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The Iberian Roma Population Variant Server(IRPVS)

Journal of Genetics and Genomics 2024年第7期51卷 769-773页

作者： Fabiola Mavillard Javier Perez-Florido Francisco M.Ortuño Amador Valladares Miren L.Álvarez-Villegas Gema Roldán Rosario Carmona Manuel Soriano Santiago Susarte Pilar Fuentes Daniel López-López Ana María Nuñez-Negrillo Alejandra Carvajal yolanda Morgado Daniel Arteaga Rosa Ufano Pablo Mir Juan F.Gamella Joaquín Dopazo Carmen Paradas Macarena Cabrera-Serrano Instituto de Biomedicina de Sevilla(IBiS) Hospital Universitario Virgen del Rocío/CSIC/Universidad de SevillaSevillaSpain centro Investigación Biomédica en Red Enfermedades Neurodegenerativas(CIBERNED) Instituto de Salud CarlosⅢSevillaSpain Plataforma Andaluza de Medicina Computacional Fundación Progreso y Salud(FPS)Hospital Virgen del RocíoSevillaSpain Grupo de medicina computacional de sistemas Instituto de Biomedicina de Sevilla(IBiS)Hospital Virgen del RocíoSevillaSpain Nodo de Genómica Funcional (INB-ELIXIR-es)Fundación Progreso y Salud(FPS)Hospital Virgen del RocíoSevilla 41013Spain bioinformática en Enfermedades raras(BiER) Centro de Investigación Biomédica en Red de Enfermedades Raras(CIBERER)Instituto de salud CarlosⅢSevillaSpain departamento de Ingeniería de Computadores Automática y RobóticaUniversidad de GranadaGranadaSpain Servicio de Urgencias de Atención Primaria Distrito SevillaSevillaSpain centro de Servicios Sociales Negociado de Servicios EspecializadosAyuntamiento de SevillaSevillaSpain departamento de Enfermería Facultad de Ciencias de la SaludUniversidad de GranadaGranadaSpain departamento de Neurología Hospital Virgen de las NievesGranadaSpain departamento de Neurología Hospital Virgen de ValmeSevillaSpain centro de Salud Utrera Sur SevillaSpain centro de Salud Polígono Sur SevillaSpain Unidad de Trastornos del Movimiento Servicio de Neurología y Neurofisiología ClínicaHospital Universitario Virgen del RocíoSevillaSpain departamento de Medicina Facultad de MedicinaUniversidad de SevillaSevilleSpain departamento de Antropología Social Universidad de GranadaSpain Unidad Enfermedades Neuromusculares Servicio de Neurología y Neurofisiología ClínicaHospital Universitario Virgen del RocíoSevillaSpain

In recent years,the number of known disease genes has exponentially grown due to the widespread adoption of cost-effective massive parallel *** identify new disease variants,especially in monogenic disorders,a frequen... 详细信息

关键词： Server filtering massive

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The fungal UmSrt1 and maize ZmSUT1 sucrose transporters battle for plant sugar resources

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Journal of Integrative Plant Biology 2017年第6期59卷 422-435页

作者： Anke Wittek Ingo Dreyer Khaled A.S. Al-Rasheid Norbert Sauer Rainer Hedrich Dietmar Geiger Institute for molecular Plant Physiology and Biophysics Julius-von-Sachs-lnstitute Biocenter University of Wurzburg 97082 Wurzburg Germany centro de bioinformatica y simulacion molecular Facultad de Ingenieria Universidad de Talca Talca Chile College of Science King Saud University Riyadh 11451 Saudi Arabia molecular Plant Physiology University Erlangen-Nurnberg 91058 Erlangen Germany

The biotrophic fungus Ustilago maydis causes corn smut disease, inducing tumor formation in its host Zea mays. Upon infection, the fungal hyphae invaginate the plasma membrane of infected maize ceils, establishing an interface where pathogen and host are separated only by their plasma membranes. At this interface the fungal and maize sucrose transporters, UmSrtl and ZmSUT1, compete for extracellular sucrose in the corn smut/maize pathos- ystem. Here we biophysically characterized ZmSUT1 and UmSrtl in Xenopus oocytes with respect to their voltage-, pH- and substrate-dependence and determined affinities toward protons and sucrose. In contrast to ZmSUT% UmSrtl has a high affinity for sucrose and is relatively pH- and voltage-independent. Using these quantitative parameters, we developed a mathematical model to simulate the competition for extracellular sucrose at the contact zone between the fungus and the host plant. This approach revealed that UmSrtl exploits the apoplastic sucrose resource, which forces the plant transporter into a sucrose export mode providing the fungus with sugar from the phloem. Importantly, the high sucrose concen- tration in the phloem appeared disadvantageous for the ZmSUT1 preventing sucrose recovery from the apoplastic space in the fungus/plant interface.

关键词： William J. Lucas, University of California, Davis, USAReceived Mar. 1, 2017 Accepted Mar. 10, 2017 Online on Mar. 15,2017

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Distributed Differences Structures Underlie Gating between the Kin Channel KAT1 and the Kout Channel SKOR

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molecular Plant 2010年第1期3卷 236-245页

作者： Janin Riedelsberger Tripti Sharma Wendy Gonzalez Pawel Gajdanowicz Samuel Elias Morales-Navarro Carlos Garcia-Mata Bernd Mueller-Roeber Fernando Danilo Gonzalez-Nilo Michael R. Blatt Ingo Dreyer Universitat Potsdam Institut for Biochemie und Biologie Molekularbiologie Heisenberg-Gruppe Biophysik und Molekulare Pflanzenbiologie BPMPB Karl-Liebknecht-Strasse 24-25 Haus 20 D-14476 Potsdam-Golm Germany Max-Planck Institute of molecular Plant Physiology 14476 Potsdam-Golm Germany centro de bioinformatica y simulacion molecular Universidad de Talca Casilla 721 Talca Chile Laboratory of Plant Physiology and Biophysics IBLS Plant Sciences Bower Building University of Glasgow Glasgow G12 8QQ UK Laboratorio de Fisiologia molecular e Integrativa Institutos de Investigaciones Biologicas Universidad Nacional de Mar del Plata 7600 Mar del Plata Buenos Aires Argentina Universitat Potsdam Institut for Biochemie und Biologie Abteilung Molekularbiologie 14476 Potsdam-Golm Germany

The family of voltage-gated （Shaker-like） potassium channels in plants includes both inward-rectifying （Kin） channels that allow plant cells to accumulate K＋ and outward-rectifying （Kout） channels that mediate K＋ efflux. despite their dose structural similarities, Kin and Kout channels differ in their gating sensitivity towards voltage and the extracellular K＋ concentration. We have carried out a systematic program of domain swapping between the Kout channel SKOR and the Kin channel KAT1 to examine the impacts on gating of the pore regions, the S4, S5, and the S6 helices. We found that, in particular, the N-terminal part of the S5 played a critical role in KAT1 and SKOR gating. Our findings were supported by molecular dynamics of KAT1 and SKOR homology models. In silico analysis revealed that during channel opening and closing, displacement of certain residues, especially in the S5 and S6 segments, is more pronounced in KAT1 than in SKOR. From our analysis of the S4-S6 region, we conclude that gating （and K＋-sensing in SKOR） depend on a number of structural elements that are dispersed over this -145-residue sequence and that these place additional constraints on configurational rearrangement of the channels during gating.

关键词： Arabidopsis K+ channel outward rectifier inward rectifier channel protein structure channel protein-cation interaction gating, K+-dependent.

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Theoretical and Experimental Exploration of Organic Synthesis Routes to Obtain Natural Rubber Analogues

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材料科学与工程（中英文A版） 2014年第9期4卷 290-296页

作者： David Ramirez-Sanchez Danilo Gonzalez Pablo Ramos Luis-Carlos Garcia centro de bioinform6tica y simulacion molecular Universidad de Talca Talca 346-0000 Chile departamento de Quimica Universidad Nacional de Colombia Bogota 11001 Colombia Theoretical Chemistry Rutgers University Newark 10032 United States of America Proyecto Curricular Licenciatura en Quimica Universidad Distrital Francisco Jose de Caldas Bogota 11001 Colombia

In the present work, synthesis routes and the reactions involved in the polymerization of two organic compounds similar to natural rubber were studied. To these routes and reactions, modifications related with the previously reported in the literature were performed in order to study them through theoretical tools and determine their prediction capability for the design of those analogs. The semi-empirical method Austin Model 1 (AM1) was used for the study of electronic configurations and it was shown that the synthesis of the polystyrene polymer (PS) and the poly copolymer (styrene-butadiene) (SBR) is possible through the use of free radicals from styrene and 1,3-butadiene monomers using benzoyl peroxide as the catalyst in both cases; going through the intermediates 1-phenyl-2-[(phenylcarbonyl)oxy]ethyl and (2E)-4(oxy (phenylcarbonyl))2-buten-1-yl. The results show that the higher electronic densities are found over the active atom in the radical compared to the electronic densities over the ions and the interest atoms in a possible condensation. Additionally, the study of the reaction mechanisms for the designed organic synthesis routes was performed by applying the frontier orbitals theory developed by R. B. Woodward, and R. Hoffmann and the respective correlation diagrams that showed thermal viability were built demonstrating the consistency between the characteristics of the orbital symmetry in the concerted reactions of the reactants and products; therefore it is seen that the free radical synthesis do not show symmetry restrictions, and it is possible to make it by a thermal route with low activation energy thresholds. The experimental yields of polymerizations were 90% and 75% for polystyrene (PS) and poly (styrene-butadiene) (SBR) respectively. Additionally mechanical tests were performed to the synthesized polymers and it was proved that the properties of the synthesized compounds are consistent with those reported in the literature. In the future it is ex

关键词：有机合成路线天然橡胶类似物实验苯乙烯聚合物有机化合物轨道对称性聚合反应

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<i>In Silico</i>and <i>in Vitro</i>Approach for the Understanding of the Xanthine Oxidase Inhibitory Activity of Uruguayan Tannat Grape Pomace and Propolis Poliphenols

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Journal of Biophysical Chemistry 2019年第1期10卷 1-14页

作者： Elena Alvareda Federico Iribarne Victoria Espinosa Pablo Miranda Daniela Santi Sara Aguilera S. Bustos Margot Paulino Zunini centro de bioinformática Estructural DETEMA Facultad de Química Universidad de la República Montevideo Uruguay centro Universitario Región Noroeste Sede Salto Universidad de la República Salto Uruguay centro de Investigaciones Biomédicas y Aplicadas Escuela de Medicina Facultad de Ciencias Médicas Universidad de Santiago de Chile Santiago Chile departamento de Ciencias Farmacéuticas Facultad de Ciencias Químicas Universidad Nacional de Córdoba Ciudad Universitaria Córdoba Argentina Instituto Multidisciplinario de Biología Vegetal (IMBIV-CONICET) Ciudad Universitaria Córdoba Argentina Faculty of Sciences Universidad Católica del Norte Antofagasta Chile

The use of food additives with xanthine oxidase (XO) inhibitory activity offers an alternative approach to hyperuricemic and gout disease treatment, and provides an example of antioxidant nutraceutics. The in vitro and in silico XO inhibitory activity of polyphenols from Uruguayan Tannat grape pomaces and propolis extracts was evaluated as well as the scavenging capacity of said compounds. When comparing propolis and grape pomace samples, the in vitro studies demonstrated that polyphenols extracted from propolis are more active as free radical scavengers than those from Tannat grape pomace. Both natural products effectively inhibited XO but the capacity of phenols present in GP is higher than the one present in P. The high content of anthocyanins in GP, absent in P, could account for this observation. In silico assays allowed us to determine relevant ligand-receptor interactions between polyphenols, from a database built with previously reported polyphenols from both natural products, and the active site of XO. The in silico results showed that compound (E)-isoprenylcaffeate from propolis was the best potential XO inhibitor displaying hydrophobic aromatic interaction between the conjugated ring of the caffeate moiety and polar interactions between hydroxyl groups from caffeate with the active site polar residues. Among grape pomaces, the Cyanidin-3-O-(6-(E)-p-coumaroyl)-glucoside was the best XO inhibitor;its moiety oxychromenyl being relevant to the docking stabilization. All these results lead us to propose Uruguayan propolis and Tannat grape pomace extracts as food additives as well as phytopharmaceuticals to decrease the uric acid levels in gout disease and to act against oxidative stress.

关键词： Propolis Tannat Grape Pomace Xanthine Oxidase Inhibition Polyphenols Functional Foods

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Clinical Profiles at the Time of Diagnosis of SARS-CoV-2 Infection in Costa Rica During the Pre-vaccination Period Using a Machine Learning Approach

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Phenomics 2022年第5期2卷 312-322页

作者： Jose Arturo Molina-Mora Alejandra González Sergio Jiménez-Morgan Estela Cordero-Laurent Hebleen Brenes Claudio Soto-Garita Jorge Sequeira-Soto Francisco Duarte-Martínez centro de Investigación en Enfermedades Tropicales(CIET)and Facultad de Microbiología Universidad de Costa RicaSan José2060Costa Rica Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud(INCIENSA) Tres Ríos 30301Costa Rica Escuela de Medicina Universidad de Costa RicaSan José2060Costa Rica

The clinical manifestations of COVID-19,caused by the SARS-CoV-2,define a large spectrum of symptoms that are mainly dependent on the human host *** Costa Rica,more than 169,000 cases and 2185 deaths were reported during the year 2020,the pre-vaccination *** describe the clinical presentations at the time of diagnosis of SARS-CoV-2 infection in Costa Rica during the pre-vaccination period,we implemented a symptom-based clustering using machine learning to identify clusters or clinical profiles at the population level among 18,974 records of positive *** were compared based on symptoms,risk factors,viral load,and genomic features of the SARS-CoV-2 sequence.A total of 18 symptoms at time of diagnosis of SARS-CoV-2 infection were reported with a frequency>1%,and those were used to identify seven clinical profiles with a specific composition of clinical *** the comparison between clusters,a lower viral load was found for the asymptomatic group,while the risk factors and the SARS-CoV-2 genomic features were distributed among all the *** other distribution patterns were found for age,sex,vital status,and *** conclusion,during the pre-vaccination time in Costa Rica,the symptoms at the time of diagnosis of SARS-CoV-2 infection were described in clinical *** host co-morbidities and the SARS-CoV-2 genotypes are not specific of a particular profile,rather they are present in all the groups,including asymptomatic *** addition,this information can be used for decision-making by the local healthcare institutions(first point of contact with health professionals,case definition,or infrastructure).In further analyses,these results will be compared against the profiles of cases during the vaccination period.

关键词： COVID-19 Costa Rica Machine learning Diagnosis SARS-CoV-2 Clinical profiles

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FungalTraits:a user-friendly traits database of fungi and fungus-like stramenopiles

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Fungal Diversity 2020年第2期105卷 I0001-I0016页

作者： Sergei Põlme Kessy Abarenkov RHenrik Nilsson Björn D.Lindahl Karina Engelbrecht Clemmensen Havard Kauserud Nhu Nguyen Rasmus Kjøller Scott T.Bates Petr Baldrian Tobias Guldberg Frøslev Kristjan Adojaan Alfredo Vizzini Ave Suija Donald Pfister Hans-Otto Baral Helle Järv Hugo Madrid Jenni Nordén Jian-Kui Liu Julia Pawlowska Kadri Põldmaa Kadri Pärtel Kadri Runnel Karen Hansen Karl-Henrik Larsson Kevin David Hyde Marcelo Sandoval-denis Matthew E.Smith Merje Toome-Heller Nalin N.Wijayawardene Nelson Menolli Jr Nicole K.Reynolds Rein Drenkhan Sajeewa S.N.Maharachchikumbura Tatiana B.Gibertoni Thomas Læssøe William Davis yuri Tokarev Adriana Corrales Adriene Mayra Soares Ahto Agan Alexandre Reis Machado Andrés Argüelles-Moyao Andrew detheridge Angelina de Meiras-Ottoni Annemieke Verbeken Arun Kumar Dutta Bao-Kai Cui C.K.Pradeep César Marín Daniel Stanton Daniyal Gohar Dhanushka N.Wanasinghe Eveli Otsing Farzad Aslani Gareth W.Griffith Thorsten H.Lumbsch Hans-Peter Grossart Hossein Masigol Ina Timling Inga Hiiesalu Jane Oja John y.Kupagme József Geml Julieta Alvarez-Manjarrez Kai Ilves Kaire Loit Kalev Adamson Kazuhide Nara Kati Küngas Keilor Rojas-Jimenez Krišs Bitenieks Laszlo Irinyi LászlóGNagy Liina Soonvald Li-Wei Zhou Lysett Wagner M.Catherine Aime MaarjaÖpik María Isabel Mujica Martin Metsoja Martin Ryberg Martti Vasar Masao Murata Matthew PNelsen Michelle Cleary Milan C.Samarakoon Mingkwan Doilom Mohammad Bahram Niloufar Hagh-Doust Olesya Dulya Peter Johnston Petr Kohout Qian Chen Qing Tian Rajasree Nandi Rasekh Amiri Rekhani Hansika Perera Renata dos Santos Chikowski Renato L.Mendes-Alvarenga Roberto Garibay-Orijel Robin Gielen Rungtiwa Phookamsak Ruvishika S.Jayawardena Saleh Rahimlou Samantha C.Karunarathna Saowaluck Tibpromma Shawn P.Brown Siim-Kaarel Sepp Sunil Mundra Zhu-Hua Luo Tanay Bose Tanel Vahter Tarquin Netherway Teng yang Tom May Torda Varga Wei Li Victor Rafael Matos Coimbra Virton Rodrigo Targino de Oliveira Vitor Xavier de Lima Vladimir S.Mikryukov yongzhong Lu yosuke Matsuda yumiko Miyamoto Urm Institute of Ecology and Earth Sciences University of Tartu14A Ravila50411 TartuEstonia Natural History Museum University of Tartu46 Vanemuise Str51003 TartuEstonia Gothenburg Global Biodiversity Centre Box 46140530 GothenburgSweden department of Biological and Environmental Sciences University of GothenburgGothenburgSweden department of Soil and Environment Swedish University of Agricultural SciencesBox 701475007 UppsalaSweden department of Forest Mycology and Plant Pathology Swedish University of Agricultural SciencesBox 702675007 UppsalaSweden Section for Genetics and Evolutionary Biology(EvoGene) Department of BiosciencesUniversity of OsloP.O.Box 1066BlindernNO-0316 OsloNorway University of Hawaiʻi at Mānoa 3190 Maile WaySt.John 102HonoluluHIUSA department of Biology University of CopenhagenUniversitetsparken 152100 CopenhagenØDenmark Purdue University Northwest WestvilleIN 46391USA Institute of Microbiology Czech Academy of SciencesVidenska 108314220 Praha 4Czech Republic GLOBE Institute University of CopenhagenØster Farimagsgade 5KH7.2.321353 CopenhagenDenmark Dipartimento di Scienze della Vita e Biologia dei Sistemi Universitàdi TorinoViale Mattioli 2510125 TorinoItaly department of Organismic and Evolutionary Biology and Farlow Library and Herbarium Harvard University22 Divinity AveCambridgeMA 02138USA Blaihofstr.42 72074 TübingenGermany SyNLAB Estonia Veerenni 53aTallinn 11313Estonia Escuela de Tecnología Médica Universidad Santo TomásLos Carreras 753OsornoChile centro de Genómica y bioinformática Universidad MayorCamino La Pirámide 5750HuechurabaSantiagoChile Norwegian Institute for Nature Research(NINA) Sognsveien 680855 OsloNorway School of Life Science and Technology University of Electronic Science and Technology of ChinaChengdu 611731People’s Republic of China Evolutionary Biology Faculty of BiologyBiological and Chemical Research CentreUniversity of Warsawul.Zwirki i Wigury 10102-089 WarsawPoland department of Botany Swedish Museum of

The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental *** the past decades,rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and ***,in spite of the progress of molecular methods,knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains *** order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis *** the information from previous efforts such as FUNGuild and FunFun together with involvement of expert knowledge,we reannotated 10,210 and 151 fungal and Stramenopila genera,*** resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera,designed for rapid functional assignments of environmental *** order to assign the trait states to fungal species hypotheses,the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS *** the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1%dissimilarity threshold.

关键词： Fungal traits Trophic modes Function Guild bioinformatics High-throughput sequencing Community ecology

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