant Species for Downstream Molecular Analyses by Tadeo, Francisco R., Agustí, Manuel, Merelo, Paz, Talón, Manuel

“…The functions performed by each of these particular cell types must be associated with specific transcriptomic, proteomic, and metabolic profiles that cannot be disentangled by analyzing whole plant organs and tissues. …”
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The International Rice Information System. A platform for meta-analysis of rice crop data by McLaren, Christopher Graham, Bruskiewich, Richard M., Portugal, Arllet M., Cosico, Alexander B.

“…New components are now being added to the International Rice Information System to handle the diversity of rice functional genomics data including genomic sequence data, molecular genetic data, expression data, and proteomic information. Users access information in the database through stand-alone programs and Web interfaces, which offer specialized applications and customized views to researchers with different interests.…”
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Matrix-assisted laser desorption/ionization time of flight mass spectrometry for comprehensive indexing of East African Ixodid tick species by Rothen, J., Githaka, Naftaly W., Kanduma, Esther G., Olds, Cassandra L., Pflueger, V., Mwaura, S., Bishop, Richard P., Daubenberger, C.A.

“…The objective was to determine the utility of this proteomic tool for reliable species identification of closely related afrotropical ticks.…”
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Identification of resistanceassociated proteins in closelyrelated maize lines varying in aflatoxin accumulation by Chen, Z., Brown, R.L., Menkir, A., Cleveland, T.E.

“…Five pairs of closely-related lines that had 75–94% genetic similarity within each pair and which varied within each pair in aflatoxin accumulation were selected for proteomic investigation. Kernel embryo and endosperm protein profile differences within the pair and across pairs were compared using two-dimensional polyacrylamide gel electrophoresis. …”
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The ÓMICAS alliance, an international research program on multi-omics for crop breeding optimization by Jaramillo Botero, Andres, Colorado, Julian D., Quimbaya, Mauricio, Rebolledo, María Camila, Lorieux, Mathias, Ghneim-Herrera, Thaura, Arango, Carlos A., Tobón, Luis E., Finke, Jorge, Rocha, Camilo, Muñoz, Fernando, Riascos, John J., Silva, Fernando, Chirinda, Ngonidzashe, Caccamo, Mario Jose, Vandepoele, Klaas, Goddard, William A.

“…The strategy and methods described in this article, involve the characterization of different crop models, using high-throughput, real-time phenotyping technologies as well as experimental tissue characterization at different levels of the omics hierarchy and under contrasting conditions, to elucidate epigenome-, genome-, proteome- and metabolome-phenome relationships. The massive data sets are used to derive in-silico models, methods and tools to discover complex underlying structure-function associations, which are then carried over to the production of new germplasm with improved agricultural traits. …”
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First draft genome assembly of the Peruvian creole cattle breed (Bos taurus) and its comparative genomics among the Bovinae subfamily by Estrada Cañari, Richard, Corredor Arizapana, Flor Anita, Figueroa Venegas, Deyanira Antonella, Salazar Coronel, Wilian, Quilcate Pairazamán, Carlos Enrique, Vásquez Pérez, Héctor Vladimir, Maicelo Quintana, Jorge Luis, Gonzales, Jhony, Arbizu Berrocal, Carlos Irvin

“…A total of 19,803 protein-coding genes were annotated in the PCC genome. We downloaded proteomes and genomes of the Bovinae subfamily, and conducted a comparative analysis with our draft genome. …”
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High antibody titres against predicted Mycoplasma surface proteins do not prevent sequestration in infected lung tissue in the course of experimental contagious bovine pleuropneumo... by Schieck, Elise, Liljander, Anne M., Hamsten, Carl, Gicheru, Nimmo, Scacchia, Massimo, Sacchini, Flavio, Heller, Martin, Schnee, Christiane, Sterner-Kock, Anja, Hlinak, Andreas, Naessens, Jan, Poole, Elizabeth J., Persson, Anna S., Jores, Joerg

“…Interestingly we found that animals that developed Mycoplasma-containing sequestra had significantly higher antibody levels against proteins comprising the surface proteome than the animals that cleared Mycoplasma from their lungs. …”
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Selective pressure against horizontally acquired prokaryotic genes as a driving force of plastid evolution by Llorente, Briardo, de Souza, Flavio S. J., Soto, Gabriela Cynthia, Meyer, Cristian, Alonso, Guillermo D., Flawia, Mirtha M., Bravo Almonacid, Fernando Felix, Ayub, Nicolás Daniel, Rodríguez-Concepción, Manuel

“…Our results reveal a possible evolutionary mechanism of how selection against heterologous genes encoding cytosolic proteins contributed in incrementing plastid proteome complexity from non-endosymbiotic gene sources, a process that may also impact mitochondrial evolution.…”
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BioMoby extensions to the Taverna workflow management and enactment software by Kawas, Edward, Senger, Martin, Wilkinson, Mark D.

“…As biology becomes an increasingly computational science, it is critical that we develop software tools that support not only bioinformaticians, but also bench biologists in their exploration of the vast and complex data-sets that continue to build from international genomic, proteomic, and systems-biology projects. The BioMoby interoperability system was created with the goal of facilitating the movement of data from one Web-based resource to another to fulfill the requirements of non-expert bioinformaticians. …”
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Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases by Staton, Margaret, Cannon, Ethalinda K.S., Sanderson, Lacey-Anne, Wegrzyn, Jill, Anderson, Tavis, Buehler, Sean, Cobo-Simón, Irene, Faaberg, Kay, Grau, Emily, Guignon, Valentin, Gunoskey, Jessica, Inderski, Blake, Jung, Sook, Lager, Kelly, Main, Dorrie, Poelchau, Monica F., Ramnath, Risharde, Richter, Peter, West, Joe, Ficklin, Stephen

“…With increasing volumes, complexity and the need to integrate genomic, transcriptomic, metabolomic, proteomic, phenomic and environmental data, community databases face tremendous challenges in ongoing maintenance, expansion and upgrades. …”
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Stress response and detoxification mechanisms involved in non-target-site herbicide resistance in sunflower by Vega, Tatiana, Gil, Mercedes, Martin, Gabriela, Moschen, Sebastian Nicolas, Picardi, Liliana, Nestares, Graciela

“…Roots were collected, and label-free quantitation (LFQ) proteomic analysis was carried out to characterize the NTSR mechanisms involved in the IMI resistance trait in sunflower. …”
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Proteins Related to Stress and Redox State of 'Moncada' Mandarin Leaves with Contrasting Fruit Load by Munoz-Fambuena, Natalia, Mesejo, Carlos, Agustí, Manuel, Tarraga, Susana, Iglesias, Domingo J., Primo-Millo, Eduardo, González-Mas, María C.

“…A proteomic study was used to know more about the Citrus redox state and stress response related to fruit load. …”
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A USA Africa collaborative strategy for identifying, characterising and developing maize germplasm with resistance to aflatoxin contamination by Menkir, A., Brown, R.L., Bandyopadhyay, Ranajit, Chen, Z.Y., Cleveland, T.E.

“…These pairs of lines are currently being used for proteome analysis to identify resistance-associated proteins and the corresponding genes underlying resistance to aflatoxin accumulation. …”
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Gut-expressed vitellogenin facilitates the movement of a plant virus across the midgut wall in its insect vector by He, Ya-Zhou, Wang, Yu-Meng, Yin, Tian-Yan, Cuéllar, Wilmer Jose, Liu, Shu-Sheng, Wang, Xiao-Wei

“…Here, in order to identify whitefly midgut proteins that interact with a devastating begomovirus, tomato yellow leaf curl virus (TYLCV), we performed midgut-specific TYLCV coat protein (CP) immunoprecipitation followed by high-throughput mass spectrometry proteomic analysis. We find that vitellogenin (Vg), a critical insect reproductive protein that has been considered to be synthesized by the fat body, is also synthesized by and interacts with TYLCV CP in the whitefly midgut. …”
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Post-translational signal peptide cleavage controls differential epitope recognition in the QP-rich domain of recombinant Theileria parva PIM by Casanova, C.L., Xue, G., Taracha, E.L.N., Dobbelaere, D.A.E.

“…A recent analysis of the proteomes of T. parva and T. annulata revealed the presence of a large family of potentially secreted proteins, characterized by the presence of large stretches of amino acids that are also particularly rich in QP-residues.…”
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Identification of novel vaccine candidates against cryptosporidiosis of neonatal bovines by reverse vaccinology by 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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Next-generation biological control: the need for integrating genetics and genomics by Leung, Kelley, Ras, Erica, Ferguson, Kim B., Arïens, Simone, Babendreier, Dirk, Bijma, Piter, Bourtzis, Kostas, Brodeur, Jacques, Bruins, Margreet A., Centurión, Alejandra, Chattington, Sophie R., Chinchilla-Ramírez, Milena, Dicke, Marcel, Fatouros, Nina E., González-Cabrera, Joel, Groot, Thomas V. M., Haye, Tim, Knapp, Marcus, Koskinioti, Panagiota, Le Hesran, Sophie, Lyrakis, Manolis, Paspati, Angeliki, Pérez-Hedo, Mertixell, Plouvier, Wouter N., Schlötterer, Christian, Stahl, Judith M., Thiel, Andra, Urbaneja, Alberto, Van-De-Zande, Louis, Verhulst, Eveline C., Vet, Louise E. M., Visser, Sander, Werren, John H., Xia, Shuwen, Zwaan, Bas J., Magalhaes, Sara, Beukeboom, Leo W., Pannebakker, Bart A.

“…Gene discovery involves quantitative trait loci analyses, transcriptomic and proteomic studies, and gene editing. Improving biocontrol practices includes marker‐assisted selection, genomic selection and microbiome manipulation of biocontrol agents, and monitoring for genetic variation during rearing and post‐release. …”
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Insights into microbially induced salt tolerance and endurance mechanisms (stem) in plants by Kaushal, M.

“…Molecular research in MI plants under salt stress conditions has found variations in the expression profiles of genes such as HKT1, NHX, and SOS1 (ion transporters), PIPs and TIPs (aquaporins), RBCS, RBCL (RuBisCo subunits), Lipoxygenase2 [jasmonic acid (JA) signaling], ABA (abscisic acid)-responsive gene, and APX, CAT, and POD (involved in antioxidant defense). Proteomic analysis in arbuscular mycorrhizal fungi-inoculated plants revealed upregulated expression of signal transduction proteins, including Ca2+ transporter ATPase, calcium-dependent protein kinase, calmodulin, and energy-related proteins (NADH dehydrogenase, iron-sulfur protein NADH dehydrogenase, cytochrome C oxidase, and ATP synthase). …”
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Designing bovine T cell vaccines via reverse immunology by Nene, Vishvanath M., Svitek, Nicholas, Toye, Philip G., Golde, W.T., Barlow, J., Buus, Soren, Nielsen, Morten

“…When retrained, NetMHCpan may be used to predict parasite peptide epitopes by scanning the predicted T. parva proteome and known parasite CTL antigens. A range of pMHC tetramers, made “on-demand”, will then be used to assay cattle that are immune to ECF or in vaccine trials to determine if CTLs of the predicted epitope specificity are present or not. …”
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Evaluation of cross-protection of African swine fever vaccine ASFV-G-ΔI177L between ASFV biotypes by Borca, M.V., Ramirez-Medina, E., Mutisya, Christine, Ojuok, Rose, Odaba, Josiah, Dihbol, M., Lacasta, Anna, Gladue, D.P.

“…Biotyping, considering the entire virus proteome, appears to be a more promising prediction tool, although additional gathering of experimental data will be necessary to fully validate it; until then, the presence of cross-protection needs to be confirmed in efficacy trials challenging vaccinated animals.…”
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