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- Kattge, Jens, et al.
(author)
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TRY plant trait database - enhanced coverage and open access
- 2020
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In: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Journal article (peer-reviewed)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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| 4. |
- Elsik, Christine G., et al.
(author)
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The Genome Sequence of Taurine Cattle : A Window to Ruminant Biology and Evolution
- 2009
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 324:5926, s. 522-528
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Journal article (peer-reviewed)abstract
- To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
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| 5. |
- Madrigal-Ruiz, P. M., et al.
(author)
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The unbalance of adiponectin oligomers, RvE1 and chemerin levels are associate with increase of adiposopathy status and insulin resistance in obesity
- 2019
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In: Journal of Translational Science. - : Open Access Text. - 2059-268X. ; 5
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Journal article (other academic/artistic)abstract
- Objective: The aim was to establish if the balance adiponectin-oligomers, resolvin-E1 and chemerin levels could contribute to the insulin resistance (IR) setting of subjects with obesity, based on their serum levels and its relationship with inflammatory markers, metabolic profile and adiposopathy status.Methods: This study included 230 individuals, classified according to World Health Organization criteria by body mass index (BMI) kg/m2 in two groups: without-obesity (from 18.5 to 29.9) and with-obesity (from 30.0 to 39.9). Body fat mass distribution, metabolic and inflammatory markers were measured by anthropometric, enzymatic and immuno-turbidimetry methods, respectively. Serum insulin, resolvin-E1, chemerin, and adiponectin-oligomers were evaluating by ELISA method. Analysis performed were correlations IR-indexes with adiposity, receiver operating characteristic (ROC) curves and the adiponectin-oligomers, resolvin-E1 and chemerin tertiles.Results: Subjects’ with-obesity showed adiposopathy status, characterized by metabolic dysregulation and a subclinical inflammatory profile. They presented higher levels (`x ±SD, ng/mL) of resolvin-E1 (1227 ±668 versus 909 ±769, P= 0.017), chemerin (91 ±31 versus 79 ±23, P= 0.013) and LMW-Adiponectin (2257 ±797 versus 1030 ±1055, P= 0.011), whereas HMW-Adiponectin was lower (2470 ±1095 versus 3236 ±1848, P= 0.010), compared to the without-obesity individuals. Individuals’ with-obesity also displayed positive correlation of IR markers (rho from 0.163 to 0.479) along body fat measurements, metabolic and inflammation profiles. Moreover, a negative correlation of HMW-Adiponectin (rho from –0.564 to –0.214) with body fat measurements, metabolic and inflammation profiles. IR-indexes, LMW-Adiponectin and resolvin-E1/chemerin relationship showed differences between groups’ with-obesity and without-obesity, but not with gender. ROC curves shown potential ability of the LMW-Adiponectin levels to differentiate IR from non-IR individuals, with AUC of 0.815, P<0.0001 (95%, CI: 0.726-0.903).Conclusion: The present study shown that LMW-Adiponectin-resolvinE1-chemerin serum unbalance establishes a specific relationship with adiposopathy in individuals with obesity, which could be a way to identify risk factors in early stages of IR.
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| 6. |
- Osoegawa, Kazutoyo, et al.
(author)
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Quality control project of NGS HLA genotyping for the 17th International HLA and Immunogenetics Workshop
- 2019
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In: Human Immunology. - : ELSEVIER SCIENCE INC. - 0198-8859 .- 1879-1166. ; 80:4, s. 228-236
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Journal article (peer-reviewed)abstract
- The 17th International HLA and Immunogenetics Workshop (IHIW) organizers conducted a Pilot Study (PS) in which 13 laboratories (15 groups) participated to assess the performance of the various sequencing library preparation protocols, NGS platforms and software in use prior to the workshop. The organizers sent 50 cell lines to each of the 15 groups, scored the 15 independently generated sets of NGS HLA genotyping data, and generated "consensus" HLA genotypes for each of the 50 cell lines. Proficiency Testing (PT) was subsequently organized using four sets of 24 cell lines, selected from 48 of 50 PS cell lines, to validate the quality of NGS HLA typing data from the 34 participating IHIW laboratories. Completion of the PT program with a minimum score of 95% concordance at the HLA-A, HLA-B, HLA-C, HLA-DRB1 and HLA-DQB1 loci satisfied the requirements to submit NGS HLA typing data for the 17th IHIW projects. Together, these PS and PT efforts constituted the 17th IHIW Quality Control project. Overall PT concordance rates for HLA-A, HLA-B, HLA-C, HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQB1, HLA-DRB1, HLA-DRB3, HLA-DRB4 and HLA-DRB5 were 98.1%, 97.0% and 98.1%, 99.0%, 98.6%, 98.8%, 97.6%, 96.0%, 99.1%, 90.0% and 91.7%, respectively. Across all loci, the majority of the discordance was due to allele dropout. The high cost of NGS HLA genotyping per experiment likely prevented the retyping of initially failed HLA loci. Despite the high HLA genotype concordance rates of the software, there remains room for improvement in the assembly of more accurate consensus DNA sequences by NGS HLA genotyping software.
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