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  • Biodiversity Research  (397)
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  • 1
    Online Resource
    Online Resource
    Genome-wide screening reveals the genetic basis of mammalian embryonic eye development
    Springer Science and Business Media LLC ; 2023
    In:  BMC Biology Vol. 21, No. 1 ( 2023-02-03)
    Details
    In: BMC Biology, Springer Science and Business Media LLC, Vol. 21, No. 1 ( 2023-02-03)
    Abstract: Microphthalmia, anophthalmia, and coloboma (MAC) spectrum disease encompasses a group of eye malformations which play a role in childhood visual impairment. Although the predominant cause of eye malformations is known to be heritable in nature, with 80% of cases displaying loss-of-function mutations in the ocular developmental genes OTX2 or SOX2, the genetic abnormalities underlying the remaining cases of MAC are incompletely understood. This study intended to identify the novel genes and pathways required for early eye development. Additionally, pathways involved in eye formation during embryogenesis are also incompletely understood. This study aims to identify the novel genes and pathways required for early eye development through systematic forward screening of the mammalian genome. Results Query of the International Mouse Phenotyping Consortium (IMPC) database (data release 17.0, August 01, 2022) identified 74 unique knockout lines (genes) with genetically associated eye defects in mouse embryos. The vast majority of eye abnormalities were small or absent eyes, findings most relevant to MAC spectrum disease in humans. A literature search showed that 27 of the 74 lines had previously published knockout mouse models, of which only 15 had ocular defects identified in the original publications. These 12 previously published gene knockouts with no reported ocular abnormalities and the 47 unpublished knockouts with ocular abnormalities identified by the IMPC represent 59 genes not previously associated with early eye development in mice. Of these 59, we identified 19 genes with a reported human eye phenotype. Overall, mining of the IMPC data yielded 40 previously unimplicated genes linked to mammalian eye development. Bioinformatic analysis showed that several of the IMPC genes colocalized to several protein anabolic and pluripotency pathways in early eye development. Of note, our analysis suggests that the serine-glycine pathway producing glycine, a mitochondrial one-carbon donator to folate one-carbon metabolism (FOCM), is essential for eye formation. Conclusions Using genome-wide phenotype screening of single-gene knockout mouse lines, STRING analysis, and bioinformatic methods, this study identified genes heretofore unassociated with MAC phenotypes providing models to research novel molecular and cellular mechanisms involved in eye development. These findings have the potential to hasten the diagnosis and treatment of this congenital blinding disease.
    Type of Medium: Online Resource
    ISSN: 1741-7007
    URL: Article
    DOI: 10.1186/s12915-022-01475-0
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
    detail.hit.zdb_id: 2133020-7
    SSG: 12
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    Online Resource
  • 2
    Online Resource
    Online Resource
    Using dynamic vegetation models to simulate plant range shifts
    Wiley ; 2014
    In:  Ecography Vol. 37, No. 12 ( 2014-12), p. 1184-1197
    Details
    In: Ecography, Wiley, Vol. 37, No. 12 ( 2014-12), p. 1184-1197
    Abstract: Dynamic vegetation models (DVMs) follow a process‐based approach to simulate plant population demography, and have been used to address questions about disturbances, plant succession, community composition, and provisioning of ecosystem services under climate change scenarios. Despite their potential, they have seldom been used for studying species range dynamics explicitly. In this perspective paper, we make the case that DVMs should be used to this end and can improve our understanding of the factors that influence species range expansions and contractions. We review the benefits of using process‐based, dynamic models, emphasizing how DVMs can be applied specifically to questions about species range dynamics. Subsequently, we provide a critical evaluation of some of the limitations and trade‐offs associated with DVMs, and we use those to guide our discussions about future model development. This includes a discussion on which processes are lacking, specifically a mechanistic representation of dispersal, inclusion of the seedling stage, trait variability, and a dynamic representation of reproduction. We also discuss upscaling techniques that offer promising solutions for being able to run these models efficiently over large spatial extents. Our aim is to provide directions for future research efforts and to illustrate the value of the DVM approach.
    Type of Medium: Online Resource
    ISSN: 0906-7590 , 1600-0587
    URL: Issue
    URL: Article
    DOI: 10.1111/ecog.2014.v37.i12
    DOI: 10.1111/ecog.00580
    Language: English
    Publisher: Wiley
    Publication Date: 2014
    detail.hit.zdb_id: 2024917-2
    detail.hit.zdb_id: 1112659-0
    SSG: 12
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    Online Resource
  • 3
    Online Resource
    Online Resource
    The effects of feeding flaxseed during the receiving period on morbidity, mortality, performance, and carcass characteristics of heifers1
    Oxford University Press (OUP) ; 2008
    In:  Journal of Animal Science Vol. 86, No. 11 ( 2008-11-01), p. 3054-3061
    Details
    In: Journal of Animal Science, Oxford University Press (OUP), Vol. 86, No. 11 ( 2008-11-01), p. 3054-3061
    Type of Medium: Online Resource
    ISSN: 0021-8812 , 1525-3163
    URL: Article
    DOI: 10.2527/jas.2007-0271
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2008
    detail.hit.zdb_id: 1490550-4
    SSG: 12
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    Online Resource
  • 4
    Online Resource
    Online Resource
    Impacts of climate change on national biodiversity population trends
    Wiley ; 2017
    In:  Ecography Vol. 40, No. 10 ( 2017-10), p. 1139-1151
    Details
    In: Ecography, Wiley, Vol. 40, No. 10 ( 2017-10), p. 1139-1151
    Abstract: Climate change has had well‐documented impacts on the distribution and phenology of species across many taxa, but impacts on species’ abundance, which relates closely to extinction risk and ecosystem function, have not been assessed across taxa. In the most comprehensive multi‐taxa comparison to date, we modelled variation in national population indices of 501 mammal, bird, aphid, butterfly and moth species as a function of annual variation in weather variables, which through time allowed us to identify a component of species’ population growth that can be associated with post‐1970s climate trends. We found evidence that these climate trends have significantly affected population trends of 15.8% of species, including eight with extreme ( 〉 30% decline per decade) negative trends consistent with detrimental impacts of climate change. The modelled effect of climate change could explain 48% of the significant across‐species population decline in moths and 63% of the population increase in winged aphids. The other taxa did not have significant across‐species population trends or consistent climate change responses. Population declines in species of conservation concern were linked to both climatic and non‐climatic factors respectively accounting for 42 and 58% of the decline. Evident differential impacts of climate change between trophic levels may signal the potential for future ecosystem disruption. Climate change has therefore already driven large‐scale population changes of some species, had significant impacts on the overall abundance of some key invertebrate groups and may already have altered biological communities and ecosystems in Great Britain.
    Type of Medium: Online Resource
    ISSN: 0906-7590 , 1600-0587
    URL: Issue
    URL: Article
    DOI: 10.1111/ecog.2017.v40.i10
    DOI: 10.1111/ecog.02411
    Language: English
    Publisher: Wiley
    Publication Date: 2017
    detail.hit.zdb_id: 2024917-2
    detail.hit.zdb_id: 1112659-0
    SSG: 12
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  • 5
    Online Resource
    Online Resource
    Efficacy of monensin and tylosin in finishing diets based on steam-flaked corn with and without corn wet distillers grains with solubles1
    Oxford University Press (OUP) ; 2008
    In:  Journal of Animal Science Vol. 86, No. 9 ( 2008-09-01), p. 2270-2276
    Details
    In: Journal of Animal Science, Oxford University Press (OUP), Vol. 86, No. 9 ( 2008-09-01), p. 2270-2276
    Type of Medium: Online Resource
    ISSN: 0021-8812 , 1525-3163
    URL: Article
    DOI: 10.2527/jas.2007-0017
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2008
    detail.hit.zdb_id: 1490550-4
    SSG: 12
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  • 6
    Online Resource
    Online Resource
    Savanna Vegetation-Fire-Climate Relationships Differ Among Continents
    American Association for the Advancement of Science (AAAS) ; 2014
    In:  Science Vol. 343, No. 6170 ( 2014-01-31), p. 548-552
    Details
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 343, No. 6170 ( 2014-01-31), p. 548-552
    Abstract: Ecologists have long sought to understand the factors controlling the structure of savanna vegetation. Using data from 2154 sites in savannas across Africa, Australia, and South America, we found that increasing moisture availability drives increases in fire and tree basal area, whereas fire reduces tree basal area. However, among continents, the magnitude of these effects varied substantially, so that a single model cannot adequately represent savanna woody biomass across these regions. Historical and environmental differences drive the regional variation in the functional relationships between woody vegetation, fire, and climate. These same differences will determine the regional responses of vegetation to future climates, with implications for global carbon stocks.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
    URL: Article
    DOI: 10.1126/science.1247355
    RVK:
    TA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2014
    detail.hit.zdb_id: 128410-1
    detail.hit.zdb_id: 2066996-3
    detail.hit.zdb_id: 2060783-0
    SSG: 11
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    Online Resource
  • 7
    Online Resource
    Online Resource
    A model system to study genomic imprinting of human genes
    Proceedings of the National Academy of Sciences ; 1998
    In:  Proceedings of the National Academy of Sciences Vol. 95, No. 25 ( 1998-12-08), p. 14857-14862
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 95, No. 25 ( 1998-12-08), p. 14857-14862
    Abstract: Somatic-cell hybrids have been shown to maintain the correct epigenetic chromatin states to study developmental globin gene expression as well as gene expression on the active and inactive X chromosomes. This suggests the potential use of somatic-cell hybrids containing either a maternal or a paternal human chromosome as a model system to study known imprinted genes and to identify as-yet-unknown imprinted genes. Testing gene expression by using reverse transcription followed by PCR, we show that functional imprints are maintained at four previously characterized 15q11–q13 loci in hybrids containing a single human chromosome 15 and at two chromosome 11p15 loci in hybrids containing a single chromosome 11. In contrast, three γ-aminobutyric acid type A receptor subunit genes in 15q12–q13 are nonimprinted. Furthermore, we have found that differential DNA methylation imprints at the SNRPN promoter and at a CpG island in 11p15 are also maintained in somatic-cell hybrids. Somatic-cell hybrids therefore are a valid and powerful system for studying known imprinted genes as well as for rapidly identifying new imprinted genes.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.95.25.14857
    RVK:
    TA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 1998
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
    SSG: 11
    SSG: 12
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  • 8
    Online Resource
    Online Resource
    Identification of a black yeast isolated from oak bark as belonging to the genus Phaeococcomyces sp. Analysis of melanin produced by the yeast
    Canadian Science Publishing ; 1989
    In:  Canadian Journal of Microbiology Vol. 35, No. 7 ( 1989-07-01), p. 728-734
    Details
    In: Canadian Journal of Microbiology, Canadian Science Publishing, Vol. 35, No. 7 ( 1989-07-01), p. 728-734
    Abstract: A black fungus isolated from oak bark was identified as a member of the yeast-like genus Phaeococcomyces. While no sexual reproduction was observed, the isolate showed characteristics associated with basidiomycetous yeasts: it was non-fermentative, produced extracellular urease, was positive with the diazonium blue B colony colour test, and had an enteroblastic form of budding. The isolate produced a black pigment constitutively which was shown to be a melanin. Production of the pigment was inhibited by the incorporation of low levels of the fungicide tricyclazole in growth media, inidicating that it was a pentaketide melanin. Pigmentation mutants were produced. Albino mutants did not produce melanin. Diffusion mutants accumulated the pentaketide melanin pathway oxidation products flaviolin and 2-hydroxyjuglone in culture media. Cross-feeder mutants accumulated scytalone, a pentaketide melanin pathway intermediate, in culture media, and caused albino mutants to melanize when grown in proximity to them on agar plates. A single mutant was isolated which excreted 1,8-dihydroxy naphthalene, the end product of the pathway. Broth cultures of Phaeococcomyces sp. in stationary growth phase released melanin in the form of granules, with an average diameter of 30 nm.Key words: black yeast, melanin production, Phaeococcomyces sp.
    Type of Medium: Online Resource
    ISSN: 0008-4166 , 1480-3275
    URL: Article
    DOI: 10.1139/m89-118
    RVK:
    WA 15000
    Language: English
    Publisher: Canadian Science Publishing
    Publication Date: 1989
    detail.hit.zdb_id: 280534-0
    detail.hit.zdb_id: 1481972-7
    SSG: 12
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    Online Resource
  • 9
    Online Resource
    Online Resource
    Construction of the physical map for three loci in chromosome band 13q14: comparison to the genetic map.
    Proceedings of the National Academy of Sciences ; 1990
    In:  Proceedings of the National Academy of Sciences Vol. 87, No. 9 ( 1990-05), p. 3415-3419
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 87, No. 9 ( 1990-05), p. 3415-3419
    Abstract: Pulsed-field gel electrophoresis (PFGE) and deletion mapping are being used to construct a physical map of the long arm of human chromosome 13. The present study reports a 2700-kilobase (kb) Not I long-range restriction map encompassing the 13q14-specific loci D13S10, D13S21, and D13S22, which are detected by the cloned DNA markers p7D2, pG24E2.4, and pG14E1.9, respectively. Analysis of a panel of seven cell lines that showed differential methylation at a Not I site between D13S10 and D13S21 proved physical linkage of the two loci to the same 875-kb Not I fragment. D13S22 mapped to a different Not I fragment, precluding the possibility that D13S22 is located between D13S10 and D13S21. PFGE analysis of Not I partial digests placed the 1850-kb Not I fragment containing D13S22 immediately adjacent to the 875-kb fragment containing the other two loci. The proximal rearrangement breakpoint in a cell line carrying a del13(q14.1q21.2) was detected by D13S21 but not by D13S10, demonstrating that D13S21 lies proximal to D13S10. Quantitative analysis of hybridization signals of the three DNA probes to DNA from the same cell line indicated that only D13S10 was deleted, establishing the order of these loci to be cen-D13S22-D13S21-D13S10-tel. Surprisingly, this order was estimated to be 35,000 times less likely than that favored by genetic linkage analysis.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.87.9.3415
    RVK:
    TA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 1990
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
    SSG: 11
    SSG: 12
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  • 10
    Online Resource
    Online Resource
    Intracellular sites of synthesis and processing of lectin in developing pea cotyledons.
    Elsevier BV ; 1983
    In:  Journal of Biological Chemistry Vol. 258, No. 15 ( 1983-08), p. 9550-9552
    Details
    In: Journal of Biological Chemistry, Elsevier BV, Vol. 258, No. 15 ( 1983-08), p. 9550-9552
    Type of Medium: Online Resource
    ISSN: 0021-9258
    URL: Article
    DOI: 10.1016/S0021-9258(17)44702-8
    Language: English
    Publisher: Elsevier BV
    Publication Date: 1983
    detail.hit.zdb_id: 2141744-1
    detail.hit.zdb_id: 1474604-9
    SSG: 12
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