Recent Submissions

  • DEF8 and Autophagy-Associated Genes are Altered in Mild Cognitive Impairment, Probable Alzheimer’s Disease Patients and a Transgenic Model of the Disease 

    Leyton, Esteban [Chile. Universidad Mayor. Centro de Biología Integrativa]; Matus, Diego [Chile. Universidad Mayor. Centro de Biología Integrativa]; Espinoza, Sandra [Chile. Universidad Mayor. Centro de Biología Integrativa]; Benítez, José Matías [Chile. Universidad Mayor. Centro de Biología Integrativa]; Cortés, Bastián [Chile. Universidad Mayor. Centro de Biología Integrativa]; Gómez, Wileidy [Chile. Universidad Mayor. Centro de Biología Integrativa]; Arévalo, Nohela B. [Chile. Universidad Mayor. Centro de Biología Integrativa]; Murgas, Paola [Chile. Universidad Mayor. Centro de Biología Integrativa]; Manque Ramírez, Patricio [Chile. Universidad Mayor. Centro de Genómica y Bioinformática]; Woehlbier, Ute [Chile. Universidad Mayor. Centro de Biología Integrativa]; Durán-Aniotz, Claudia; Hetz, Claudio; Behrens, María Isabel; San Martín, Carol D. [Chile. Universidad Mayor. Centro de Biología Integrativa]; Nassif, Melissa [Chile. Universidad Mayor. Centro de Biología Integrativa] (IOS Press, 2021-02-19)
    Background:Disturbances in the autophagy/endolysosomal systems are proposed as early signatures of Alzheimer’s disease (AD). However, few studies are available concerning autophagy gene expression in AD patients. Objective:To ...
  • Rule-Based Models and Applications in Biology 

    Bustos, Álvaro; Fuenzalida, Ignacio; Santibáñez, Rodrigo; Pérez-Acle, Tomás; Martin, Alberto J M [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile] (Humana Press, 2018-11-13)
    Complex systems are governed by dynamic processes whose underlying causal rules are difficult to unravel. However, chemical reactions, molecular interactions, and many other complex systems can be usually represented as ...
  • The protein architecture in Bacteria and Archaea identifies a set of promiscuous and ancient domains 

    Hernández-Guerrero, Rafael; Galán-Vásquez, Edgardo; Pérez-Rueda, Ernesto [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile] (Public Library of Science, 2019-12-19)
    In this work, we describe a systematic comparative genomic analysis of promiscuous domains in genomes of Bacteria and Archaea. A quantitative measure of domain promiscuity, the weighted domain architecture score (WDAS), ...
  • Single-Nucleotide Polymorphisms (SNP) Mining and Their Effect on the Tridimensional Protein Structure Prediction in a Set of Immunity-Related Expressed Sequence Tags (EST) in Atlantic Salmon (Salmo salar) 

    Vallejos-Vidal, Eva; Reyes-Cerpa, Sebastián [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile]; Rivas-Pardo, Jaime Andrés [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile]; Maisey, Kevin; Yañez, José M.; Valenzuela, Héctor; Cea, Pablo A.; Castro-Fernández, Víctor; Tort, Lluis; Sandino, Ana M.; Imarai, Mónica; Reyes-López, Felipe E. (Frontiers Media S.A., 2020-02-27)
    Single-nucleotide polymorphisms (SNPs) are single genetic code variations considered one of the most common forms of nucleotide modifications. Such SNPs can be located in genes associated to immune response and, therefore, ...
  • Interleukin-35 inhibits alveolar bone resorption by modulating the Th17/Treg imbalance during periodontitis 

    Cafferata, Emilio A.; Terraza-Aguirre, Claudia; Barrera, Romina; Faúndez, Nicolás; González, Nicolás; Rojas, Carolina; Melgar-Rodríguez, Samanta; Hernández, Marcela; Carvajal, Paola; Cortez, Cristian [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile]; González, Fermin E.; Covarrubias, Cristian; Vernal, Rolando (Blackwell Munksgaard, 2020-04)
    Aim T lymphocytes play a central role during the pathogenesis of periodontitis, and the imbalance between the pathogenic T-helper type 17 (Th17) and protective T-regulatory (Treg) lymphocytes determines the tooth-supporting ...
  • Evolution of Predicted Acid Resistance Mechanisms in the Extremely Acidophilic Leptospirillum Genus 

    Vergara, Eva; Neira, Gonzalo; González, Carolina [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile]; Cortez, Diego; Dopson, Mark; Holmes, David S. [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile] (MDPI Multidisciplinary Digital Publishing Institute, 2020-04)
    Organisms that thrive in extremely acidic environments (<= pH 3.5) are of widespread importance in industrial applications, environmental issues, and evolutionary studies. Leptospirillum spp. constitute the only extremely ...
  • A HaloTag-TEV genetic cassette for mechanical phenotyping of proteins from tissues 

    Rivas-Pardo, Jaime Andrés [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile]; Li, Yong; Martonfalvi, Zsolt; Tapia-Rojo, Rafael; Unger, Andreas; Fernández-Trasancos, Angel; Herrero-Galán, Elías; Velázquez-Carreras, Diana; Fernández, Julio M.; Linke, Wolfgang A.; Alegre-Cebollada, Jorge (Nature Publishing Group, 2020-04-28)
    Single-molecule methods using recombinant proteins have generated transformative hypotheses on how mechanical forces are generated and sensed in biological tissues. However, testing these mechanical hypotheses on proteins ...
  • Draft Genome Sequence of Blautia luti DSM 14534(T), Isolated from Human Stool 

    Ortiz, Rodrigo L.; Melis-Arcos, Felipe; Covarrubias, Paulo C.; Ugalde, Juan A.; Apte, Zachary S.; Pérez-Donoso, José; Cárdenas, Juan P. [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile]; Almonacid, Daniel E. (Chile. Universidad Mayor, 2020-05)
    Here, we report the draft sequence of Blautia luti strain DSM 14534T, originally isolated from human feces. This draft contains 74 contigs, comprising 3,718,760 bp with a G+C content of 42.87%. The annotated draft contains ...
  • Unlocking Survival Mechanisms for Metal and Oxidative Stress in the Extremely Acidophilic, Halotolerant Acidihalobacter Genus 

    Khaleque, Himel Nahreen; Fathollazadeh, Homayoun; González, Carolina [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile]; Shafique, Raihan; Kaksonen, Anna H.; Holmes, David S. [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile]; Watkin, Elizabeth L.J. (MDPI Multidisciplinary Digital Publishing Institute, 2020-11-24)
    Microorganisms used for the biohydrometallurgical extraction of metals from minerals must be able to survive high levels of metal and oxidative stress found in bioleaching environments. The Acidihalobacter genus consists ...
  • Boldine inhibits the alveolar bone resorption during ligature-induced periodontitis by modulating the Th17/Treg imbalance 

    Cafferata, Emilio A.; Castro-Saavedra, Sebastián; Fuentes-Barros, Gonzalo; Melgar-Rodriguez, Samanta; Rivera, Felipe; Carvajal, Paola; Hernández, Marcela; Cortés, Bastian, I [Centro de Biología Integrativa, Facultad de Ciencias, Universidad Mayor, Chile]; Cortez, Cristian [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile]; Cassels, Bruce K.; Vernal, Rolando (Chile. Universidad Mayor, 2020-06)
    Background During periodontitis, tooth-supporting alveolar bone is resorbed when there is an increased expression of the pro-osteolytic factor termed receptor activator of nuclear factor kappa B ligand (RANKL), which is ...
  • Aggregatibacter actinomycetemcomitans Induces Autophagy in Human Junctional Epithelium Keratinocytes 

    Cordero, Esteban M. [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile]; Cortes, Bastian I. [Centro de Biología Intergrativa, Facultad de Ciencias, Universidad Mayor, Chile]; Palominos, Sebastián [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile]; Parra, Pedro [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile]; Mella, Tania [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile]; Henrríquez, Constanza [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile]; Salazar, Nelda [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile]; Monasterio, Gustavo; Cafferata, Emilio A.; Murgas, Paola [Centro de Biología Intergrativa, Facultad de Ciencias, Universidad Mayor, Chile]; Vernal, Rolando; Cortez, Cristian Andres [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile] (MDPI, 2020-05)
    The adverse environmental conditions found in the periodontium during periodontitis pathogenesis stimulate local autophagy responses, mainly due to a continuous inflammatory response against the dysbiotic subgingival ...
  • Interfering with the Folding of Group A Streptococcal pili Proteins 

    Contreras, Fernanda [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile]; Rivas-Pardo, Jaime Andrés [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile] (Chile. Universidad Mayor, 2020-05-20)
    Gram-positive bacteria use their adhesive pili to attach to host cells during early stages of a bacterial infection. These extracellular hair-like appendages experience mechanical stresses of hundreds of picoNewtons; ...
  • Nutrient dose-responsive transcriptome changes driven by Michaelis Menten kinetics underlie plant growth rates 

    Swift, Joseph; Alvarez, Jose M. [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile]; Araus, Viviana; Gutiérrez, Rodrigo A.; Coruzzi, Gloria M. (National Academy of Sciences, 2020-06-09)
    An increase in nutrient dose leads to proportional increases in crop biomass and agricultural yield. However, the molecular underpinnings of this nutrient dose-response are largely unknown. To investigate, we assayed changes ...
  • Transient genome-wide interactions of the master transcription factor NLP7 initiate a rapid nitrogen-response cascade 

    Alvarez, Jose M. [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile]; Schinke, Anna-Lena; Brooks, Matthew D.; Pasquino, Angelo; Leonelli, Lauriebeth; Varala, Kranthi; Safi, Alaeddine; Krouk, Gabriel; Krapp, Anne; Coruzzi, Gloria M. (Nature Publishing Group, 2020-03-02)
    Dynamic reprogramming of gene regulatory networks (GRNs) enables organisms to rapidly respond to environmental perturbation. However, the underlying transient interactions between transcription factors (TFs) and genome-wide ...
  • A balancing act: how plants integrate nitrogen and water signals 

    Araus, Viviana; Swift, Joseph; Alvarez, Jose M. [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile]; Henry, Amelia; Coruzzi, Gloria M. (Oxford University Press, 2020-07-25)
    Nitrogen (N) and water (W) are crucial inputs for plant survival as well as costly resources for agriculture. Given their importance, the molecular mechanisms that plants rely on to signal changes in either N or W status ...
  • IL-22-expressing CD4(+)AhR(+) T lymphocytes are associated with RANKL-mediated alveolar bone resorption during experimental periodontitis 

    Monasterio, Gustavo; Budini, Victoria; Fernández, Baltasar; Castillo, Francisca; Rojas, Carolina; Alvarez, Carla; Cafferata, Emilio A.; Vicencio, Emiliano [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile]; Cortés, Bastian I. [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile]; Cortez, Cristian Andres [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile]; Vernal, Rolando (Blackwell Munksgaard, 2019-10)
    Background and Objective Over the past few years, the importance of interleukin-22 (IL-22) and T-helper (Th)22 lymphocytes in the pathogenesis of periodontitis has become apparent; however, there are still aspects that are ...
  • Engineering a single-chain antibody against Trypanosoma cruzi metacyclic trypomastigotes to block cell invasion 

    Kalempa Demeu, Lara Maria; Soares, Rodrigo Jahn; Miranda, Juliana Severo; Pacheco-Lugo, Lisandro A.; Oliveira, Kelin Goncalves; Cortez Plaza, Cristian Andres [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile]; Billiald, Philippe; de Moura, Juliana Ferreira; Yoshida, Nobuko; Alvarenga, Larissa Magalhaes; DaRocha, Wanderson Duarte (Chile. Universidad Mayor, 2019-10-16)
    Trypanosoma cruzi is a flagellate protozoan pathogen that causes Chagas disease. Currently there is no preventive treatment and the efficiency of the two drugs available is limited to the acute phase. Therefore, there is ...
  • Draft genome of Chilean honeybee (Apis mellifera) gut strain Lactobacillus kunkeei MP2 

    Olmos, Alejandro [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile]; Henríquez-Piskulich, Patricia [Ceapi Mayor, Universidad Mayor, Chile]; Sanchez, Carolina [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile]; Rojas-Herrera, Marcelo [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile]; Moreno-Pino, Mario [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile]; Gómez, Marcela [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile]; Rodríguez Da Silva, Rafael [CEAPI Mayor, Universidad Mayor, Chile]; Maracaja-Coutinho, Vinicius [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile]; Aldea, Patricia [CEAPI Mayor, Universidad Mayor, Chile]; Trombert, Annette N. [Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile] (American Society for Microbiology, 2014)
    Here, we report the first draft genome sequence of Lactobacillus kunkeei strain MP2, isolated from a Chilean honeybee gut. The sequenced genome has a total size of 1.58 Mb distributed into 44 contigs and 1,356 protein-coding ...
  • Whole Genome Sequence, Variant Discovery and Annotation in Mapuche-Huilliche Native South Americans 

    Vizoso, Paula [Univ Mayor, Fac Ciencias, Ctr Propagac Conservac Vegetal CEPROVEG, Santiago, Chile]; Vidal, Elena A. [Univ Mayor, Fac Ciencias, Ctr Geneim Bioinformat, Santiago, Chile]; Moyano, Tomás C.; Bustos, Bernabe, I; Pérez-Palma, Eduardo; Moraga, Carol; Riveras, Eleodoro; Montecinos, Alejandro; Azocar, Lorena; Soto, Daniela C.; Vidal, Mabel; Di Genoval, Alex; Puschel, Klaus; Nurnberg, Peter; Buch, Stephan; Hampe, Jochen; Allende, Miguel L.; Cambiazo, Veronica; González, Mauricio; Hodar, Christian; Montecino, Martin; Muñoz-Espinoza, Claudia; Orellana, Ariel; Reyes-Jara, Angelica; Travisanyl, Dante; Moraga, Mauricio; Eyheramendy, Susana; Maass, Alejandro; De Ferrari, Giancarlo, V; Mique, Juan Francisco; Gutiérrez, Rodrigo A. (NATURE PUBLISHING GROUP, 2019)
    Whole human genome sequencing initiatives help us understand population history and the basis of genetic diseases. Current data mostly focuses on Old World populations, and the information of the genomic structure of Native ...
  • Non-lysosomal Activation in Macrophages of Atlantic Salmon (Salmo salar) After Infection With Piscirickettsia salmonis 

    Reyes-Cerpa, Sebastián [Univ Mayor, Ctr Genom & Bioinformat, Fac Ciencias, Santiago, Chile]; Valdés, Jorge [Univ Mayor, Ctr Genom & Bioinformat, Fac Ciencias, Santiago, Chile]; Ibaceta, Valentina [Univ Mayor, Ctr Genom & Bioinformat, Fac Ciencias, Santiago, Chile]; Brianson, Bernardo [Univ Mayor, Ctr Genom & Bioinformat, Fac Ciencias, Santiago, Chile]; Espinoza, Allison [Univ Mayor, Ctr Genom & Bioinformat, Fac Ciencias, Santiago, Chile]; Ahumada, Diego E. [Univ Mayor, Ctr Genom & Bioinformat, Fac Ciencias, Santiago, Chile]; Tapia, Sebastián [Univ Mayor, Ctr Genom & Bioinformat, Fac Ciencias, Santiago, Chile]; Pérez-Stuardo, Diego [Univ Mayor, Ctr Genom & Bioinformat, Fac Ciencias, Santiago, Chile]; Morales-Reyes, Jonathan; Espinoza, Allison; Soto-Herrera, Valentina; Sandino, Ana M.; Spencer, Eugenio; Vallejos-Vidal, Eva; Reyes-López, Felipe E. (FRONTIERS MEDIA SA, 2019)
    Piscirickettsia salmonis is a facultative intracellular pathogen and etiological agent of the systemic disease salmonid rickettsial septicemia. It has been suggested that P salmonis is able to survive in host macrophages, ...

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