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Molecular determinants of Antibiotic Resistance in the Costa Rican Pseudomonas aeruginosa AG1 by a Multi-omics Approach:A Review of 10 Years of Study

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Phenomics 2021年第3期1卷 129-142页

作者： Jose Arturo Molina-Mora Fernando García centro de Investigación en Enfermedades tropicales(CIET)&Facultad de Microbiología Universidad de Costa RicaSan JoséCosta Rica

Pseudomonas aeruginosa AG1(PaeAG1)is a Costa Rican strain that was isolated in 2010 in a major *** strain has resistance to multiple antibiotics such asβ-lactams(including carbapenems),aminoglycosides,and ***1 is considered critical(Priority 1)due to its resistance to carbapenems,and it was the first report of a *** isolate carrying both VIM-2 and IMP-18 genes encoding for metallo-β-lactamases(MBL)enzymes(both with carbapenemase activity).Owing to these traits,we have studied this model for 10 years using diverse approaches including *** this review,we summarize the main points of the different steps that we have studied in PaeAG1:preliminary analyses of this strain at the genomic and phenomic levels revealed that this microorganism has particular features of antibiotic *** the multi-omics approach,the genome assembly was the initial step to identify the genomic determinants of this strain,includ-ing virulence factors,antibiotic resistance genes,as well as a complex accessory ***,a comparative genomic approach was implemented to define and update the phylogenetic relationship among complete *** genomes,the genomic island content in other strains,and the architecture of the two MBL-carrying ***,the proteomic profile of PaeAG1 was studied after exposure to antibiotics using 2-dimensional gel electrophoresis(2D-GE).Fourth,to study the central response to multiple perturbations in ***,i.e.,the core perturbome,a machine learning approach was *** analysis revealed biological functions and determinants that are shared by different ***,to evaluate the effects of ciprofloxacin(CIP)on PaeAG1,a growth curve comparison,differential expression analysis(RNA-Seq),and network analysis were *** the results of the core perturbome(pathways that also were found in this perturbation with CIP),it was possible to identify the“exclusive”response and determina

关键词： Pseudomonas aeruginosa PaeAG1 Antibiotic resistance Multi-omics High risk

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Influence of soil and elevation on roadside cryptogam diversity in the tropical Andes

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Forest Ecosystems 2022年第5期9卷 639-646页

作者： Paul Salinas Marina Mazon Vinicio Carrion-Paladines Nixon Cumbicus Patricio Guzman Paolo Giordani Angel Benítez Maestría en Biología de la Conservacion y Ecología Tropical Universidad Tecnica Particular deLojaSan Cayetano Alto s/nLoja1101608Ecuador centro de investigaciones tropicales del Ambiente y Biodiversidad–CITIAB Universidad Nacional de LojaCiudadela Universitariasector La ArgeliaEC 110101LojaEcuador Biodiversidad de Ecosistemas tropicales-BIETROP Herbario HUTPLDepartamento de Ciencias Biologicas y AgropecuariasUniversidad Tecnica Particular de LojaSan Cayetano Alto s/nLoja1101608Ecuador departament of Pharmacy University of GenoaViale Cembrano 416148GenoaItaly

Background: The deforestation caused by road construction is one of the main drivers for both biodiversity and function loss in tropical ecosystems. Terricolous cryptogams are pioneers in colonizing roadside and they are limited by environmental and edaphic factors, thus, cryptogams may act as pioneers for ecosystem rehabilitation at ***: This research was aimed at determining the diversity and composition of terricolous cryptogams, as well as their relationship with elevation and soil properties among roadside of the tropical Andes of Ecuador, in order to establish indicator species of this anthropized ecosystems. Five elevations were selected and in each one 50grids of 20 cm×30 cm were sampled(250 in total along the road), where occurrence, cover and identification of every cryptogam species were recorded. To evaluate the effect of elevation and soil properties on cryptogam richness, a linear model was conducted. Species composition among elevations was compared by non-metric multidimensional scaling(NMDS), and their relationship with the environmental variables through a correlation with adjusted axes was performed. A total of 72 species were recorded, those being 44 bryophytes and 28lichens. Species richness and composition of terricolous cryptogams were influenced by elevation and soil properties, thus the richness is higher at elevations E1, E2 and E3(2600, 2200 and 1800 m a.s.l.), differing from low elevations E4 and E5(1400 and 1000 m a.s.l.). Higher elevations with specific soil conditions(e.g bulk density, nitrogen and silt) harbored different cryptogam communities than those in lower ***: A combination of both elevation and soil properties are shaping the colonization by terricolous cryptogams commnunities. As such, 18 species were identified as the best indicators for all sets of environmental conditions at the roadside, which can therefore be considered for monitoring ecological processes in tropical areas. Use of biocrus

关键词： Bryophytes Indicator species Beta diversity Lichens Richness Ecuador

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The role of shaded cocoa plantations in the maintenance of epiphytic orchids and their interactions with phorophytes

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Journal of Plant Ecology 2020年第1期13卷 27-35页

作者： Jonas Morales-Linares JoséGGarcía-Franco Alejandro Flores-Palacios Thorsten Krömer Tarin Toledo-Aceves Red de Ecología Funcional Instituto de EcologíaA.C.Carretera Antigua a Coatepec 351El HayaXalapa 91070VeracruzMexico centro de Investigación en Biodiversidad y Conservación Universidad Autónoma del Estado de MorelosAv.Universidad 1001Col.ChamilpaCuernavaca 62209MorelosMexico Present address:centro de Investigación en Biodiversidad y Conservación Universidad Autónoma del Estado de MorelosAv.Universidad 1001Col.ChamilpaCuernavaca 62209MorelosMéxico centro de investigaciones tropicales Universidad VeracruzanaJoséMaría Morelos 44-46Zona CentroXalapa 91000VeracruzMexico

Aims Habitat loss and fragmentation are the main threats to biodiversity in tropical *** such as shaded cocoa plantations(SCP)provide refuge for tropical forest ***,it is poorly known whether the interspecific ecological interactions are also maintained in these transformed *** evaluated the diversity,reproductive status and photosynthetic metabolism(CAM or C3)of the epiphytic orchid community,and their interactions with host trees(phorophytes)in SCP compared to tropical rainforest(TRF).Methods In southeastern Mexico,three sites each in TRF and SCP were studied,with four 400 m2 plots established at each site to record all orchids and their *** determined the reproductive(adult)or non-reproductive(juvenile)status of each orchid individual in relation to the presence or absence,respectively,of flowers/fruits(or remnants),and assigned the photosynthetic pathway of each orchid species based in *** used true diversity and ecological networks approaches to analyze orchid diversity and orchid–phorophyte interactions,*** Findings In total,607 individuals belonging to 47 orchid species were *** diversity was higher in TRF(19 effective species)than in SCP(11 effective species)and only seven species were shared between the two *** orchid species were more frequent in SCP(53%)than in TRF(14%).At the community level the proportion of non-reproductive and reproductive orchid species and the nested structure and specialization level of the TRF orchid–phorophyte network were maintained in ***,only a subset of TRF epiphytic orchids remains in SCP,highlighting the importance of protecting *** this difference,shaded agroecosystems such as SCP can maintain some of the diversity and functions of natural forests,since the SCP epiphytic orchid community,mainly composed of CAM species,and its phorophytes constitute a nested interaction network,which would confer robustness to d

关键词： agroecosystem ecological networks Mexico photosynthetic pathway tropical rainforest

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In Silico Pipeline to Identify Tumor‑Specific Antigens for Cancer Immunotherapy Using Exome Sequencing Data

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Phenomics 2023年第2期3卷 130-137页

作者： Diego Morazán‑Fernández Javier Mora Jose Arturo Molina‑Mora Caja Costarricense de Seguro Social San José10104Costa Rica centro de Investigación de Enfermedades tropicales Centro de Investigación en Cirugía y Cáncerand Facultad de MicrobiologíaUniversidad de Costa RicaSan José2060Costa Rica

Tumor-specific antigens or neoantigens are peptides that are expressed only in cancer cells and not in healthy *** of these molecules can induce an immune response,and therefore,their use in immunotherapeutic strategies based on cancer vaccines has been extensively *** based on these approaches have been triggered by the current high-throughput DNA sequencing ***,there is no universal nor straightforward bioinformatic protocol to discover neoan-tigens using DNA sequencing ***,we propose a bioinformatic protocol to detect tumor-specific antigens associated with single nucleotide variants(SNVs)or“mutations”in tumoral *** this purpose,we used publicly available data to build our model,including exome sequencing data from colorectal cancer and healthy cells obtained from a single case,as well as frequent human leukocyte antigen(HLA)class I alleles in a specific *** data from Costa Rican Central Valley population was selected as an *** strategy included three main steps:(1)pre-processing of sequencing data;(2)variant calling analysis to detect tumor-specific SNVs in comparison with healthy tissue;and(3)prediction and characterization of peptides(protein fragments,the tumor-specific antigens)derived from the variants,in the context of their affinity with frequent alleles of the selected *** our model data,we found 28 non-silent SNVs,present in 17 genes in chromosome *** protocol yielded 23 strong binders peptides derived from the SNVs for frequent HLA class I alleles for the Costa Rican *** the analyses were performed as an example to implement the pipeline,to our knowledge,this is the first study of an in silico cancer vaccine using DNA sequencing data in the context of the HLA *** is concluded that the standardized protocol was not only able to identify neoantigens in a specific but also provides a complete pipeline for the eventual design of cancer vaccines using

关键词： Neopeptide Colorectal cancer Cancer vaccine Neoantigens Human leukocyte antigen Costa Rica

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Ethnobotany, Pharmacology and Chemistry of Medicinal Orchids from Veracruz

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Journal of Agricultural Science and Technology(A) 2015年第9期5卷 745-754页

作者： Leticia Margarita Cano Asseleih Rebeca Alicia Menchaca Garcia Jose Yader Sageth Ruiz Cruz centro de lnvestigaciones tropicales (ClTRO) Universidad Veracruzana Xalapa 91000 Mexico

Orchidaceae is a large family of 1,260 species in Mexico, of which 433 grow in the state of Veracruz, Mexico. Although economically important in horticulture because of the beauty of their flowers, researches have done little work regarding their medicinal properties. This paper aimed to present the results of ethnobotanical, pharmacological and active compounds research on Veracruz medicinal orchids. The ethnobotanical information was obtained by consulting the Atlas of the Mexican Traditional Medicine Plants, Veracruz Medicinal Flora Database （CITRO-UV project） and through field work in the Nahuatl community of Cuautlajapa, Veracruz. To obtain pharmacological and active compounds information of registered species, a search was carded out through MEDLINE （USA National Library of Medicine Journal Citation database）. Twelve medicinal orchids were recorded for Veracruz, i.e., Epidendrum chlorocorymbos Schltr., Habenaria floribunda Lindl., Isochillus latibracteatus A. Rich. ＆ Galeotti, lsochillus major Schltdl. ＆ Cham., Mormodes maculata var. unicolor （Hook.） L. O. Williams, Oestlundia luteorosea （A. Rich. ＆ Galeotti） W. E. Higgins, Oncidium ascendens Lindl., Scaphyglottis fasciculata Hook., Sobralia macrantha Lindl., Spiranthes eriophora （Rob. ＆ Greenm.）, Stanhopea oculata （G. Lodd.） Lindl. and Vanilla planifolia Andrews. Only two species have been investigated in terms of their pharmacology and active compounds. Also, information for another five species closely related to already identified ones was obtained. Given the relative poverty of current information on the topic, this paper demonstrates the need to further study the ethnobotanical, pharmacological and chemical aspects of the region＇s medicinal orchids.

关键词： Orchids medicinal orchids traditional medicine Veracruz medicinal orchids.

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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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银屑病患者中链球菌M蛋白引发的外周血单核细胞增生及Th1/Th2细胞因子产物

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世界核心医学期刊文摘（皮肤病学分册） 2006年第8期2卷 32-33页

作者： Pérez-Lorenzo R. Núez-Oreza L.A. Garma-Quen P.M. 潘敏 centro de investigaciones en Enfermedades tropicales Universidad Autó noma de Campeche Ciudad Universitaria s/n 24030 Campeche Mexico

Background: Psoriasis is a chronic skin disease that is probably a T cell-mediated autoimmune condition which is strongly associated with streptococcal throat infections. Although some groups have associated the involved response with different streptococcal antigens, M protein has been described as the major virulence factor of Streptococcus pyogenes. Thus, it is necessary to describe some features of the cellular responses to this streptococcal antigen. Methods: Proliferation and Th1/Th2 cytokine production of peripheral blood mononuclear cells (PBMC) in response to total soluble extracts from type M5 S. pyogenes with (TSE37Sp) and without (M-TSESp) M protein were analyzed in 10 psoriatic patients and 10 healthy controls. Results: PBMC from both patients and controls proliferated to both extracts. Responses to M-TSESp were significantly lower than those to TSE37Sp (P ded to TSE37Sp with a much higher production of this cytokine as compared to the responses showed to M-TSESp while the cells from psoriatic patients responded without differences in the production of IL- 10. Conclusion: Results obtained suggest an important Th1 response to M protein in psoriatic patients which could be associated with the cellular responses involved in psoriasis, while healthy subjects respond in a probably non-Th2 IL- 10 producing regulatory T cells fashion.

关键词：细胞因子产物 Th1/Th2 外周血单核细胞单核细胞增生链球菌M蛋白银屑病患者化脓性链球菌链球菌抗原反应特征慢性皮肤病

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Evaluation of the Synergistic Effect of EDTA-Functionalized Chitosan Nanoparticles on Imipenem delivery in Pseudomonas aeruginosa Carbapenem-Resistant Strain AG1

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Journal of Biomaterials and Nanobiotechnology 2018年第1期9卷 64-78页

作者： Marilyn Porras-Gomez Jose Vega-Baudrit Fernando Garcia Santiago Nunez-Corrales Sergio Madrigal-Carballo National Nanotechnology Laboratory(LANOTEC) National Center for Advanced Technology Studies(CeNAT)San JoseCosta Rica centro de investigaciones en Enfermedades tropicales(CIET) Facultad de MicrobiologiaUniversidad de Costa RicaSan PedroCosta Rica National Center for Biotechnological Innovations(CENIBiot) National Center for Advanced Technology Studies(CeNAT)San JoseCosta Rica

Metallo-β-lactamases are bacterial zinc-dependent enzymes involved in the hydrolysis of β-lactamic antibiotics representing the main cause of bacterial resistance to carbapenems, drugs of last resort for treating infections caused by multiresistant bacteria. We elaborated the hypothesis that it is possible to inhibit the enzymatic activity of metallo-β-lactamases by lowering the availability of zinc in the extracellular medium using metal chelating agents such as EDTA carried on nanoparticles. Chitosan, as linear cationic polysaccharide is frequently used in biomedical and pharmaceutical applications, has been studied as a biocompatible encapsulating agent in drug delivery systems and is an ideal transport agent for bioactive molecular complexes in antibiotic applications due to its ability to associate with negatively charged substances. We developed novel nanoparticles using chitosan as a transport matrix for β-lactamic antibiotics. Nanoparticles were synthesized according to the ion gelation method using tripolyphosphate as crosslinking agent. Nanoparticles were functionalized by the adsorption of EDTA, which acts as complexifying agent for Zn2+ ions causing inhibition of metallo-β-lactamases activity. We evaluate the antimicrobial effects of EDTA-functionalized nanoparticles with an imipenem cargo on the clinical isolate P. aeruginosa AG1, a carbapenem-resistant high-risk clone ST-111 carrying both blaIMP-18 and blaVIM-2 metallo-β-lactamases genes.

关键词： Chitosan EDTA Nanoparticles Drug-Resistant Imipenem

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Communities and service providers address access to perinatal care in postconflict Northern Uganda:socialising evidence for participatory action

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Family Medicine and Community Health 2021年第2期9卷 1-10页

作者： Loubna Belaid Pamela Atim Eunice Atim Emmanuel Ochola Martin Ogwang Pontius Bayo Janet Oola Isaac Wonyima Okello Ivan Sarmiento Laura Rojas-Rozo Kate Zinszer Christina Zarowsky Neil Andersson CIET/PRAM Family Medicine McGill UniversityMontrealQuébecCanada Public Health Gulu UniversityGuluUganda Maternal and child health Nwoya Health DistrictNwoyaUganda St Mary's Lacor Hospital GuluUganda Family Medicine McGill UniversityMontrealQuébecCanada Preventive and social medicine University of MontrealMontrealQuébecCanada Universidad Autónoma de Guerrero Centro de Investigación de Enfermedades TropicalesAcapulcoMexico

Objectives describe participatory codesign of interventions to improve access to perinatal care services in Northern *** design Mixed-methods participatory research to codesign increased access to perinatal *** cognitive mapping,focus groups and a household survey identified and documented the extent of obstructions to *** dialogue focused stakeholder discussions of this evidence to address the obstacles to *** significant change stories explored the participant experience of this *** Three parishes in Nwoya district in the Gulu region,Northern *** Purposively sampled groups of women,men,female youth,male youth,community health workers,traditional midwives and service *** of seven stakeholder categories included 5-8 participants in each of three *** Stakeholders identified several obstructions to accessing perinatal care:lack of savings in preparation for childbirth in facility costs,lack of male support and poor service provider *** suggested joining saving groups,practising saving money and income generation to address the short-term financial *** recommended increasing spousal awareness of perinatal care and they proposed improving service provider *** described their own improved care-seeking behaviour and patient-provider relationships as short-term gains of the *** Participatory service improvement is feasible and acceptable in postconflict settings like Northern *** communities in identifying perinatal service delivery issues and reflecting on local evidence about these issues generate workable community-led solutions and increases trust between community members and service providers.

关键词： service services action

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