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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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Intense pulsed light‑based treatment for the improvement of symptoms in glaucoma patients treated with hypotensive eye drops

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Eye and Vision 2024年第2期10卷 12-21页

作者： Jose Maria Martinez‑de‑la‑Casa Carlos Oribio‑Quinto almudena Milans‑del‑Bosch Pilar Perez‑Garcia Laura Morales‑fernandez Javier Garcia‑Bella Jose Manuel Benitez‑del‑Castillo Julian Garcia‑Feijoo David P.Pinero Ophthalmology Unit Department of Ophthalmology and ORLFaculty of MedicineHospital Clinico San-CarlosUniversidad Complutense de MadridInstituto de Investigacion Sanitaria del Hospital Clinico San-Carlos(IdISSC)28040 MadridSpain Department of Immunology Ophthalmology and ORLSchool of MedicineInstituto de Investigaciones Oftalmologicas Ramon CastroviejoUniversidad Complutense de MadridMadridSpain Department of Optics Pharmacology and AnatomyUniversity of AlicanteAlicanteSpain

Background:Ocular surface disease in glaucoma patients is a significant ocular co-morbidity that can affect 40%to 59%of these patients worldwide.The current study was aimed at evaluating the potential clinical benefit of an intense pulsed light(IPL)-based treatment in glaucomatous patients with ocular surface disease due to prolonged hypotensive eyedrop treatments.To our knowledge,this is the first series analyzing the therapeutic effect of this treatment option in this type of patients.Methods:This non-comparative prospective case series study enrolled a total of 30 glaucoma patients ranging in age from 57 to 94 years old and treated with hypotensive eyedrops for years with dry eye symptomatology.All patients received four sessions of IPL treatment using the Optima IPL system(Lumenis,Yokneam,Israel)adjusted to the official optimized Lumenis setting.Changes in symptomatology,corneal staining,conjunctival hyperemia,non-invasive break-up time(NIBUT),tear osmolarity,tear meniscus height(TMH),meiboscore and meibomian gland expressibility was analyzed after treatment.Results:Statistically significant reductions were observed after IPL treatment in the symptomatology scores measured with different questionnaires[ocular surface disease index(OSDI),standard patient evaluation of eye dryness(SPEED)and symptom assessment questionnaire in dry eye(SANDE)]as well as with the visual analogue scale(P<0.001).Mean change in OSDI was−15.0±11.3.A significant reduction was found after treatment in the corneal staining score(P<0.001).A significant reduction was found in tear film meniscus height(P=0.012),as well as in tear film osmolarity(P=0.001).A significant reduction was also found in meibomian gland expressibility(P=0.003),changing the percentage of grade 3 eyes from 44.4%before IPL to 17.2%after treatment.Conclusions:IPL therapy combined with meibomian gland expression(MGX)seems to be an effective option to improve symptomatology in glaucomatous patients with ocular surface disease due to prolonged hypotensive eyedrop treatment

关键词： Glaucoma Intense pulsed light Dry eye Meibomian glands

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Anchoring of 10-phenylphenothiazine to mesoporous silica materials:A water compatible organic photocatalyst for the degradation of pollutants

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Journal of Materials Science & Technology 2022年第8期103卷 134-143页

作者： Daniel González-Muñoz almudena Gómez-Avilés Carmen B.Molina Jorge Bedia Carolina Belver Jose Alemán Silvia Cabrera Organic Chemistry Department Science FacultyUniversidad Autónoma de Madrid28049 MadridSpain Chemical Engineering Department Science FacultyUniversidad Autónoma de Madrid28049 MadridSpain Institute for Advanced Research in Chemical Sciences(IAdChem) Universidad Autónoma de Madrid28049 MadridSpain Inorganic Chemistry Department Science FacultyUniversidad Autónoma de Madrid28049 MadridSpain

The application of organic photocatalysts towards the oxidation of pollutants in water is hampered by different limitations such as their insolubility in the media.Herein,we report that the grafting of a photoorganocatalyst into mesoporous silica materials is an ideal approach to obtain effective catalysts.Thereby,the photocatalyst 10-phenylphenothiazine(PTH)was easily anchored into three different mesoporous silica-based materials(MSN,MSU-2 and SBA-15)with different particle sizes and pore sizes through an amide bond formation.The materials were characterized using IR analysis,solid-state X-ray diffraction,porosity and microscopy(SEM and TEM)techniques,showing that PTH is immobilized inside the pores of the materials and its optical properties are maintained after the anchoring.Although homogeneous PTH was inactive in water media,the three photocatalytic materials were active for the degradation of pollutants.SBA-15-AP-PTH exhibited the highest catalytic performance towards the degradation of acetaminophen and diclofenac under solar irradiation,finding in this manner a new strategy for the decontamination of pollutants.

关键词： Organic semiconductors Silica support Solar photocatalysis Water treatment Pharmaceuticals

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Genomic patterns of homozygosity and inbreeding depression in MurcianoGranadina goats

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Journal of Animal Science and Biotechnology 2022年第3期13卷 721-734页

作者： María Gracia Luigi-Sierra almudena Fernández Amparo Martínez Dailu Guan Juan Vicente Delgado Javier FernándezÁlvarez Vincenzo Landi Francesc Xavier Such Jordi Jordana María Saura Marcel Amills Centre for Research in Agricultural Genomics(CRAG) CSIC-IRTA-UAB-UBUniversitat Autònoma de Barcelona08193 BellaterraSpain Departamento de Mejora Genética Animal INIACarretera de la Coruña km 7528040 MadridSpain Departamento de Genética Universidad de Córdoba14071 CórdobaSpain Department of Veterinary Medicine University of Bari“Aldo Moro”62 per Casamassima km.370010 ValenzanoSPItaly Group of Research in Ruminants(G2R) Department of Animal and Food ScienceUniversitat Autònoma de Barcelona(UAB)BellaterraBarcelonaSpain Departament de Ciència Animal i dels Aliments Facultat de VeterinàriaUniversitat Autònoma de Barcelona08193 BellaterraSpain

Background:Inbreeding depression can adversely affect traits related to fitness,reproduction and productive performance.Although current research suggests that inbreeding levels are generally low in most goat breeds,the impact of inbreeding depression on phenotypes of economic interest has only been investigated in a few studies based on genealogical data.Results:We genotyped 1040 goats with the Goat SNP50 BeadChip.This information was used to estimate different molecular inbreeding coefficients and characterise runs of homozygosity and homozygosity patterns.We detected38 genomic regions with increased homozygosity as well as 8 ROH hotspots mapping to chromosomes 1,2,4,6,14,16 and 17.Eight hundred seventeen goats with available records for dairy traits were analysed to evaluate the potential consequences of inbreeding depression on milk phenotypes.Four regions on chromosomes 8 and 25were significantly associated with inbreeding depression for the natural logarithm of the somatic cell count.Notably,these regions contain several genes related with immunity,such as SYK,IL27,CCL19 and CCL21.Moreover,one region on chromosome 2 was significantly associated with inbreeding depression for milk yield.Conclusions:Although genomic inbreeding levels are low in Murciano-Granadina goats,significant evidence of inbreeding depression for the logarithm of the somatic cell count,a phenotype closely associated with udder health and milk yield,have been detected in this population.Minimising inbreeding would be expected to augment economic gain by increasing milk yield and reducing the incidence of mastitis,which is one of the main causes of dairy goat culling.

关键词： Goat Inbreeding Milk yield Murciano-Granadina Somatic cell score

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Spermiogram and sperm head morphometry assessed by multivariate cluster analysis results during adolescence （12-18 years） and the effect of varicocele

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Asian Journal of Andrology 2016年第6期18卷 824-830页

作者： Fernando Vasquez Caries Soler Patricia Camps Anthony Valverde almudena Garcia-Molina Research Group on Reproductive and Sexual Health Health Sciences Division Universidad del Norte EO. Box 1569 Barranquilla Colombia Department of Functional Biology and Physical Anthropology University of Valencia 46100 Burjassot Valencia Spain R+D Department Proiser R+D Scientific Park University of Valencia 46980 Paterna Valencia Spain Technological Institute of Costa Rica Agronomy School Animal Reproduction Department San Carlos Campus 223-21001 San Carlos Costa Rica

This work evaluates sperm head morphometric characteristics in adolescents from 12 to 18 years of age, and the effect of varicocele. Volunteers between 150 and 224 months of age （mean 191, n = 87）, who had reached oigarche by 12 years old, were recruited in the area of Barranquilla, Colombia. Morphometric analysis of sperm heads was performed with principal component （PC） and discriminant analysis, Combining seminal fluid and sperm parameters provided five PCs： two related to sperm morphometry, one to sperm motility, and two to seminal fluid components. Discriminant analysis on the morphometric results of varicocele and nonvaricocele groups did not provide a useful classification matrix. Of the semen-related PCs, the most explanatory （40%） was related to sperm motility. Two PCs, including sperm head elongation and size, were sufficient to evaluate sperm morphometric characteristics. Most of the morphometric variables were correlated with age, with an increase in size and decrease in the elongation of the sperm head. For head size, the entire sperm population could be divided into two morphometric subpopulations, SP1 and SP2, which did not change during adolescence. In general, for varicocele individuals, SP1 had larger and more elongated sperm heads than SP2, which had smaller and more elongated heads than in nonvaricocele men. In summary, sperm head morphometry assessed by CASA-Morph and multivariate cluster analysis provides a better comprehension of the ejaculate structure and possibly sperm function. Morphometric analysis provides much more information than data obtained from conventional semen analysis.

关键词： adolescence CASA-Morph system seminal quality sperm head morphometry spermiogram subpopulation

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Efficiency of white lupin in the removal of mercury from contaminated soils: Soil and hydroponic experiments

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Journal of Environmental Sciences 2010年第3期22卷 421-427页

作者： Pilar Zornoza Rocío Milln M. Jos Sierra almudena Seco Elvira Esteban Department of Agricultural Science Autonomous University of Madrid Francisco Tomsy Valiente 7. E-28049 Madrid Spain Research Center for Energy Environment and Technology Environmental Department. Soil Degradation Research Unit. Av. Complutense 22. E-28040 Madrid Spain

This study examined the ability of the white lupin to remove mercury （Hg） from a hydroponic system （Hg concentrations 0, 1.25, 2.5, 5 and 10 μmol/L） and from soil in pots and lysimeters （total Hg concentration （19.2 ± 1.9） mg/kg availability 0.07%, and （28.9 ± 0.4） mg/kg availability 0.09%, respectively）, and investigated the accumulation and distribution of Hg in different parts of the plant. White lupin roots efficiently took up Hg, but its translocation to the harvestable parts of the plant was low. The Hg concentration in the seeds posed no risk to human health according to the recommendations of the World Health Organization, but the shoots should not be used as fodder for livestock, at least when unmixed with other fodder crops. The accumulation of Hg in the hydroponically-grown plants was linear over the concentration range tested. The amount of Hg retained in the roots, relative to the shoots, was almost constant irrespective of Hg dose （90%）. In the soil experiments, Hg accumulation increased with exposure time and was the greater in the lysimeter than in the pot experiments. Although Hg removal was the greater in the hydroponic system, revealing the potential of the white lupin to extract Hg, bioaccumulation was the greatest in the lysimeter-grown plants; the latter system more likely reflects the true behaviour of white lupin in the field when Hg availability is a factor that limits Hg removal. The present results suggest that the white lupin could be used in long-term soil reclamation strategies that include the goal of profitable land use in Hg-polluted areas.

关键词： edible plant parts hydroponic-soil-lysimeter experiments Lupinus albus L. mercury

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Morphometric comparison by the ISAS CASA-DNAf system of two techniques for the evaluation of DNA fragmentation in human spermatozoa

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Asian Journal of Andrology 2016年第6期18卷 835-839页

作者： Sara Sadeghi almudena Garcia-Molina Ferran Celma Anthony Valverde Sogol Fereidounfar Caries Soler Department of Functional Biology and Physical Anthropology University of Valencia 46100 Burjassot Valencia Spain R+D Department Proiser R+D Scientific Park Universitat de Valencia 46980 Paterna Valencia Spain Technological Institute of Costa Rica San Carlos Campus School of Agronomy 223-21001 Alajuela Costa Rica Department of Botany Kharazmi University Tehran Iran

DNA fragmentation has been shown to be one of the causes of male infertility, particularly related to repeated abortions, and different methods have been developed to analyze it. In the present study, two commercial kits based on the SCD technique （Halosperm~ and SDFA） were evaluated by the use of the DNA fragmentation module of the ISAS vl CASA system. Seven semen samples from volunteers were analyzed. To compare the results between techniques, the Kruskal-Wallis test was used. Data were used for calculation of Principal Components （two PCs were obtained）, and subsequent subpopulations were identified using the Halo, Halo/Core Ratio, and PC data. Results from both kits were significantly different （P 〈 0.001）. In each case, four subpopulations were obtained, independently of the classification method used. The distribution of subpopulations differed depending on the kit used. From the PC data, a discriminant analysis matrix was obtained and a good a posterioriclassification was obtained （97.1% for Halosperm and 96.6% for SDFA）. The present results are the first approach on morphometric evaluation of DNA fragmentation from the SCD technique. This approach could be used for the future definition of a classification matrix surpassing the current subjective evaluation of this important sperm factor.

关键词： DNA fragmentation Halosperm morphometry principal component analysis SDFA subpopulation

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Sperm kinematic, head morphometric and kinetic- morphometric subpopulations in the blue fox （Alopex lagopus）

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Asian Journal of Andrology 2017年第2期19卷 154-159页

作者： Caries Soler Jesus Contell Lorena Bori Maria Sancho almudena Garcia-Molina Anthony Valverde Jan Segarvall Department of Functional Biology and Physical Anthropology University of Valencia 46100 Burjassot Spain R+D Department Proiser R+D Scientific Park University of Valencia 46980 Paterna Spain Technological Institute of Costa Rica San Carlos Campus School of Agronomy 223-21001 Alajuela Costa Rica Finnish Fur Breeders Association ProFur 65101 Vaasa Finland

This work provides information on the blue fox ejaculated sperm quality needed for seminal dose calculations. Twenty semen samples, obtained by masturbation, were analyzed for kinematic and morphometric parameters by using CASA-Mot and CASA-Morph system and principal component （PC） analysis. For motility, eight kinematic parameters were evaluated, which were reduced to PC1, related to linear variables, and PC2, related to oscillatory movement. The whole population was divided into three independent subpopulations： SP1, fast cells with linear movement; SP2, slow cells and nonoscillatory motility; and SP3, medium speed cells and oscillatory movement. In almost all cases, the subpopulation distribution by animal was significantly different. Head morphology analysis generated four size and four shape parameters, which were reduced to PC 1, related to size, and PC2, related to shape of the cells. Three morphometric subpopulations existed. SPI： large oval cells; SP2： medium size elongated cells; and SP3. small and short cells. The subpopulation distribution differed between animals. Combining the kinematic and morphometric datasets produced PC1, related to morphometric parameters, and PC2, related to kinematics, which generated four sperm subpopulations - SPI.. high oscillatory motility, large and short heads; SP2; medium velocity with small and short heads; SP3. slow motion small and elongated cells; and SP4. high linear speed and large elongated cells. Subpopulation distribution was different in all animals. The establishment of sperm subpopulations from kinematic, morphometric, and combined variables not only improves the well-defined fox semen characteristics and offers a good conceptual basis for fertility and sperm preservation techniques in this species, but also opens the door to use this approach in other species, included humans.

关键词： integration of motility and morphology principal component analysis sperm morphometry subpopulation

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Physical activation of graphene: An effective, simple and clean procedure for obtaining microporous graphene for high-performance Li/S batteries

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Nano Research 2019年第4期12卷 759-766页

作者： almudena Benitez Alvaro Caballero Julian Morales Jusef Hassoun Enrique Rodriguez-Castellon Jesus Canales-Vazquez Dpto. Quimica Inorganica e Ingenieria Qutmica Instituto de Quimica Fina y Nanoquimica Universidad de Cordoba 14071 Cordoba Spain Departm ent of Chemical and Pharmaceutical Sciences University of Ferrara Via Fossato di Mortara 17 44121 Ferrara Italy Dpto. de Quimica Inorganica Cristalografia y Mineralogia Facultad de Ciencias Universidad de Malaga 29071 Malaga Spain Instituto de Energias Renovables Universidad de Castilla-La Mancha Paseo de La Investigacion 1 Albacete 02071 Spain

Graphe ne nano sheets are a promising scaffold to accommodate S for achievi ng high performa nee Li/S battery. Nano sheet activation is used as a viable strategy to induce a micropore system and further improve the battery performance. Accordingly, chemical activation methods dominate despite the need of multiple stages, which slow down the process in addition to making them tiresome. Here, a three-dimensional (3D) N-doped graphene specimen was physically activated with CO2, a clean and single step process, and used for the preparation of a sulfur composite (A-3DNG/S). The A-3DNG/S composite exhibited outstanding electrochemical properties such as an excellent rate capability (1,000 mAh·g^-1 at 2C), high reversible capacity and cycling stability (average capacity ~ 800 mAh·g^-1 at 1C after 200 cycles), values which exceed those measured in chemically activated graphene. Therefore, these results support the use of physical activation as a simple and efficient alternative to improve the performance of carbons as an S host for high-performance Li-S batteries.

关键词： physical activation 3D-graphene solvothermal microwave synthesis Li-S battery

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Dog sperm head morphometry： its diversity and .=volution

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Asian Journal of Andrology 2017年第2期19卷 149-153页

作者： Caries Soler Ana Alambiaga Maria A Marti almudena Garcia-Molina Anthony Valverde Jesus Contell Marcos Campos Department of Functional Biology and Physical Anthropology University of Valencia 46100 Burjassot Spain R+D Department Proiser R+D Scientific Park University of Valencia 46980 Paterna Spain 3Technological Institute of Costa Rica San Carlos Campus School of Agronomy 223-21001 Alajuela Costa Rica Department of Medicine and Animal Surgery University CardenaI-Herrera-CEU 46113 Moncada Valencia Spain Global Veterinaria (Reprovalcan) 46500 Sagunto Valencia Spain Clinica Veterinaria Sangueso 46009 Valencia Spain

Dogs have been under strong artificial selection as a consequence of their relationship with man. Differences between breeds are evident that could be reflected in seminal characteristics. The present study was to evaluate differences in sperm head morphometry between seven well-defined breeds of dog： the British Bulldog, Chihuahua, German Shepherd, Labrador Retriever, Spanish Mastiff, Staffordshire Terrier, and Valencian Rat Hunting dog. Semen samples were obtained by masturbation and smears stained with Diff-Quik. Morphometric analysis （CASA-Morph） produced four size and four shape parameters. Length, Ellipticity, and Elongation showed higher differences between breeds. MANOVA revealed differences among all breeds. Considering the whole dataset, principal component analysis （PCA） showed that PC1 was related to head shape and PC2 to size. Procluster analysis showed the British Bulldog to be the most isolated breed, followed by the German Shepherd. The PCA breed by breed showed the Chihuahua, Labrador Retriever, Spanish Mastiff, and Staffordshire Terrier to have PC1 related to shape and PC2 to size, whereas the British Bulldog, Valencia Rat Hunting dog, and German Shepherd had PC1 related to size and PC2 to shape. The dendrogram for cluster groupings and the distance between them showed the British Bulldog to be separated from the rest of the breeds. Future work on dog semen must take into account the large differences in the breeds＇ sperm characteristics. The results provide a base for future work on phylogenetic and evolutionary studies of dogs, based on their seminal characteristics.

关键词： Canis familiaris cluster analysis diversity sperm morphometry

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