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Why and how to use the SeqCode

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mLife 2024年第1期3卷 1-13页

作者： Wiliam B.Whitman maria Chuvochina Brian P.Hedlund Konstantinos T.Konstantinidis marike Palmer Luis m.rodriguez-R lain Sutcliffe Fengping Wang Deparment of microbioogy University of GeorgiaAthensGeorgiaUAA Schoolof Chemistry and molecular Biosciences Australian CentreforEogenomicsThe Universty of QueenslandSt LuciaAustralia University of Nevada Las Vegas Las VegasNevadaUSA Schol of Civil and Environmental Engineering and School of Biological SciencesGeorgia Institute of TechnologyAtlantaGeorgiaUSA Department of microbiology University of ManitobaWinnipegManitobaCanada School of Life Sciences University of Nevada Las VegasLas VegasNevadaUSA Department of microbiology and Digital Science Center(DiSC) University of InnsbruckInnsbruckAustria Faculty of Health&Life Sciences Northumbria UniversityNewcastle upon TyneUK School of Oceanography International Center for Deep Life InvestigationShanghai Jiao Tong UniversityShanghaiChina

The SeqCode,formally called the Code of Nomenclature of Prokaryotes Described from Sequence Data,is a new code of nomenclature in which genome sequences are the nomenclatural types for the names of prokaryotic *** similar to the International Code of Nomenclature of Prokaryotes(ICNP)in structure and rules of priority,it does not require the deposition of type strains in international culture ***,it allows for the formation of permanent names for uncultured prokaryotes whose nearly complete genome sequences have been obtained directly from environmental DNA as well as other prokaryotes that cannot be deposited in culture *** the diversity of uncultured prokaryotes greatly exceeds that of readily culturable prokaryotes,the SeqCode is the only code suitable for naming the majority of prokaryotic *** start date of the SeqCode was January 1,2022,and the online Registry(https://***)was created to ensure valid publication of *** SeqCode recognizes all names validly published under the ICNP before *** that date,names validly published under the SeqCode compete with ICNP names for *** a result,species can have only one name,either from the SeqCode or ICNP,enabling effective communication and the creation of unified taxonomies of uncultured and cultured *** SeqCode is administered by the SeqCode Committee,which is comprised of the SeqCode Community and elected administrative *** with an interest in the systematics of prokaryotes is encouraged to join the SeqCode Community and participate in the development of this resource.

关键词： genome sequences metagenome-assembled genomes nomenclature SeqCode

Energy model based on solar potential and the production of electrical energy through living plants’photosynthesis

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Clean Energy 2024年第3期8卷 116-126页

作者： Raymond Daniel rodriguez martinez Department of Industrial Production Faculty of EngineeringUniversidad Metropolitana1073 CaracasVenezuela

Developing a sustainable energy model is imperative considering the current trend towards decarbonizing sectors *** this purpose,Venezuela was used as a reference to propose an energy model focused on taking advantage of plant photosynthesis through microbial-vegetable fuel cells together with an agro-photovoltaic system to enhance energy and agricultural *** production from the cells was estimated using an average power density of 264 mW/m^(2) over 4%of the areas destined for crops in the entire Venezuelan region,obtaining an annual production of 19.889 GWh/*** contrast,the energy production of the agro-photovoltaic system was modelled using PVsyst software on 50%of the area used for the cells distributed throughout the states of Anzoátegui,Guárico,monagas and Portuguesa according to their meteorological conditions,solar irradiation and agricultural activity,resulting in 3703417 GWh/*** resulting whole system proved to be able to cover>10 times the installed electricity generation capacity at a national level and,together with the tremendous scalability of the microbial fuel cells,it shows that Venezuela has a high potential for the production and distribution of clean energy.

关键词： ecosystems microbial fuel cell microorganisms renewable sustainability

microRNA-502-3p regulates GABAergic synapse function in hippocampal neurons

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Neural Regeneration Research 2024年第12期19卷 2698-2707页

作者： Bhupender Sharma melissa mTorres Sheryl rodriguez Laxman Gangwani Subodh Kumar Center of Emphasis in Neuroscience Department of Molecular and Translational MedicinePaul L.Foster School of MedicineTexas Tech University Health Sciences CenterEl PasoTXUSA Bond Life Sciences Center and Department of Veterinary Pathobiology University of MissouriColumbiaMOUSA L.Frederick Francis Graduate School of Biomedical Sciences Texas Tech University Health Sciences CenterEl PasoTXUSA

Gamma-aminobutyric acid(GABA)ergic neurons,the most abundant inhibitory neurons in the human brain,have been found to be reduced in many neurological disorders,including Alzheimer's disease and Alzheimer's disease-related *** previous study identified the upregulation of microRNA-502-3p(miR-502-3p)and downregulation of GABA type A receptor subunitα-1 in Alzheimer's disease *** study investigated a new molecular relationship between miR-502-3p and GABAergic synapse *** vitro studies were perfo rmed using the mouse hippocampal neuronal cell line HT22 and miR-502-3p agomiRs and *** silico analysis identified multiple binding sites of miR-502-3p at GABA type A receptor subunitα-1 *** assay confirmed that miR-502-3p targets the GABA type A receptor subunitα-1 gene and suppresses the luciferase ***,quantitative reve rse transcription-polymerase chain reaction,miRNA in situ hybridization,immunoblotting,and immunostaining analysis confirmed that overexpression of miR-502-3p reduced the GABA type A receptor subunitα-1 level,while suppression of miR-502-3p increased the level of GABA type A receptor subunitα-1 ***,as a result of the overexpression of miR-502-3p,cell viability was found to be reduced,and the population of necrotic cells was found to be *** whole cell patch-clamp analysis of human-GABA receptor A-α1/β3/γ2L human embryonic kidney(HEK)recombinant cell line also showed that overexpression of miR-502-3p reduced the GABA current and overall GABA function,suggesting a negative correlation between miR-502-3p levels and GABAergic synapse ***,the levels of proteins associated with Alzheimer s disease were high with miR-502-3p overexpression and reduced with miR-502-3p *** present study provides insight into the molecular mechanism of regulation of GABAergic synapses by *** propose that micro-RNA,in particular miR-502-3p,could be a potential the

关键词： Alzheimer's disease GABAergic synapse gamma-aminobutyric acid type A receptor subunitα-1(GABRα1) microRNA-502-3p(miR-502-3p) miRNA in situ hybridization Patch-clamp

In‑depth proteome characterization of endometrium and extraembryonic membranes during implantation in pig

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Journal of Animal Science and Biotechnology 2024年第3期15卷 1027-1055页

作者： maria A.Gil Josep m.Cambra Heriberto rodriguez‑martinez Cristina Cuello Inmaculada Parrilla Emilio A.martinez Department of medicine and Animal Surgery International Excellence Campus for Higher Education and Research“Campus Mare Nostrum”University of MurciaMurciaSpain Institute for Biomedical Research of murcia(ImIB-Pascual Parrilla) MurciaSpain Technical University of munich MunichGermany Department of Biomedical&Clinical Sciences(BKV) BKH/Obstetrics&GynaecologyLinkoping UniversityLinkopingSweden

Background Proteome characterization of the porcine endometrium and extraembryonic membranes is important to understand mother-embryo *** this study,the proteome of the endometrium and cho-rioallantoic membrane was characterized in pregnant sows(PS)during early gestation(d 18 and 24 of gestation)and in the endometrium of non-pregnant sows(NPS)during the same days using LC-mS/mS *** UniProtKB database and ClueGO were used to obtain functional Gene Ontology annotations and biological and functional networks,*** Our analysis yielded 3,254 and 3,457 proteins identified in the endometrium of PS and NPS,respectively;of these,1,753 being common while 1,501 and 1,704 were exclusive to PS and NPS,*** addition,we iden-tified 3,968 proteins in the extraembryonic membranes of *** analyses of function revealed some proteins had relevance for the immune system process and biological adhesion in endometrium while the embryonic chorion displayed abundance of proteins related to cell adhesion and cytoskeletal organization,suggesting they dominated the moment of endometrial remodeling,implantation and adhesion of the lining *** are available via Pro-teomeXchange with identifier *** This is the first in-depth proteomic characterization of the endometrium and extraembryonic mem-branes during weeks 3 to 4 of gestation;data that contribute to the molecular understanding of the dynamic environ-ment during this critical period,associated with the majority of pregnancy losses.

关键词： Endometrium Extraembryonic membranes Implantation Pig Proteome

Identific tion of quantitative trait loci and associated candidate genes for pregnancy success in Angus–Brahman crossbred heifers

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Journal of Animal Science and Biotechnology 2024年第1期15卷 162-170页

作者： Quinn A.Hoorn Gabriel A.Zayas Eduardo E.rodriguez Laura m.Jensen Raluca G.mateescu Peter J.Hansen Department of Animal Sciences Donald Henry Barron Reproductive and Perinatal Biology Research Programand the Genetics InstituteUniversity of FloridaGainesvilleFLUSA School of Applied Systems Biology La Trobe UniversityBundooraVIC 3083Australia

Background In beef cattle, more than 50% of the energy input to produce a unit of beef is consumed by the female that produced the calf. Development of genomic tools to identify females with high genetic merit for reproductive function could increase the profitability and sustainability of beef *** Genome-wide association studies(GWAS) were performed using a single-step genomic best linear unbiased prediction approach on pregnancy outcome traits from a population of Angus–Brahman crossbred heifers. Furthermore, a validation GWAS was performed using data from another farm. Heifers were genotyped with the Bovine GGP F250 array that contains 221,077 SNPs. In the discovery population, heifers were bred in winter breeding seasons involving a single round of timed artificial insemination(AI) followed by natural mating for 3 months. Two phenotypes were analyzed: pregnancy outcome to first-service AI(PAI;n = 1,481) and pregnancy status at the end of the breeding season(PEBS;n = 1,725). The heritability was estimated as 0.149 and 0.122 for PAI and PEBS, respectively. In the PAI model, one quantitative trait locus(QTL), located between 52.3 and 52.5 mb on BTA7, explained about 3% of the genetic variation, in a region containing a cluster of γ-protocadherin genes and SLC25A2. Other QTLs explaining between 0.5% and 1% of the genetic variation were found on BTA12 and 25. In the PEBS model, a large QTL on BTA7 was synonymous with the QTL for PAI, with minor QTLs located on BTA5, 9, 10, 11, 19, and 20. The validation population for pregnancy status at the end of the breeding season were Angus–Brahman crossbred heifers bred by natural mating. In concordance with the discovery population, the large QTL on BTA7 and QTLs on BTA10 and 12 were *** In summary, QTLs and candidate SNPs identified were associated with pregnancy outcomes in beef heifers, including a large QTL associated with a group of protocadherin genes. Confirmation of these associations

关键词： Beef cattle Fertility GWAS QTL

Efficient removal of the recalcitrant metamizole contaminant from drinking water by using a CaLaCoO_(9) perovskite supported on recycled polyethylene

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Journal of Environmental Sciences 2024年第2期136卷 56-67页

作者： Ernesto Valadez-Renteria Christian Perez-Carrasco Dulce Yolotzin medina-Velazquez Vicente rodriguez-Gonzalez Jorge Oliva CONACYT-División de materiales Avanzados Instituto Potosino de Investigación Científica y Tecnológica A.C.San Luis PotosíSLP 78216México División de Ciencias Básicas e Ingeniería Universidad Autónoma Metropolitana AzcapotzalcoCol.Reynosa-TamaulipasC.P.MéxicoDF 02200México

metamizole(mZ)is a widely used anti-inflammatory *** to its common use,this contaminant is found in sewage and *** order to reduce the contamination produced by the mZ,we fabricated in this work a photocatalytic composite using recycled polyethylene(RPE)and the CaLaCoO_(9)(LCCO)*** nanoparticles had a microplate-like morphology and sizes of 1.4–5.5μm according to the analysis of *** photocatalytic properties of the LCCO powders were evaluated under ultraviolet-visible(UV-Vis)irradiation and found a removal efficiency of 96%.When the RPE+LCCO composite was employed for the photocatalytic degradation of mZ,a maximum degradation of 92.5%was *** influence of the pH on the photocatalytic activity was also studied and found that an initial pH=3 produced a total degradation of mZ after 240 min of UV-Vis ***,three reuse cycles were carried out for the pure LCCO powders and for the RPE+LCCO composites and found that the maximum loss of degradation was 5%.Furthermore,scavenger experiments demonstrated that the super oxide and hydroxyl radicals are formed during the photocatalytic reaction and were responsible for the degradation of ***,the X-ray photoelectron-spectroscopy and Raman analysis demonstrated the formation of defects(oxygen vacancies),those ones delayed the electron-hole recombination,which in turn,enhanced the degradation of the ***,the studies performed in this work proved that composites made with recycled plastics and LCCO perovskites are a low-cost and feasible alternative for the cleaning of water sources polluted with pharmaceutical compounds.

关键词： Photocatalysis metamizole Pharmaceutical contaminant UV-Vis irradiation Perovskite

Pelleting and particle size reduction of corn increase net energy and digestibility of fiber,protein,and fat in corn-soybean meal diets fed to group-housed pigs

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Journal of Animal Science and Biotechnology 2024年第4期15卷 1751-1760页

作者： Su A Lee Diego A.rodriguez Chad B.Paulk Hans H.Stein Department of Animal Sciences University of IllinoisUrbanaIL 61801USA Department of Grain Sciences and Industry Kansas State UniversityManhattanKS 66506USA

Background Reduction of the particle size of corn increases energy digestibility and concentrations of digestible and metabolizable *** may also reduce particle size of grain,but it is not known if there are interactions between particle size reduction and *** objective of this experiment was to test the hypothesis that particle size reduction and pelleting,separately or in combination,increase N balance,apparent total tract digestibility(ATTD)of fiber and fat,and net energy(NE)in corn-soybean meal diets fed to group-housed *** Six corn-soybean meal-based diets were used in a 3×2 factorial design with 3 particle sizes of corn(i.e.,700,500,or 300μm)and 2 diet forms(i.e.,meal or pelleted).Pigs were allowed ad libitum access to feed and ***-four castrated male pigs(initial weight:29.52 kg;standard diviation:1.40)were allotted to the 6 diets using a 6×6 Latin square design with 6 calorimeter chambers(i.e.,4 pigs/chamber)and 6 *** consumption and CO_(2)and CH_(4)productions were measured during fed and fasting states and fecal and urine samples were *** Regardless of particle size of corn,the ATTD of gross energy(GE),N,and acid-hydrolyzed ether extract(AEE),and the concentration of NE were greater(Pmeal *** of diet form,the ATTD of GE,N,and AEE,and the concentration of NE were increased(linear;Pmeal diets than in pelleted diets(interaction;Pmeal diets than in pelleted diets.

关键词： Corn Digestibility Feed technology Net energy Particle size Pelleting

Histopathological impact of SARS-CoV-2 on the liver:Cellular damage and long-term complications

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World Journal of Gastroenterology 2024年第22期30卷 2866-2880页

作者： Alfonso rodriguez-Espada moises Salgado-de la mora Briana mariette rodriguez-Paniagua Nathaly Limonde la Rosa monica Itzel martinez-Gutierrez Santiago Pastrana-Brandes Nalu Navarro-Alvarez Department of molecular Biology Universidad Panamericana School of MedicineCampus MéxicoMexico 03920Mexico Department of Internal medicine Instituto Nacional de Ciencias Médicas y Nutrición Salvador ZubiránMexico 14080Mexico Department of Surgery University of Colorado Anschutz Medical CampusDenverCO 80045United States PECEm Facultad de MedicinaUniversidad Nacional Autónoma de MéxicoMexico 04360Mexico Department of Gastroenterology Instituto Nacional de Ciencias Médicas y Nutrición Salvador ZubiránMexico 14080Mexico

Coronavirus disease 2019(COVID-19),caused by the highly pathogenic severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),primarily impacts the respiratory tract and can lead to severe outcomes such as acute respiratory distress syndrome,multiple organ failure,and *** extensive studies on the pathogenicity of SARS-CoV-2,its impact on the hepatobiliary system remains *** liver injury is commonly indicated by reduced albumin and elevated bilirubin and transaminase levels,the exact source of this damage is not fully *** mechanisms for injury include direct cytotoxicity,collateral damage from inflammation,drug-induced liver injury,and ischemia/***,evidence often relies on blood tests with liver enzyme *** this comprehensive review,we focused solely on the different histopathological manifestations of liver injury in COVID-19 patients,drawing from liver biopsies,complete autopsies,and in vitro liver *** present evidence of the direct impact of SARS-CoV-2 on the liver,substantiated by in vitro observations of viral entry mechanisms and the actual presence of viral particles in liver samples resulting in a variety of cellular changes,including mitochondrial swelling,endoplasmic reticulum dilatation,and hepatocyte *** ly,we describe the diverse liver pathology observed during COVID-19 infection,encompassing necrosis,steatosis,cholestasis,and lobular *** also discuss the emergence of long-term complications,notably COVID-19-related secondary sclerosing *** the histopathological liver changes occurring during COVID-19 infection is pivotal for improving patient recovery and guiding decision-making.

关键词： Liver SARS-CoV-2 COVID-19 Angiotensin-converting enzyme 2 Histopathology Liver biopsies Liver autopsy In vitro

Exploring the genetic control of sweat gland characteristics in beef cattle for enhanced heat tolerance

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Journal of Animal Science and Biotechnology 2024年第5期15卷 1820-1831页

作者： Aakilah S.Hernandez Gabriel A.Zayas Eduardo E.rodriguez Kaitlyn m.Sarlo Davila Fahad Rafiq Andrea N.Nunez Cristiane Goncalves Titto Raluca G.mateescu Department of Animal Science North Carolina State UniversityRaleighNCUSA Department of Animal Sciences University of FloridaGainesvilleFLUSA. Ruminant Diseases and Immunology Research Unit National Animal Disease CentersUnited States Department of Agriculture1920 Dayton AvenueAmesIA 50010USA. Department of Animal Science Iowa StateAmesIAUSA School of Animal Sciences and Food Engineering University of Sao PauloAv Duque de Caxias Norte 225PirassunungaSao Paulo 13635‑900Brazil

Background Thermal stress in subtropical regions is a major limiting factor in beef cattle production systems with around$369 million being lost annually due to reduced *** stress causes numerous physiological and behavioral disturbances including reduced feed intake and decreased production *** utilize various physiological mechanisms such as sweating to regulate internal *** in these traits can help identify genetic variants that control sweat gland properties and subsequently allow for genetic selection of cattle with greater *** This study used 2,401 Brangus cattle from two commercial ranches in *** phenotypes that contribute to an animal's ability to manage heat stress were calculated from skin biopsies and included sweat gland area,sweat gland depth,and sweat gland *** animals were genotyped with the Bovine GGP F250K,and BLUPF90 software was used to estimate genetic parameters and for Genome Wide Association *** Sweat gland phenotypes heritability ranged from 0.17 to 0.42 indicating a moderate amount of the phenotypic variation is due to genetics,allowing producers the ability to select for favorable sweat gland properties.A weighted single-step GWAS using sliding 10 kb windows identified multiple quantitative trait loci(QTLs)explaining a significant amount of genetic *** located on BTA7 and BTA12 explained over 1.0%of genetic variance and overlap the ADGRV1 and CCDC168 genes,*** variants identified in this study are implicated in processes related to immune function and cellular proliferation which could be relevant to heat *** of Origin Alleles(BOA)were predicted using local ancestry in admixed populations(LAmP-LD),allowing for identification of markers'origin from either Brahman or Angus ancestry.A BOA GWAS was performed to identify regions inherited from particular ancestral breeds that might have a significant impact on sweat gland pheno

关键词： GWAS Heritability Skin Thermotolerance