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Evaluating the potential of(epi)genotype‑by‑low pass nanopore sequencing in dairy cattle:a study on direct genomic value and methylation analysis

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Journal of Animal Science and Biotechnology 2023年第6期14卷 2276-2289页

作者： oscar gonzalez‑recio Adrian Lopez‑Catalina Ramon Peiro‑Pastor Alicia Nieto‑Valle Monica Castro Almudena Fernandez Dpt.Mejora Genetica Animal INIA-CSICCtra La Coruna Km 7.528040 MadridSpain. ETSIAAB Universidad Politecnica de Madrid.Ciudad Universitaria S/N28040 MadridSpain.

Background Genotype-by-sequencing has been proposed as an alternative to SNP genotyping arrays in genomic selection to obtain a high density of markers along the genome.It requires a low sequencing depth to be cost effective,which may increase the error at the genotype assigment.Third generation nanopore sequencing technology offers low cost sequencing and the possibility to detect genome methylation,which provides added value to genotype-by-sequencing.The aim of this study was to evaluate the performance of genotype-by-low pass nanopore sequencing for estimating the direct genomic value in dairy cattle,and the possibility to obtain methylation marks simultaneously.Results Latest nanopore chemistry(LSK14 and Q20)achieved a modal base calling accuracy of 99.55%,whereas previous kit(LSK109)achieved slightly lower accuracy(99.1%).The direct genomic value accuracy from genotype-by-low pass sequencing ranged between 0.79 and 0.99,depending on the trait(milk,fat or protein yield),with a sequencing depth as low as 2×and using the latest chemistry(LSK114).Lower sequencing depth led to biased estimates,yet with high rank correlations.The LSK109 and Q20 achieved lower accuracies(0.57-0.93).More than one million high reliable methylated sites were obtained,even at low sequencing depth,located mainly in distal intergenic(87%)and promoter(5%)regions.Conclusions This study showed that the latest nanopore technology in useful in a LowPass sequencing framework to estimate direct genomic values with high reliability.It may provide advantages in populations with no available SNP chip,or when a large density of markers with a wide range of allele frequencies is needed.In addition,low pass sequencing provided nucleotide methylation status of>1 million nucleotides at≥10×,which is an added value for epigenetic studies.

关键词： Genomic selection Genomic values Low pass sequencing Low sequencing imputation Polygenic risk score

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Glial plasticity after hexahydrobenzene exposure

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Neural Regeneration Research 2016年第3期11卷 404-405页

作者： Tania Campos-Ordonez oscar gonzalez-Perez Laboratory of Neurobiology School of PsychologyUniversity of Colima Medical Sciences PhD Program School of MedicineUniversity of Colima

The organic solvents are not only utilized in industrial processes,but also as drugs of abuse.In fact,solvent consumption represents the fourth option for drug users just after alcohol,tobacco and marijuana.In humans,... 详细信息

关键词： intentional tobacco plasticity utilized volatile alcohol exposure abuse morphological microglia

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Emerging roles of microglia cells in the regulation of adult neural stem cells

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Neuroimmunology and Neuroinflammation 2016年第1期3卷 204-206页

作者： Eduardo Lira-Diaz oscar gonzalez-Perez Laboratory of Neuroscience School of PsychologyUniversity of ColimaColima 28040Mexico Medical Sciences PhD Program School of MedicineUniversity of ColimaColima 28040Mexico

MICROGLIA CELLS Microglia cells are antigen presenting cells with myeloid origin that constituted approximately 10%of all glial cells of the adult mouse brain.^([1])In the early embryo,the microglial precursors are located in the yolk sac and progressively migrate throughout the primitive brain.^([2])In the adult brain,some of microglial cells derive from the bone marrow,but this process only takes place when the brain is lesioned.^([1])Microglial cells can display 4 morphological and functional stages:(1)resting microglia;(2)active microglia;(3)phagocytic microglia;and(4)senescent microglia.

关键词： neural migrate adult

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Portal hypertensive colopathy is associated with portal hypertension severity in cirrhotic patients

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World Journal of Gastroenterology 2009年第38期15卷 4781-4787页

作者： Antonio Diaz-Sanchez oscar Nuez-Martinez Cecilia gonzalez-Asanza Ana Matilla Beatriz Merino Diego Rincon Inmaculada Beceiro Maria Vega Catalina Magdalena Salcedo Rafael Baares Gerardo Clemente Liver Unit-CIBEREHD.Hospital General Universitario Gregorio Maraón Madrid 28007Spain Gastroenterology Unit Hospital Infanta Leonor Gastroenterology Unit Hospital Infanta Sofia Department of Gastroenterology Hospital Universitario Príncipe de Asturias

AIM:To assess the prevalence of portal hypertension (PH) related colorectal lesions in liver transplant candidates, and to evaluate its association with the severity of PH.METHODS: Between October 2004 and December 2005, colonoscopy was performed in 92 cirrhotic liver transplant candidates. We described the lesions resulting from colorectal PH and their association with the grade of PH in 77 patients who underwent measurement of hepatic venous pressure gradient (HVPG).RESULTS: Mean age was 55 years and 80.7% of patients were men. The main etiology of cirrhosis was alcoholism (45.5%). Portal hypertensive colopathy (PHC) was found in 23.9%, colonic varices in 7.6% and polyps in 38% of patients (adenomatous type 65.2%). One asymptomatic patient had a well-differentiated adenocarcinoma. The manifestations of colorectal PH were not associated with the etiology of liver disease or with the Child-Pugh grade. Ninety percent of patients with colopathy presented with gastroesopha-geal varices (GEV), and 27.5% of patients with GEV presented with colopathy (P=0.12). A relationship between higher values of HVPG and presence of col-opathy was observed (19.9±6.2 mmHg vs 16.8±5.4 mmHg, P=0.045), but not with the grade of col-opathy (P=0.13). Preneoplastic polyps and neoplasm (P=0.02) and spontaneous bacterial peritonitis (P=0.006) were more prevalent in patients with colopathy. We did not observe any association between previous β-blocker therapy and the presence of colorectal portal hypertensive vasculopathy.CONCLUSION: PHC is common in cirrhotic liver trans-plant candidates and is associated with higher portal pressure.

关键词：严重程度门静脉肝硬化患者高压结肠压性

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基于远缘学科交叉的音乐学研究与实践

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南京航空航天大学学报（社会科学版） 2022年第4期24卷 164-168页

作者：板俊荣张进孙丽君 oscar Caravaca gonzalez 南京航空航天大学艺术学院江苏南京211106

推进学科交叉已成为当前学术研究和学科特色发展领域的共识。当前近缘学科之间的交叉融合能够顺利推进,但远缘学科之间的跨度较大,交叉融合不易,成果产出非常困难。借助学校学科发展优势,从解决学科间的沟通交流障碍与学术话语分歧,组... 详细信息

推进学科交叉已成为当前学术研究和学科特色发展领域的共识。当前近缘学科之间的交叉融合能够顺利推进,但远缘学科之间的跨度较大,交叉融合不易,成果产出非常困难。借助学校学科发展优势,从解决学科间的沟通交流障碍与学术话语分歧,组建远缘学科交叉融合团队,探索创新成果形成的机理等层面入手,推进艺术学科与工科之间的交叉融合发展。

关键词：艺工融合学科交叉音乐认知

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Astrocytes:everything but the glue

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Neuroimmunology and Neuroinflammation 2015年第1期2卷 115-117页

作者： oscar gonzalez-Perez Veronica Lopez-Virgen Alfredo Quiñones-Hinojosa Laboratory of Neuroscience School of PsychologyUniversity of ColimaColimaCol 28040Mexico Department of Neurosurgery Johns Hopkins School of MedicineBaltimoreMD 21201USA

The current knowledge in neuroscience indicates that the neural tissue has two major cell populations:neurons and glia(term derived from the Greek word for glue).Neuronal population is characterized by the capacity to produce action potentials,whereas glial cells are typically identified as the subordinate cell population of neurons.Till date,this point of view has changed dramatically,and growing evidence indicates that glial cells play a crucial role in normal mental functions and the pathogenesis of neurological diseases.

关键词： neural knowledge typically

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Construction of aboveground biomass models with remote sensing technology in the intertropical zone in Mexico

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Journal of Geographical Sciences 2012年第4期22卷 669-680页

作者： AGUIRRE-SALADO Carlos Arturo TREVINO-GARZA Eduardo Javier AGUIRRE-CALDERON oscar Alberto JIMENEZ-PiEREZ Javier gonzalez-TAGLE Marco Aurelio VALDEZ-LAZALDE Jose Rene M IRANDA-ARAGON Liliana AGUIRRE-SALADO Alejandro lvan Autonomous University of Nuevo Leon Linares NL 67700 Mexico Autonomous University of San Luis Potosi SLP 78290 Mexico The College of Postgraduates Texcoco MEX 56230 Mexico

Spatially-explicit estimation of aboveground biomass （AGB） plays an important role to generate action policies focused in climate change mitigation, since carbon （C） retained in the biomass is vital for regulating Earth＇s temperature. This work estimates AGB using both chlorophyll （red, near infrared） and moisture （middle infrared） based normalized vegetation indices constructed with MCD43A4 MODerate-resolution Imaging Spectroradiometer （MODIS） and MOD44B vegetation continuous fields （VCF） data. The study area is located in San Luis Potosi, Mexico, a region that comprises a part of the upper limit of the intertropical zone. AGB estimations were made using both individual tree data from the National Forest Inventory of Mexico and allometric equations reported in scientific literature. Linear and nonlinear （expo- nential） models were fitted to find their predictive potential when using satellite spectral data as explanatory variables. Highly-significant correlations （p = 0.01 ） were found between all the explaining variables tested. NDVI62, linked to chlorophyll content and moisture stress, showed the highest correlation. The best model （nonlinear） showed an index of fit （Pseudo - r2） equal to 0.77 and a root mean square error equal to 26.00 Mg/ha using NDVI62 and VCF as explanatory variables. Validation correlation coefficients were similar for both models： linear （r = 0.87＊＊） and nonlinear （r = 0.86＊＊）.

关键词： MODIS MCD43A4 MOD44B forest inventory regression

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Sexist Prejudice of Primary School Children in Different Urban and Rural Contexts of Spain

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Journal of Contemporary Educational Research 2018年第4期2卷 6-9页

作者： oscar Navarro Juana Maria Anguita Angel Luis gonzalez Francisco Javier Sanchez-Verdejo Department of Pedagogy University of Castilla-La ManchaCiudad RealSpain

At present,a great deal of historical gender prejudice is still visible in society.It is essential to eliminate these invisible barriers that impede achieving real equality between men and women.This article seeks to provide a vision of the perception of primary school girls and boys regarding the masculine and feminine genders.A questionnaire was given to groups of schoolchildren in different locations,including rural areas and large cities such as Madrid,the capital of Spain.In addition to detect prejudice toward one of the two genders,some of the most often repeated answers were taken into account.On several occasions,one of the two sexes,or the two,was linked to intelligence or to the ideal of beauty.However,differences were not observed in all cases.Comments are made on the most relevant data regarding the predisposition among children to link girls with more passive attitudes than boys.For many years,society has fought to achieve real equality between the two sexes.However,there is still a great deal to be done,and the younger generations have the responsibility of succeeding in having the two sexes live together in a more egalitarian society.The role of education is to encourage this process.

关键词： prejudices stereotype gender children primary school

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Effect of a Protein-Energy Supplement of Low Consumption with Coconut Pulp Expeller (<i>Acrocomia aculeata</i>) of Beef Cattle at Pasture

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Open Journal of Animal Sciences 2020年第3期10卷 528-534页

作者： Julio gonzalez Javier Kanazawa Patricia Coronel Gregorio Presentado María Paz Corrales Patricia Criscioni oscar Luis Valiente Department of Bromatology Nutrition and Animal Feeding Faculty of Veterinary Sciences National University of Asunción Asunción Paraguay Department of Animal Production Faculty of Veterinary Sciences National University of Asunción Asunción Paraguay

The purpose of this study is to evaluate the effect of a low consumption protein-energy supplement that incorporates 15% of coconut pulp expeller in bovine animals. These pasture fattening cattle were checked on daily weight gain, supplement consumption and efficiency of pasture use. This study was carried out in a livestock establishment in the Department of Concepción, Paraguay. A total of 108 animals were selected;castrated male bovines, 342 ± 30.2 of body weight (BW), age average 28 months, Nelore breed distributed in 2 treatments (T1 and T2): T1 = 42 animals;control group (pasture + conventional mineral salt) and T2 = 66 animals;treatment group with a protein-energy supplement (pasture + protein-energy supplement with minerals). In both treatments, the animals grazed on pasture of Brachiaria brizantha cv. Marandú and Panincum maximaun cv. Tanzania used a system of pasture rotation of 1 - 3 days of occupation and 35 - 40 days of rest. The average daily weight gain (DG) was 0.82 and 0.83 kg/day (p > 0.05), the supplement consumption was 0.1 and 0.28 kg/day per animal and the % disappearance of the biomass of 18 and 23% for T1 and T2, respectively. In conclusion, there was no evident effect on DG of protein-energy

关键词： Supplementation Protein-Energy Mineral Bovine Fattening

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Genetic Diversity of the Pepper Pathogen <i>Phytophthora capsici</i>on Farms in the Amazonian High Jungle of Peru

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American Journal of Plant Sciences 2011年第3期2卷 461-466页

作者： Jon Hulvey oscar Hurtado-gonzalez Liliana Aragón-Caballero Daniel Gobena Dylan Storey Ledare Finley Kurt Lamour 不详

Phytophthora capsici is an important oomycete pathogen of Capsicum peppers worldwide. Populations of P. capsici recovered from coastal regions in Peru were previously shown to be dominated by a single clonal lineage referred to as PcPE-1. During 2008, 219 isolates of P. capsici were collected from Capsicum pubescens (Rocoto), C. annum (Pimento), and C. baccatum (Aji) at 9 farms in the Amazonian high jungle in the areas surrounding Oxapampa, and one coastal location, Carabayllo. Two isolates of P. capsici were also recovered from Cyclanthera pedata (Caigua fruit) near one field. All isolates were characterized using a panel of eight single nucleotide polymorphism (SNP) markers that are fixed for heterozygosity in the PcPE-1 lineage. A subset of isolates was also characterized using amplified fragment length polymorphism (AFLP) markers. Nine discreet SNP multi-locus genotypes were identified, and the PcPE-1 lineage was recovered from all of the field sites. Both A1 and A2 mating types were recovered from two sites. The implications of the genotypic diversity and distribution identified in this study are discussed.

关键词： Population Genetics DNA Markers Clonality Asexual Reproduction Sexual Reproduction

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