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  • 1
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2022
    In:  Scientific Data Vol. 9, No. 1 ( 2022-08-12)
    In: Scientific Data, Springer Science and Business Media LLC, Vol. 9, No. 1 ( 2022-08-12)
    Abstract: The Sumatran orang-utan (Pongo abelii) reference genome was first published in 2011, in conjunction with ten re-sequenced genomes from unrelated wild-caught individuals. Together, these published data have been utilized in almost all great ape genomic studies, plus in much broader comparative genomic research. Here, we report that the original sequencing Consortium inadvertently switched nine of the ten samples and/or resulting re-sequenced genomes, erroneously attributing eight of these to the wrong source individuals. Among them is a genome from the recently identified Tapanuli (P. tapanuliensis) species: thus, this genome was sequenced and published a full six years prior to the species’ description. Sex was wrongly assigned to five known individuals; the numbers in one sample identifier were swapped; and the identifier for another sample most closely resembles that of a sample from another individual entirely. These errors have been reproduced in countless subsequent manuscripts, with noted implications for studies reliant on data from known individuals.
    Type of Medium: Online Resource
    ISSN: 2052-4463
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2775191-0
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  • 2
    In: Frontiers in Ecology and Evolution, Frontiers Media SA, Vol. 9 ( 2021-5-31)
    Abstract: Microarrays can be a cost-effective alternative to high-throughput sequencing for discovering novel single-nucleotide polymorphisms (SNPs). Illumina’s iScan platform dominates the market, but their commercial microarray products are designed for model organisms. Further, the platform outputs data in a proprietary format. This cannot be easily converted to human-readable genotypes or be merged with pre-existing data. To address this, we present and validate a novel pipeline to facilitate data analysis from cross-species application of Illumina microarrays. This facilitates the generation of a compatible VCF from iScan data and the merging of this with a second VCF comprising genotypes derived from other samples and sources. Our pipeline includes a custom script, iScanVCFMerge (presented as a Python package), which we validate using iScan data from three great ape genera. We conclude that cross-species application of microarrays can be a rapid, cost-effective approach for SNP discovery in non-model organisms. Our pipeline surmounts the common challenges of integrating iScan genotypes with pre-existing data.
    Type of Medium: Online Resource
    ISSN: 2296-701X
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2021
    detail.hit.zdb_id: 2745634-1
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  • 3
    Online Resource
    Online Resource
    American Veterinary Medical Association (AVMA) ; 2021
    In:  American Journal of Veterinary Research Vol. 82, No. 1 ( 2021-01), p. 11-21
    In: American Journal of Veterinary Research, American Veterinary Medical Association (AVMA), Vol. 82, No. 1 ( 2021-01), p. 11-21
    Abstract: To determine the effects of dexmedetomidine, doxapram, and dexmedetomidine plus doxapram on ventilation ( e ), breath frequency, and tidal volume (V t ) in ball pythons ( Python regius ) and of doxapram on the thermal antinociceptive efficacy of dexmedetomidine. ANIMALS 14 ball pythons. PROCEDURES Respiratory effects of dexmedetomidine and doxapram were assessed with whole-body, closed-chamber plethysmography, which allowed for estimates of e and V t . In the first experiment of this study with a complete crossover design, snakes were injected, SC, with saline (0.9% NaCl) solution, dexmedetomidine (0.1 mg/kg), doxapram (10 mg/kg), or dexmedetomidine and doxapram, and breath frequency, e , and V t were measured before and every 30 minutes thereafter, through 240 minutes. In the second experiment, antinociceptive efficacy of saline solution, dexmedetomidine, and dexmedetomidine plus doxapram was assessed by measuring thermal withdrawal latencies before and 60 minutes after SC injection. RESULTS Dexmedetomidine significantly decreased breath frequency and increased V t but did not affect e at all time points, compared with baseline. Doxapram significantly increased e , breath frequency, and V t at 60 minutes after injection, compared with saline solution. The combination of dexmedetomidine and doxapram, compared with dexmedetomidine alone, significantly increased e at 30 and 60 minutes after injection and did not affect breath frequency and V t at all time points. Thermal withdrawal latencies significantly increased when snakes received dexmedetomidine or dexmedetomidine plus doxapram, versus saline solution. CONCLUSIONS AND CLINICAL RELEVANCE Concurrent administration of doxapram may mitigate the dexmedetomidine-induced reduction of breathing frequency without disrupting thermal antinociceptive efficacy in ball pythons.
    Type of Medium: Online Resource
    ISSN: 0002-9645
    Language: Unknown
    Publisher: American Veterinary Medical Association (AVMA)
    Publication Date: 2021
    detail.hit.zdb_id: 2056942-7
    SSG: 22
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  • 4
    In: BMC Genomics, Springer Science and Business Media LLC, Vol. 21, No. 1 ( 2020-12)
    Abstract: Orang-utans comprise three critically endangered species endemic to the islands of Borneo and Sumatra. Though whole-genome sequencing has recently accelerated our understanding of their evolutionary history, the costs of implementing routine genome screening and diagnostics remain prohibitive. Capitalizing on a tri-fold locus discovery approach, combining data from published whole-genome sequences, novel whole-exome sequencing, and microarray-derived genotype data, we aimed to develop a highly informative gene-focused panel of targets that can be used to address a broad range of research questions. Results We identified and present genomic co-ordinates for 175,186 SNPs and 2315 Y-chromosomal targets, plus 185 genes either known or presumed to be pathogenic in cardiovascular ( N  = 109) or respiratory ( N  = 43) diseases in humans – the primary and secondary causes of captive orang-utan mortality – or a majority of other human diseases ( N  = 33). As proof of concept, we designed and synthesized ‘SeqCap’ hybrid capture probes for these targets, demonstrating cost-effective target enrichment and reduced-representation sequencing. Conclusions Our targets are of broad utility in studies of orang-utan ancestry, admixture and disease susceptibility and aetiology, and thus are of value in addressing questions key to the survival of these species. To facilitate comparative analyses, these targets could now be standardized for future orang-utan population genomic studies. The targets are broadly compatible with commercial target enrichment platforms and can be utilized as published here to synthesize applicable probes.
    Type of Medium: Online Resource
    ISSN: 1471-2164
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2020
    detail.hit.zdb_id: 2041499-7
    SSG: 12
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