Antibacterial and anti-virulence potential of plant phenolic compounds against Vibrio parahaemolyticus [version 2; peer review: 1 approved, 2 approved with reservations]

Authors: A. Alexis Lopez-Zavala, J. Fernando Ayala-Zavala, Adrian Ochoa-Leyva, M. Lizeth Alvarez-Ainza, A. Thalia Bernal-Mercado, F. Javier Vazquez-Armenta, M. Olivia Aros-Corrales

Source: F1000Research, Vol 12 (2024)

Subject Terms: anti-virulence, natural compounds, vibriosis, food safety, eng, Medicine, Science

File Description: electronic resource

Relation: https://f1000research.com/articles/12-1256/v2; https://doaj.org/toc/2046-1402

Access URL: https://doaj.org/article/fe05ad8b5eed4db6933a478820afe05d

White spot syndrome virus impact on the expression of immune genes and gut microbiome of black tiger shrimp Penaeus monodon

Authors: Thapanan Jatuyosporn, Pasunee Laohawutthichai, Juan Pablo Ochoa Romo, Luigui Gallardo-Becerra, Filiberto Sánchez Lopez, Anchalee Tassanakajon, Adrian Ochoa-Leyva, Kuakarun Krusong

Source: Scientific Reports, Vol 13, Iss 1, Pp 1-12 (2023)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/9b23ed679423427785dc366e10d4fffa

Agavin induces beneficial microbes in the shrimp microbiota under farming conditions

Authors: Juan Pablo Ochoa-Romo, Fernanda Cornejo-Granados, Alonso A. Lopez-Zavala, María Teresa Viana, Filiberto Sánchez, Luigui Gallardo-Becerra, Mirna Luque-Villegas, Yesenia Valdez-López, Rogerio R. Sotelo-Mundo, Andrés Cota-Huízar, Agustín López-Munguia, Adrian Ochoa-Leyva

Source: Scientific Reports, Vol 12, Iss 1, Pp 1-16 (2022)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/416e6238602943d3b448d3ccc53e0433

Secretome characterization of clinical isolates from the Mycobacterium abscessus complex provides insight into antigenic differences

Authors: Fernanda Cornejo-Granados, Thomas A. Kohl, Flor Vásquez Sotomayor, Sönke Andres, Rogelio Hernández-Pando, Juan Manuel Hurtado-Ramirez, Christian Utpatel, Stefan Niemann, Florian P. Maurer, Adrian Ochoa-Leyva

Source: BMC Genomics, Vol 22, Iss 1, Pp 1-13 (2021)

Subject Terms: Bioinformatics, Antigenicity, M. abscessus subspecies, In silico analysis, Vaccinology, Biotechnology, TP248.13-248.65, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1471-2164

Access URL: https://doaj.org/article/3c746e9824c14e4fa23611512b8ec7f0

PmAP2-β depletion enhanced activation of the Toll signaling pathway during yellow head virus infection in the black tiger shrimp Penaeus monodon

Authors: Thapanan Jatuyosporn, Pasunee Laohawutthichai, Premruethai Supungul, Rogerio R. Sotelo-Mundo, Adrian Ochoa-Leyva, Anchalee Tassanakajon, Kuakarun Krusong

Source: Scientific Reports, Vol 11, Iss 1, Pp 1-12 (2021)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/8fcb2ceb70724e768ca80bb7361e13ff

HLA-Haplotypes Influence Microbiota Structure in Northwestern Mexican Schoolchildren Predisposed for Celiac Disease or Type 1 Diabetes

Authors: Sandra V. Aguayo-Patrón, Omar A. Trujillo-Rivera, Fernanda Cornejo-Granados, Adrian Ochoa-Leyva, Ana M. Calderón de la Barca

Source: Microorganisms, Vol 11, Iss 6, p 1412 (2023)

Subject Terms: HLA DQ2 and DQ8, celiac disease, type 1 diabetes, microbiota, schoolchildren, Northwestern Mexico, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.mdpi.com/2076-2607/11/6/1412; https://doaj.org/toc/2076-2607

Access URL: https://doaj.org/article/d0b6fbbb233e4ab19ecd7441cbacd90a

Protocol for the isolation, sequencing, and analysis of the gut phageome from human fecal samples

Authors: Shirley Bikel, Luigui Gallardo-Becerra, Fernanda Cornejo-Granados, Adrian Ochoa-Leyva

Source: STAR Protocols, Vol 3, Iss 1, Pp 101170- (2022)

Subject Terms: Bioinformatics, Sequence analysis, Health Sciences, Sequencing, Metabolism, Microbiology, Science (General), Q1-390

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2666166722000508; https://doaj.org/toc/2666-1667

Access URL: https://doaj.org/article/143cdcfbdfa34ef3b5e6d9efc838c162

Gut dsDNA virome shows diversity and richness alterations associated with childhood obesity and metabolic syndrome

Authors: Shirley Bikel, Gamaliel López-Leal, Fernanda Cornejo-Granados, Luigui Gallardo-Becerra, Rodrigo García-López, Filiberto Sánchez, Edgar Equihua-Medina, Juan Pablo Ochoa-Romo, Blanca Estela López-Contreras, Samuel Canizales-Quinteros, Abigail Hernández-Reyna, Alfredo Mendoza-Vargas, Adrian Ochoa-Leyva

Source: iScience, Vol 24, Iss 8, Pp 102900- (2021)

Subject Terms: biological sciences, physiology, microbiology, virology, endocrinology, omics, Science

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2589004221008683; https://doaj.org/toc/2589-0042

Access URL: https://doaj.org/article/4807fab776ee4520b8d44742929a9788

Metal Ions and Chemical Modification Reagents Inhibit the Enzymatic Activity of Lecithin-Dependent Hemolysin from Vibrio parahaemolyticus

Authors: Francisco Javier Vazquez-Armenta, Uriel Felipe Valdez-Olmos, Aldo Alejandro Arvizu-Flores, Jesus Fernando Ayala-Zavala, Adrian Ochoa-Leyva, Alonso Alexis Lopez-Zavala

Source: Toxins, Vol 14, Iss 9, p 609 (2022)

Subject Terms: V. parahaemolyticus, LDH, metal ions, chemical agent inhibition, Medicine

File Description: electronic resource

Relation: https://www.mdpi.com/2072-6651/14/9/609; https://doaj.org/toc/2072-6651

Access URL: https://doaj.org/article/ad9d16b8d2aa445a9dad920ba6e01a61

Transcriptome Analysis of Soursop (Annona muricata L.) Fruit under Postharvest Storage Identifies Genes Families Involved in Ripening

Authors: Yolotzin Apatzingan Palomino-Hermosillo, Guillermo Berumen-Varela, Verónica Alhelí Ochoa-Jiménez, Rosendo Balois-Morales, José Orlando Jiménez-Zurita, Pedro Ulises Bautista-Rosales, Mónica Elizabeth Martínez-González, Graciela Guadalupe López-Guzmán, Moisés Alberto Cortés-Cruz, Luis Felipe Guzmán, Fernanda Cornejo-Granados, Luigui Gallardo-Becerra, Adrian Ochoa-Leyva, Iran Alia-Tejacal

Source: Plants, Vol 11, Iss 14, p 1798 (2022)

Subject Terms: de novo assembly, differential gene expression, functional annotation, plant cell wall, refrigeration, pectin, Botany, QK1-989

File Description: electronic resource

Relation: https://www.mdpi.com/2223-7747/11/14/1798; https://doaj.org/toc/2223-7747

Access URL: https://doaj.org/article/51763c84ec734dee90b03d67a9dfce32

Functional and taxonomic classification of a greenhouse water drain metagenome

Authors: Gamaliel López-Leal, Fernanda Cornejo-Granados, Juan Manuel Hurtado-Ramírez, Alfredo Mendoza-Vargas, Adrian Ochoa-Leyva

Source: Standards in Genomic Sciences, Vol 13, Iss 1, Pp 1-9 (2018)

Subject Terms: Shotgun sequencing, Greenhouse, Metagenome, Environmental sample, Water drain, Genetics, QH426-470

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s40793-018-0326-y; https://doaj.org/toc/1944-3277

Access URL: https://doaj.org/article/3dc6c5b7e38347f6a3621b76ef96a288

Alterations of the Gut Microbiome Associated to Methane Metabolism in Mexican Children with Obesity

Authors: Sofía Magdalena Murga-Garrido, Yaneth Citlalli Orbe-Orihuela, Cinthya Estefhany Díaz-Benítez, Ana Cristina Castañeda-Márquez, Fernanda Cornejo-Granados, Adrian Ochoa-Leyva, Alejandro Sanchez-Flores, Miguel Cruz, Ana Isabel Burguete-García, Alfredo Lagunas-Martínez

Source: Children, Vol 9, Iss 2, p 148 (2022)

Subject Terms: gut microbiome, childhood, obesity, methane, energy, dietary pattern, Pediatrics, RJ1-570

File Description: electronic resource

Relation: https://www.mdpi.com/2227-9067/9/2/148; https://doaj.org/toc/2227-9067

Access URL: https://doaj.org/article/80e1e03713774dc884b09f41f79cdd04

Genome-Wide Identification of Mango (Mangifera indica L.) Polygalacturonases: Expression Analysis of Family Members and Total Enzyme Activity During Fruit Ripening

Authors: Mitzuko Dautt-Castro, Andrés G. López-Virgen, Adrian Ochoa-Leyva, Carmen A. Contreras-Vergara, Ana P. Sortillón-Sortillón, Miguel A. Martínez-Téllez, Gustavo A. González-Aguilar, J. Sergio Casas-Flores, Adriana Sañudo-Barajas, David N. Kuhn, Maria A. Islas-Osuna

Source: Frontiers in Plant Science, Vol 10 (2019)

Subject Terms: polygalacturonase, Mangifera indica L., gene expression, enzymatic activity, firmness, ripening, Plant culture, SB1-1110

File Description: electronic resource

Relation: https://www.frontiersin.org/article/10.3389/fpls.2019.00969/full; https://doaj.org/toc/1664-462X

Access URL: https://doaj.org/article/bd6849a40ce94e71a3c79b4267944f28

d-Glutamic acid hydrochloride

Authors: Leonardo Y. Fox-Uribe, Javier Hernández-Paredes, Yedith Soberanes, Ignacio Valenzuela-Chavira, Karina D. Garcia-Orozco, Adrian Ochoa-Leyva, Karen Ochoa Lara, Rosa Elena Navarro, Rogerio R. Sotelo-Mundo

Source: IUCrData, Vol 4, Iss 4, p x190458 (2019)

Subject Terms: crystal structure, amino acids, absolute structure, Flack parameter, Hooft parameter, Crystallography, QD901-999

File Description: electronic resource

Relation: http://scripts.iucr.org/cgi-bin/paper?S2414314619004589; https://doaj.org/toc/2414-3146

Access URL: https://doaj.org/article/e469a0292a0f4509aa1ac8ebf6a1ea15

A Novel Glutathione S-Transferase Gtt2 Class (VpGSTT2) Is Found in the Genome of the AHPND/EMS Vibrio parahaemolyticus Shrimp Pathogen

Authors: Ignacio Valenzuela-Chavira, David O. Corona-Martinez, Karina D. Garcia-Orozco, Melissa Beltran-Torres, Filiberto Sanchez-Lopez, Aldo A. Arvizu-Flores, Rocio Sugich-Miranda, Alonso A. Lopez-Zavala, Ramon E. Robles-Zepeda, Maria A. Islas-Osuna, Adrian Ochoa-Leyva, Michael D. Toney, Hugo Serrano-Posada, Rogerio R. Sotelo-Mundo

Source: Toxins, Vol 13, Iss 9, p 664 (2021)

Subject Terms: glutathione s-transferase (GST), Vibrio parahaemolyticus, Gtt2 class, glutathione (GSH), kinetic isotope effect, crystal structure, Medicine

File Description: electronic resource

Relation: https://www.mdpi.com/2072-6651/13/9/664; https://doaj.org/toc/2072-6651

Access URL: https://doaj.org/article/8101e59365844f9383fea967643dd1f3

Targeted RNA-Seq Reveals the M. tuberculosis Transcriptome from an In Vivo Infection Model

Authors: Fernanda Cornejo-Granados, Gamaliel López-Leal, Dulce A. Mata-Espinosa, Jorge Barrios-Payán, Brenda Marquina-Castillo, Edgar Equihua-Medina, Zyanya L. Zatarain-Barrón, Camilo Molina-Romero, Rogelio Hernández-Pando, Adrian Ochoa-Leyva

Source: Biology, Vol 10, Iss 9, p 848 (2021)

Subject Terms: transcriptome, tuberculosis, host-pathogen, RNA-seq, in vivo infection, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.mdpi.com/2079-7737/10/9/848; https://doaj.org/toc/2079-7737

Access URL: https://doaj.org/article/676d17e0a94a4973bf63c7d2dd4a08f8

Structural Basis for the Limited Response to Oxidative and Thiol-Conjugating Agents by Triosephosphate Isomerase From the Photosynthetic Bacteria Synechocystis

Authors: Eduardo Castro-Torres, Pedro Jimenez-Sandoval, Eli Fernández-de Gortari, Margarita López-Castillo, Noe Baruch-Torres, Marisol López-Hidalgo, Antolín Peralta-Castro, Corina Díaz-Quezada, Rogerio R. Sotelo-Mundo, Claudia G. Benitez-Cardoza, L. Michel Espinoza-Fonseca, Adrian Ochoa-Leyva, Luis G. Brieba

Source: Frontiers in Molecular Biosciences, Vol 5 (2018)

Subject Terms: triosephosphate isomerase, X-ray structure, thiol-based redox regulation, oxidative damage, protein evolution, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.frontiersin.org/article/10.3389/fmolb.2018.00103/full; https://doaj.org/toc/2296-889X

Access URL: https://doaj.org/article/f403151a8a024ab28ac8f9f6b7891d1e

A meta-analysis reveals the environmental and host factors shaping the structure and function of the shrimp microbiota

Authors: Fernanda Cornejo-Granados, Luigui Gallardo-Becerra, Miriam Leonardo-Reza, Juan Pablo Ochoa-Romo, Adrian Ochoa-Leyva

Source: PeerJ, Vol 6, p e5382 (2018)

Subject Terms: 16S rRNA, Shrimp microbiota, Meta-analysis, Metagenomics, High-throughput sequencing, PICRUST, Medicine, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://peerj.com/articles/5382.pdf; https://peerj.com/articles/5382/; https://doaj.org/toc/2167-8359

Access URL: https://doaj.org/article/7ad33559efc84374883a6d02280eb925

A novel thymidylate synthase from the Vibrionales, Alteromonadales, Aeromonadales, and Pasteurellales (VAAP) clade with altered nucleotide and folate binding sites

Authors: Alonso A. Lopez-Zavala, Eduardo Guevara-Hernandez, Luz H. Vazquez-Lujan, Arturo Sanchez-Paz, Karina D. Garcia-Orozco, Carmen A. Contreras-Vergara, Gamaliel Lopez-Leal, Aldo A. Arvizu-Flores, Adrian Ochoa-Leyva, Rogerio R. Sotelo-Mundo

Source: PeerJ, Vol 6, p e5023 (2018)

Subject Terms: Vibrio parahaemolyticus, Trimethoprim, Gammaproteobacteria, Alteromonadales, Enzyme, Aeromonadales, Medicine, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://peerj.com/articles/5023.pdf; https://peerj.com/articles/5023/; https://doaj.org/toc/2167-8359

Access URL: https://doaj.org/article/abf24e1c72994a058269100db07038b9

A novel approach for human whole transcriptome analysis based on absolute gene expression of microarray data

Authors: Shirley Bikel, Leonor Jacobo-Albavera, Fausto Sánchez-Muñoz, Fernanda Cornejo-Granados, Samuel Canizales-Quinteros, Xavier Soberón, Rogerio R. Sotelo-Mundo, Blanca E. del Río-Navarro, Alfredo Mendoza-Vargas, Filiberto Sánchez, Adrian Ochoa-Leyva

Source: PeerJ, Vol 5, p e4133 (2017)

Subject Terms: Microarray, Transcriptome, Human, Personalized medicine, Absolute gene expression, Transcriptomics, Medicine, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://peerj.com/articles/4133.pdf; https://peerj.com/articles/4133/; https://doaj.org/toc/2167-8359

Access URL: https://doaj.org/article/d450432259ab4802a5d0140f5780be8d