Multiocular defect has been described in different canine breeds, including the Old English Sheepdog. Affected dogs typically present with multiple and various ocular abnormalities. We carried out ...whole genome sequencing on an Old English Sheepdog that had been diagnosed with hereditary cataracts at the age of five and then referred to a board-certified veterinary ophthalmologist due to owner-reported visual deterioration. An ophthalmic assessment revealed that there was bilateral vitreal degeneration, macrophthalmos, and spherophakia in addition to cataracts. Follow-up consultations revealed cataract progression, retinal detachment, uveitis and secondary glaucoma. Whole genome sequence filtered variants private to the case, shared with another Old English Sheepdog genome and predicted to be deleterious were genotyped in an initial cohort of six Old English Sheepdogs (three affected by multiocular defect and three control dogs without evidence of inherited eye disease). Only one of the twenty-two variants segregated correctly with multiocular defect. The variant is a single nucleotide substitution, located in the collagen-type gene COL11A1, c.1775T>C, that causes an amino acid change, p.Phe1592Ser. Genotyping of an additional 14 Old English Sheepdogs affected by multiocular defect revealed a dominant mode of inheritance with four cases heterozygous for the variant. Further genotyping of hereditary cataract-affected Old English Sheepdogs revealed segregation of the variant in eight out of nine dogs. In humans, variants in the COL11A1 gene are associated with Stickler syndrome type II, also dominantly inherited.
Progressive retinal atrophies (PRAs) are a genetically heterogeneous group of inherited eye diseases that affect over 100 breeds of dog. The initial clinical sign is visual impairment in scotopic ...conditions, as a consequence of rod photoreceptor cell degeneration. Photopic vision degeneration then follows, due to progression of the disease to the cone photoreceptors, and ultimately results in complete blindness. Two full-sibling English Shepherds were diagnosed with PRA at approximately 5 years old and tested clear of all published PRA genetic variants. This study sought to identify the novel PRA-associated variant segregating in the breed. We utilised a combined approach of whole genome sequencing of the probands and homozygosity mapping of four cases and 22 controls and identified a short interspersed nuclear element within an alternatively spliced exon in FAM161A. The XP_005626197.1 c.17929_ins210 variant was homozygous in six PRA cases and heterozygous or absent in control dogs, consistent with a recessive mode of inheritance. The insertion is predicted to extend exon 4 by 39 aberrant amino acids followed by an early termination stop codon. PRA is intractable to treatment, so the development of a genetic screening test, based on the associated variant, is significant, because it provides dog breeders/owners with a means of reducing the frequency of the disease variant within this breed as well as minimising the risk of breeding puppies that will develop this blinding disease.
Genetic analysis of animals involved in captive breeding and reintroduction programmes can provide valuable information to aid in maintaining wild type genotypes and genetic variability. Hylobates ...moloch, also referred to as the silvery gibbon, is an Endangered primate species endemic to the Indonesian island of Java. As part of an overall conservation programme, a captive breeding and reintroduction programme is being organised. In order to aid both the management decisions within the breeding programme and success rates of re-introductions analyses at three genetic regions were carried out, with DNA extracted from non-invasively collated faecal samples. In order to assay if captively bred individuals were representative of their wild conspecifics, the population was split into two groups representative of wild born and captive born individuals. Genetic analyses at mitochondrial DNA hypervariable region-I (mtDNA HV-I), 15 microsatellite loci and the second exon of the major histocompatibility complex (MHC) DRB region, were carried out to ascertain genetic variability levels, levels of inbreeding, signs of selection and confirm the pedigree. Captive born individuals had markedly lower levels of variability at mtDNA HV-I, which was significant versus the wild group. The second neutral marker of microsatellites revealed no differentiation between wild and captive-born; moreover measures of standardised heterozygosity demonstrateda fairly high level of genomic variability overall. Pedigree analysis using the microsatellites produced information that differed from studbook entries. This was further supported by haplotypic data compiled from the MHC DRB exon 2 analysis. The MHC study revealed a total of 14 DRB alleles, 10 of which are from unknown lineages when compared to human and chimpanzees. As with microsatellites, no group differentiation between wild and captive has occurred but there are more rare alleles present within wild individuals. In conclusion, whilst genetic variation is both high and shows no deviation from wild-born to captive-born at neutral microsatellite loci, care should be taken to maintain rare mtDNA haplotypes and MHC DRB alleles in future generations.
Genetic analysis of animals involved in captive breeding and reintroduction programmes can provide valuable information to aid in maintaining wild type genotypes and genetic variability. Hylobates ...moloch, also referred to as the silvery gibbon, is an Endangered primate species endemic to the Indonesian island of Java. As part of an overall conservation programme, a captive breeding and reintroduction programme is being organised. In order to aid both the management decisions within the breeding programme and success rates of re-introductions analyses at three genetic regions were carried out, with DNA extracted from non-invasively collated faecal samples. In order to assay if captively bred individuals were representative of their wild conspecifics, the population was split into two groups representative of wild born and captive born individuals. Genetic analyses at mitochondrial DNA hypervariable region-I (mtDNA HV-I), 15 microsatellite loci and the second exon of the major histocompatibility complex (MHC) DRB region, were carried out to ascertain genetic variability levels, levels of inbreeding, signs of selection and confirm the pedigree. Captive born individuals had markedly lower levels of variability at mtDNA HV-I, which was significant versus the wild group. The second neutral marker of microsatellites revealed no differentiation between wild and captive-born; moreover measures of standardised heterozygosity demonstrateda fairly high level of genomic variability overall. Pedigree analysis using the microsatellites produced information that differed from studbook entries. This was further supported by haplotypic data compiled from the MHC DRB exon 2 analysis. The MHC study revealed a total of 14 DRB alleles, 10 of which are from unknown lineages when compared to human and chimpanzees. As with microsatellites, no group differentiation between wild and captive has occurred but there are more rare alleles present within wild individuals. In conclusion, whilst genetic variation is both high and shows no deviation from wild-born to captive-born at neutral microsatellite loci, care should be taken to maintain rare mtDNA haplotypes and MHC DRB alleles in future generations.
Marine scientists often assess habitats to understand the distribution and relative abundance of marine resources. Due to the spatial nature of habitats and associated temporal changes, however, ...assimilating data using traditional analytical methods is often difficult. Geographic Information Systems (GIS) are proving to be effective tools to help address problems inherent in the analysis of spatial data, GIS can be used to effectively collate, archive, display, analyze, and model spatial and temporal data. Additionally, by combining dissimilar data types, such as socio-political boundaries, bottom types, and fish distributions, for example, resource managers can use GIS to make informed management decisions. In this way, GIS provides resource managers with a means to integrate scientific data with prevailing cultural values and traditions. We have developed a working GIS for the Monterey Bay National Marine Sanctuary that allows interpretation of many terrestrial and marine data sets, including inter-tidal monitoring data, permit locations, seabird strandings, fisheries catch data, habitat types, marine political boundaries, as well as land cover classification from satellite imagery, watersheds, streams, roads, and political boundaries. We have linked terrestrial and marine data to create a broad spatial and temporal database that will be used in a variety of ways such as evaluating natural processes, permitting and monitoring coastal development and assessing environmental impacts (e.g. oil spills).
Les scientifiques déterminent souvent les habitats pour comprendre la répartition et l'abondance relative des ressources marines. Pourtant, en raison de la variabilité spatiale et temporelle des données, leur assimilation par les méthodes d'analyse traditionnelles est souvent difficile. Les systèmes d'information géographique (SIG) se révèlent efficaces pour traiter ces problèmes. Ils permettent de collecter, classer, visualiser, analyser et modéliser les données spatiales et temporelles. En combinant des données de natures différentes telles que limites socio-politiques, types d'habitats et répartition des espèces de poissons, les gestionnaires des ressources peuvent prendre leurs décisions en connaissance de cause. Ainsi, le SIG constitue un moyen d'intégrer les données scientifiques aux valeurs et traditions culturelles de l'époque. Les auteurs ont développé un SIG pour la réserve marine nationale de la baie de Monterey. Il permet d'interpréter des jeux de données terrestres et marines comprenant, entre autres, les marées, les zones de décharges autorisées, les sites d'échouage des oiseaux de mer, les captures de pêches, les types d'habitats, les limites politiques marines ; il permet aussi la classification de la couverture terrestre par imagerie satellitale, bassins hydrographiques, fleuves, routes et limites politiques. Les données terrestres et marines sont réunies dans une grande base de données spatiales et temporelles offrant un choix important d'applications pour l'évaluation des processus naturels, l'autorisation et la surveillance du dévelopement côtier et l'évaluation de leurs impacts sur l'environnement (par exemple, les marées noires).
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