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HP0953-hypothetical virulence factor overexpresion and localization during Helicobacter pylori infection of gastric epithelium

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World Journal of Gastroenterology 2022年第29期28卷 3886-3902页

作者： Nancy K Arteaga-Resendiz gerardo e rodea Rosa María Ribas-Aparicio Alma L Olivares-Cervantes Juan Arturo Castelán-Vega Joséde Jesús Olivares-Trejo Sandra Mendoza-elizalde edgar O López-Villegas Christian Colín Pamela Aguilar-rodea Alfonso Reyes-López Marcela Salazar García Norma Velázquez-Guadarrama Laboratorio de Investigación en enfermedades Infecciosas Hospital Infantil de México Federico GómezMexico City 06720Mexico Posgrado en Biomedicina y Biotecnología Molecular Laboratorio de Producción y Control de BiológicosEscuela Nacional de Ciencias BiológicasInstituto Politécnico NacionalMexico City 11340Mexico Laboratorio de Adquisición de Hierro Universidad Autónoma de la Ciudad MéxicoPosgrado Ciencias GenómicaMexico City 03100Mexico Laboratorio Central de Microscopía Escuela Nacional de Ciencias BiológicasInstituto Politécnico NacionalMexico City 11340Mexico Centro de estudios económicos y sociales en salud Hospital Infantil de México Federico GómezMexico City 06720Mexico Laboratorio de Investigación en Biología del Desarrollo y Teratogénesis experimental Hospital Infantil de México Federico GómezMexico City 06720Mexico

BACKGROUND The high prevalence and persistence of Helicobacter pylori(H. pylori) infection, as well as the diversity of pathologies related to it, suggest that the virulence factors used by this microorganism are varied. Moreover, as its proteome contains 340hypothetical proteins, it is important to investigate them to completely understand the mechanisms of its virulence and survival. We have previously reported that the hypothetical protein HP0953 is overexpressed during the first hours of adhesion to inert surfaces, under stress conditions, suggesting its role in the environmental survival of this bacterium and perhaps as a virulence factor.AIM To investigate the expression and localization of HP0953 during adhesion to an inert surface and against gastric(AGS) cells.MeTHODS expression analysis was performed for HP0953 during H. pylori adhesion. HP0953 expression at 0,3, 12, 24, and 48 h was evaluated and compared using the Kruskal-Wallis equality-of-populations rank test. Recombinant protein was produced and used to obtain polyclonal antibodies for immunolocalization. Immunogold technique was performed on bacterial sections during adherence to inert surfaces and AGS cells, which was analyzed by transmission electron microscopy. HP0953 protein sequence was analyzed to predict the presence of a signal peptide and transmembrane helices, both provided by the exPASy platform, and using the GLYCOPP platform for glycosylation sites. Different programs, via, I-TASSeR, RaptorX, and HHalign-Kbest, were used to perform three-dimensional modeling.ReSULTS HP0953 exhibited its maximum expression at 12 h of infection in gastric epithelium cells.Immunogold technique revealed HP0953 localization in the cytoplasm and accumulation in some peripheral areas of the bacterial body, with greater expression when it is close to AGS cells.Bioinformatics analysis revealed the presence of a signal peptide that interacts with the transmembrane region and then allows the release of the protein to the external environment. The programs also

关键词： Hypothetical protein HP0953 Adherence Helicobacter pylori Glycocalyx Virulence factor Persistence

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A Systematic Review of Cannabidiol effects in Coronary Syndromes: Challenges to Clinical Translation

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Journal of Biosciences and Medicines 2024年第4期12卷 246-263页

作者： Mario e. Zuñiga-Ayala Alejandra Meaney-Martínez Alejandro Alcocer-Chauvet Vidal Gonzalez-Coronado Nestor Rubio-Infante gerardo Garcia-Rivas Department of Cardiology Instituto de Seguridad Social and Trabajadores del Estado (ISSSTE) Hospital Regional Primero de Octubre Mexico City Mexico Department of Interventional Cardiology Instituto de Seguridad Social y Trabajadores del Estado (ISSSTE) Hospital Regional Primero de Octubre Mexico City Mexico Instituto Tecnó logico de Monerrey Escuela de Medicina and Ciencias de la Salud C&#225tedra de Cardiolog&#237a and Medicina Vascular Monterrey Mexico

Background: Myocardial ischemia in addition to other several cardiac syndromes represent a pathological proinflammatory state alongside a complex cellular microenvironment that can be modified by using cannabinoids. Cannabidiol (CBD), a non-psychoactive compound of cannabis has been recently proposed as an immudomodulatory and cardioprotective drug. Objectives: In this systematic review we sought to clarify and summarize the clinical and preclinical evidence of potential benefit of the use of CBD in coronary syndromes. Methods: We conducted a systematic search and review according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) and Review of Animal Data from experimental Studies (CAMARADeS) guidelines, in the electronic database from PubMed, Web of Science and Scopus up to April 2022 using predefined search terms. Pre-specified exclusion and inclusion criteria were considered, finally 11 articles were chosen to be included for this peer review. Results: Currently there are no good-quality clinical trials with the use of CBD in acute or chronic coronary syndromes. A total of 11 preclinical studies where prescreened and 5 demonstrated reproducible positive cardiovascular outcomes on in-vivo models treated with CBD. Mechanisms of CBD cardioprotection observed: 1) reduction in oxidative stress and inflammation, 2) activation of adenosine receptors and 3) increased expression of angiotensin type 2-receptor. experimental models included ischemia/reperfusion injury, myocardial infarction, arrhythmias, and metabolic syndrome-like conditions. Conclusion: No clinical recommendation can be issued with the current evidence, on the use of CBD in acute and chronic coronary syndromes. Based on preclinical evidence, we considered there is enough evidence to propose the development of well-designed clinical trials that include CBD in the management of coronary syndromes.

关键词： Cannabis Cannabidiol Acute Coronary Syndromes Myocardial Infarction Myocardial Ischemia and Oxidative Stress

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The protein-protein interaction landscape of transcription factors during gynoecium development in Arabidopsis

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Molecular Plant 2023年第1期16卷 260-278页

作者： Humberto Herrera-Ubaldo Sergio e.Campos Pablo López-Gómez Valentín Luna-García Víctor M.Zúñiga-Mayo gerardo e.Armas-Caballero Karla L.González-Aguilera Alexander DeLuna Nayelli Marsch-Martínez Carlos espinosa-Soto Stefan de Folter Unidad de Genómica Avanzada(UGA-LANGeBIO) Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional(CINVESTAV-IPN)IrapuatoGuanajuato 36824México Departamento de Biotecnología y Bioquímica Unidad IrapuatoCINVESTAV-IPNIrapuatoGuanajuato 36824México Instituto de Física Universidad de San Luis PotosíSan Luis PotosíSLP 78290México Present address:Department of Plant Sciences University of CambridgeCambridgeUK Present address:Department of Molecular and Cellular Biology University of California DavisDavisCAUSA Present address:CONACYT Instituto de FitosanidadColegio de PostgraduadosCampus MontecilloTexcocoMéxico

Flowers are composed of organs whose identity is defined by the combinatorial activity of transcription factors(TFs).The interactions between MADS-box TFs and protein complex formation have been schematized in the floral quartet model of flower development.The gynoecium is the flower’s female reproductive part,crucial for fruit and seed production and,hence,for reproductive success.After the establishment of carpel identity,many tissues arise to form a mature gynoecium.TFs have been described as regulators of gynoecium development,and some interactions and complexes have been identified.However,broad knowledge about the interactions among these TFs and their participation during development remains scarce.In this study,we used a systems biology approach to understand the formation of a complex reproductive unit—as the gynoecium—by mapping binary interactions between well-characterized TFs.We analyzed almost 4500 combinations and detected more than 250 protein-protein interactions(PPIs),resulting in a process-specific interaction map.Topological analyses suggest hidden functions and novel roles for many TFs.In addition,we observed a close relationship between TFs involved in auxin and cytokinin-signaling pathways and other TFs.Furthermore,we analyzed the network by combining PPI data,expression,and genetic data,which helped us to dissect it into several dynamic spatio-temporal subnetworks related to gynoecium development processes.Finally,we generated an extended PPI network that predicts new players in gynoecium development.Taken together,all these results serve as a valuable resource for the plant community.

关键词： interactome networks transcription factors gynoecium development

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Influence of flooding and vegetation on carbon,nitrogen,and phosphorus dynamics in the pore water of a Spartina alterniflora salt marsh

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Journal of environmental Sciences 2011年第2期23卷 212-221页

作者： Vanesa L.Negrin Carla V.Spetter Raúl O.Asteasuain gerardo M.e.Perillo Jorge e.Marcovecchio Argentine Institute of Oceanography (IADO CONICETCCT-Bahía Blanca)Camino La Carrindanga km 75Building E-1 CC 804Bahía Blanca 8000Argentina Department of Chemistry Southern National Institute of Chemistry (INQUISUR)Southern National University (UNS)Av Alem 1253Bahía Blanca 8000Argentina Department of Geology Southern National University (UNS)San Juan 670Bahía Blanca 8000Argentina National Technological University Regional Faculty of Bahía Blanca (UTN-FRBB)11 de Abril 461Bahía Blanca 8000Argentina University of the Fraternity of Associations Santo Toms de Aquino (FASTA) Gascón 3145Mar del Plata 7600Argentina

Four sites were selected in a salt marsh in the Bahia Blanca estuary （Argentina）：（1） low marsh （flooded by the tide twice daily） vegetated by S. alterniflora; （2） non-vegetated low marsh; （3） high marsh （flooded only in spring tides） vegetated by S. alterniflora; （4） non-vegetated high marsh. The pH and eh were measured in sediments, while dissolved nutrients （ammonium, nitrate, nitrite and phosphate） and particulate organic matter （POM） were determined in pore water, pH （6.2-8.7） was only affected by vegetation in low areas. eh （from -300 to 250 mV） was lower at low sites than at high ones; in the latter, the values were higher in the non-vegetated sediments. The POM concentration was greater in the high marsh than in the low marsh, with no effect of vegetation. Ammonium was the most abundant nitrogen nutrient species in pore water, except in the non-vegetated high marsh where nitrate concentration was higher. All nitrogen nutrients were affected by both flooding and vegetation. Phosphate was always present in pore water at all sites throughout the year and its concentration varied within narrow limits, with no effect of flooding and greater values always at non-vegetated sites. Our results showed that the variability of the pore water composition within the marsh is greater than the temporal variation, meaning that both tidal flooding and vegetation are important in the dynamics of nutrients and organic matter in the sediment pore water.

关键词： organic matter nutrients flooding Spartina alterniflora

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Transmission potential of the novel coronavirus (COVID-19) onboard the diamond Princess Cruises Ship, 2020

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Infectious Disease Modelling 2020年第1期5卷 264-270页

作者： Kenji Mizumoto gerardo Chowell Graduate School of Advanced Integrated Studies in Human Survivability Kyoto University Yoshida-Nakaadachi-choSakyo-kuKyotoJapan Hakubi Center for Advanced Research Kyoto UniversityYoshidahonmachiSakyo-kuKyotoJapan Department of Population Health Sciences School of Public HealthGeorgia State UniversityAtlantaGeorgiaUSA Division of International epidemiology and Population Studies Fogarty International CenterNational Institutes of HealthBethesdaUSA

An outbreak of COVID-19 developed aboard the Princess Cruises Ship during January eFebruary 2020.Using mathematical modeling and time-series incidence data describing the trajectory of the outbreak among passengers and crew members,we characterize how the transmission potential varied over the course of the outbreak.Our estimate of the mean reproduction number in the confined setting reached values as high as^11,which is higher than mean estimates reported from community-level transmission dynamics in China and Singapore(approximate range:1.1e7).Our findings suggest that Rt decreased substantially compared to values during the early phase after the Japanese government implemented an enhanced quarantine control.Most recent estimates of Rt reached values largely below the epidemic threshold,indicating that a secondary outbreak of the novel coronavirus was unlikely to occur aboard the Diamond Princess Ship.

关键词： Corona epidemic Confined settings Cruise Next generation matrix

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Host-parasite interactions in perpetual darkness:Macroparasite diversity in the cavefish Astyanax mexicanus

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Zoological Research 2023年第4期44卷 782-792页

作者： Ana Santacruz David Hernández-Mena Ramses Miranda-Gamboa gerardo Pérez-Ponce De León Claudia Patricia Ornelas-García Departamento de Zoología Instituto de BiologíaUniversidad Nacional Autónoma de MéxicoMéxico City CP 04510México Departamento de Sistemas y Procesos Naturales Escuela Nacional de Estudios Superiores Unidad MéridaUcúYucatán CP 97357México Instituto de energías Renovables Universidad Nacional Autónoma de MéxicoTemixcoMorelos CP 62580México Colección Nacional de Peces Departamento de ZoologíaInstituto de BiologíaUniversidad Nacional Autónoma de MéxicoMéxico City CP 04510México Stowers Institute for Medical Research Kansas CityMO 64110USA

Astyanax mexicanus has repeatedly colonized cave environments,displaying evolutionary parallelisms in many troglobitic traits.Despite being a model system for the study of adaptation to life in perpetual darkness,the parasites that infect cavefish are practically unknown.In this study,we investigated the macroparasite communities in 18 cavefish populations from independent lineages and compared them with the parasite diversity found in their sister surface fish populations,with the aim of better understanding the role that parasites play in the colonization of new environments.Within the cavefish populations,we identified 13 parasite taxa,including a subset of 10 of the 27 parasite taxa known for the surface populations.Parasites infecting the cavefish belong to five taxonomic groups,including trematodes,monogeneans,nematodes,copepods,and acari.Monogeneans are the most dominant group,found in 14 caves.The macroparasites include species with direct life cycles and trophic transmission,including invasive species.Surprisingly,paired comparisons indicate higher parasite richness in the cavefish than in the surface fish.Spatial variation in parasite composition across the caves suggests historical and geographical contingencies in the host-parasite colonization process and potential evolution of local adaptations.This base-line data on parasite diversity in cavefish populations of A.mexicanus provides a foundation to explore the role of divergent parasite infections under contrasting ecological pressures(cave vs.surface environments)in the evolution of cave adaptive traits.

关键词： Adaptation Metazoan parasites Niche change Parasite assemblage Prevalence

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Gridded 20-year climate parameterization of Africa and South America for a stochastic weather generator (CLIGeN)

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Big earth Data 2023年第2期7卷 349-374页

作者： Andrew Fullhart Guillermo e.Ponce-Campos Menberu B.Meles Ryan P.McGehee gerardo Armendariz Paulo Tarso S.Oliveira Cristiano Das Neves Almeida José C.de Araújo Werner Nel David C.Goodrich Southwest Watershed Research Center USDA-ARS TucsonAZUSA School of Natural Resources and the environment University of ArizonaTucsonAZUSA Sustainable Agricultural Water Systems Unit USDA-ARS DavisCAUSA Agricultural and Biological engineering Purdue UniversityWest LafayetteINUSA Faculty of engineering Architecture and Urbanism and GeographyFederal University of Mato Grosso do Sul(UFMS)Campo GrandeMSBrazil Water Resources and environmental engineering Laboratory Federal University of ParaíbaJoao PessoaPBBrazil Federal University of Fortaleza Department of Agricultural EngineeringFortalezaBrazil Department of Geography and environmental Science University of Fort HareAliceSouth Africa

CLIGeN is a stochastic weather generator that creates statistically representative timeseries of daily and sub-daily point-scale weather variables from observed monthly statistics and other parameters. CLIGeN precipitation timeseries are used as climate input for various risk-assessment modelling applications as an alternative to observe long-term, high temporal resolution records. Here, we queried gridded global climate datasets (TerraClimate, eRA5, GPM-IMeRG, and GLDAS) to estimate various 20-year climate statistics and obtain complete CLIGeN input parameter sets with coverage of the African and South American continents at 0.25 arc degree resolution. The estimation of CLIGeN precipitation parameters was informed by a ground-based dataset of >10,000 locations worldwide. The ground observations provided target values to fit regression models that downscale CLIGeN precipitation input parameters. Aside from precipitation parameters, CLIGeN’s parameters for temperature, solar radiation, etc. were in most cases directly calculated according to the original global datasets. Cross-validation for estimated precipitation parameters quantified errors that resulted from applying the estimation approach in a predictive fashion. Based on all training data, the RMSe was 2.23 mm for the estimated monthly average single-event accumulation and 4.70 mm/hr for monthly maximum 30-min intensity. This dataset facilitates exploration of hydrological and soil erosional hypotheses across Africa and South America.

关键词： Climate CLIGeN Africa South America

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Is it growing exponentially fast? -Impact of assuming exponential growth for characterizing and forecasting epidemics with initial near-exponential growth dynamics

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Infectious Disease Modelling 2016年第1期1卷 71-78页

作者： gerardo Chowell Cecile Viboud School of Public Health Georgia State UniversityAtlantaGAUSA Division of International epidemiology and Population Studies Fogarty International CenterNational Institutes of HealthBethesdaMDUSA

The increasing use of mathematical models for epidemic forecasting has highlighted the importance of designing models that capture the baseline transmission characteristics in order to generate reliable epidemic forecasts.Improved models for epidemic forecasting could be achieved by identifying signature features of epidemic growth,which could inform the design of models of disease spread and reveal important characteristics of the transmission process.In particular,it is often taken for granted that the early growth phase of different growth processes in nature follow early exponential growth dynamics.In the context of infectious disease spread,this assumption is often convenient to describe a transmission process with mass action kinetics using differential equations and generate analytic expressions and estimates of the reproduction number.In this article,we carry out a simulation study to illustrate the impact of incorrectly assuming an exponential-growth model to characterize the early phase(e.g.,3e5 disease generation intervals)of an infectious disease outbreak that follows near-exponential growth dynamics.Specifically,we assess the impact on:1)goodness of fit,2)bias on the growth parameter,and 3)the impact on short-term epidemic forecasts.Our findings indicate that devising transmission models and statistical approaches that more flexibly capture the profile of epidemic growth could lead to enhanced model fit,improved estimates of key transmission parameters,and more realistic epidemic forecasts.

关键词： dynamics. process. exponential

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A primer on stable parameter estimation and forecasting in epidemiology by a problem-oriented regularized least squares algorithm

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Infectious Disease Modelling 2017年第2期2卷 268-275页

作者： Alexandra Smirnova gerardo Chowell Department of Mathematics and Statistics Georgia State UniversityAtlantaUSA School of Public Health Georgia State UniversityAtlantaUSA Division of International epidemiology and Population Studies Fogarty International CenterNational Institutes of HealthBethesdaMDUSA

Public health officials are increasingly recognizing the need to develop disease-forecasting systems to respond to epidemic and pandemic outbreaks.For instance,simple epidemic models relying on a small number of parameters can play an important role in characterizing epidemic growth and generating short-term epidemic forecasts.In the absence of reliable information about transmission mechanisms of emerging infectious diseases,phenomenological models are useful to characterize epidemic growth patterns without the need to explicitly model transmission mechanisms and the natural history of the disease.In this article,our goal is to discuss and illustrate the role of regularization methods for estimating parameters and generating disease forecasts using the generalized Richards model in the context of the 2014e15 ebola epidemic in West Africa.

关键词： Generalized Richards model Parameter estimation Regularization methods epidemic forecasting ebola

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Systematic comparison of epidemic growth patterns using two different estimation approaches

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Infectious Disease Modelling 2021年第1期6卷 5-14页

作者： Yiseul Lee Kimberlyn Roosa gerardo Chowell Department of Population Health Sciences School of Public HealthGeorgia State UniversityAtlantaGA30303USA Division of International epidemiology and Population Studies Fogarty International CenterNational Institute of HealthBethesdaMD20892USA UT One Health Initiative University of TennesseeKnoxvilleTN37996USA

Background:Different estimation approaches are frequently used to calibrate mathematical models to epidemiological data,particularly for analyzing infectious disease outbreaks.Here,we use two common methods to estimate parameters that characterize growth patterns using the generalized growth model(GGM)calibrated to real outbreak datasets.Materials and methods:Data from 31 outbreaks are used to fit the GGM to the ascending phase of each outbreak and estimate the parameters using both least squares(LSQ)and maximum likelihood estimation(MLe)methods.We utilize parametric bootstrapping to construct confidence intervals for parameter estimates.We compare the results including RMSe,Anscombe residual,and 95%prediction interval coverage.We also evaluate the correlation between the estimates from both methods.Results:Comparing LSQ and MLe estimates,most outbreaks have similar parameter estimates,RMSe,Anscombe,and 95%prediction interval coverage.Parameter estimates do not differ across methods when the model yields a good fit to the early growth phase.However,for two outbreaks,there are systematic deviations in model fit to the data that explain differences in parameter estimates(e.g.,residuals represent random error rather than systematic deviation).Conclusion:Our findings indicate that utilizing LSQ and MLe methods produce similar results in the context of characterizing epidemic growth patterns with the GGM,provided that the model yields a good fit to the data.

关键词： Parameter estimation Generalized growth model Least squares estimation Maximum likelihood estimation epidemiological models

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