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571.
Jakob Hemmer‐Hansen Einar E. Nielsen Nina O. Therkildsen Martin I. Taylor Rob Ogden Audrey J. Geffen Dorte Bekkevold Sarah Helyar Christophe Pampoulie Torild Johansen FishPopTrace Consortium Gary R. Carvalho 《Molecular ecology》2013,22(10):2653-2667
The genomic architecture underlying ecological divergence and ecological speciation with gene flow is still largely unknown for most organisms. One central question is whether divergence is genome‐wide or localized in ‘genomic mosaics’ during early stages when gene flow is still pronounced. Empirical work has so far been limited, and the relative impacts of gene flow and natural selection on genomic patterns have not been fully explored. Here, we use ecotypes of Atlantic cod to investigate genomic patterns of diversity and population differentiation in a natural system characterized by high gene flow and large effective population sizes, properties which theoretically could restrict divergence in local genomic regions. We identify a genomic region of strong population differentiation, extending over approximately 20 cM, between pairs of migratory and stationary ecotypes examined at two different localities. Furthermore, the region is characterized by markedly reduced levels of genetic diversity in migratory ecotype samples. The results highlight the genomic region, or ‘genomic island’, as potentially associated with ecological divergence and suggest the involvement of a selective sweep. Finally, we also confirm earlier findings of localized genomic differentiation in three other linkage groups associated with divergence among eastern Atlantic populations. Thus, although the underlying mechanisms are still unknown, the results suggest that ‘genomic mosaics’ of differentiation may even be found under high levels of gene flow and that marine fishes may provide insightful model systems for studying and identifying initial targets of selection during ecological divergence. 相似文献
572.
Yoshiyuki Tanaka Emma S. Data Shohei Hirose Takeshi Taniguchi Ikuzo Uritani 《Bioscience, biotechnology, and biochemistry》2013,77(4):693-700
Bluish fluorescent and phenolic components were produced in cassava roots in response to cut- injury, and in relation to physiological deterioration and microbial deterioration. The former roved to consist of five coumarin components, the main three of which were scopoletin, scopolin and esculin, and the other two were scopoletin- and esculetin-containing conjugates. A main component of the latter was (+)-catechin. Some enzymes pertaining to the production of the secondary metabolites such as acid invertase, phenylalanine ammonia lyase and peroxidase were formed in cut-injured tissue and in non-infected tissue adjacent to the soft-rotten part. 相似文献
573.
Anne van der Vorst G. A. Rixt Zijlstra Nico De Witte Ruth G. M. Vogel Jos M. G. A. Schols Gertrudis I. J. M. Kempen D-SCOPE Consortium 《Tijdschrift voor gerontologie en geriatrie》2018,49(5):174-186
Most research on (multidimensional) frailty focuses on deficits and risks of adverse outcomes. However, frail older people can still report positive outcomes, such as a relatively high QoL. In order to develop more positively oriented prevention strategies, this exploratory study aimed (a) to identify characteristics related to QoL among frail older people; and (b) to explain discrepancies between higher and lower levels of QoL, with a specific focus on strengths frail older people with a higher QoL still may have. Quantitative and qualitative data was gathered by means of semi-structured interviews with Flemish community-dwelling, frail older people with higher (n?=?16) and lower QoL levels (n?=?18). Quantitative analyses showed that frail older people with a higher QoL were older, had lower levels of psychological frailty, and reported higher meaning in life compared to those with a lower QoL. Outcomes of qualitative analysis showed that participants in the high QoL subgroup adapted more effectively to difficulties, had more things in prospect, performed more activities, and were more satisfied with their social network compared to the low QoL subgroup. To conclude, this exploratory study suggests possibilities to promote and improve QoL by strengthening specific resources among frail older people.Please note that an English version of this article has been published in BMC Geriatrics: van der Vorst A, Zijlstra GAR, De Witte N, Vogel RGM, Schols JMGA, Kempen GIJM, D?SCOPE Consortium. Explaining discrepancies in self-reported quality of life in frail older people: a mixed-methods study. BMC Geriatr. 2017;17(1): 251. https://doi.org/10.1186/s12877-017-0641-y. 相似文献
574.
Transcriptome reprogramming due to the introduction of a barley telosome into bread wheat affects more barley genes than wheat
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Elodie Rey Michael Abrouk Gabriel Keeble‐Gagnère Miroslava Karafiátová Jan Vrána Sandrine Balzergue Ludivine Soubigou‐Taconnat Véronique Brunaud Marie‐Laure Martin‐Magniette Takashi R. Endo Jan Barto? International Wheat Genome Sequencing Consortium Rudi Appels Jaroslav Dole?el 《Plant biotechnology journal》2018,16(10):1767-1777
575.
Elisabeth E. Mlynarski Michael Xie Deanne Taylor Molly B. Sheridan Tingwei Guo Silvia E. Racedo Donna M. McDonald-McGinn Eva W. C. Chow Jacob Vorstman Ann Swillen Koen Devriendt Jeroen Breckpot Maria Cristina Digilio Bruno Marino Bruno Dallapiccola Nicole Philip Tony J. Simon Amy E. Roberts Ma?gorzata Piotrowicz Carrie E. Bearden Stephan Eliez Doron Gothelf Karlene Coleman Wendy R. Kates Marcella Devoto Elaine Zackai Damian Heine- Su?er Elizabeth Goldmuntz Anne S. Bassett Bernice E. Morrow Beverly S. Emanuel The International Chromosome q. Consortium 《Human genetics》2016,135(3):273-285
576.
Michael?Raess Ana?Ambrosio?de Castro Valérie?Gailus-Durner Sabine?Fessele Martin?Hrabě de AngelisEmail author the INFRAFRONTIER Consortium 《Mammalian genome》2016,27(7-8):445-450
Ageing research and more generally the study of the functional basis of human diseases profit enormously from the large-scale approaches and resources in mouse functional genomics: systematic targeted mutation of the mouse genome, systemic phenotyping in mouse clinics, and the archiving and distribution of the mouse resources in public repositories. INFRAFRONTIER, the European research infrastructure for the development, systemic phenotyping, archiving and distribution of mammalian models, offers access to sustainable mouse resources for biomedical research. INFRAFRONTIER promotes the global sharing of high-quality resources and data and thus contributes to data reproducibility and animal welfare. INFRAFRONTIER puts great effort into international standardisation and quality control and into technology development to improve and expand experimental protocols, reduce the use of animals in research and increase the reproducibility of results. In concert with the research community and the International Mouse Phenotyping Consortium (IMPC), INFRAFRONTIER is currently developing new pilot platforms and services for the research on ageing and age-related diseases. 相似文献
577.
Eugenia Migliavacca Christelle Golzio Katrin M?nnik Ian Blumenthal Edwin?C. Oh Louise Harewood Jack A. Kosmicki Maria?Nicla Loviglio Giuliana Giannuzzi Loyse Hippolyte Anne?M. Maillard Ali?Abdullah Alfaiz p. European Consortium Mieke M. van Haelst Joris Andrieux James F. Gusella Mark J. Daly Jacques S. Beckmann Sébastien Jacquemont Michael E. Talkowski Nicholas Katsanis Alexandre Reymond 《American journal of human genetics》2015,96(5):784-796
578.
Sarah Louise Mackie John C. Taylor Lubna Haroon-Rashid Stephen Martin Bhaskar Dasgupta Andrew Gough Michael Green Lesley Hordon Stephen Jarrett Colin T. Pease Jennifer H. Barrett Richard Watts Ann W. Morgan UK GCA Consortium UKRAG Consortium 《Arthritis research & therapy》2015,17(1)
IntroductionGiant cell arteritis (GCA) is an autoimmune disease commonest in Northern Europe and Scandinavia. Previous studies report various associations with HLA-DRB1*04 and HLA-DRB1*01; HLA-DRB1 alleles show a gradient in population prevalence within Europe. Our aims were (1) to determine which amino acid residues within HLA-DRB1 best explained HLA-DRB1 allele susceptibility and protective effects in GCA, seen in UK data combined in meta-analysis with previously published data, and (2) to determine whether the incidence of GCA in different countries is associated with the population prevalence of the HLA-DRB1 alleles that we identified in our meta-analysis.MethodsGCA patients from the UK GCA Consortium were genotyped by using single-strand oligonucleotide polymerization, allele-specific polymerase chain reaction, and direct sequencing. Meta-analysis was used to compare and combine our results with published data, and public databases were used to identify amino acid residues that may explain observed susceptibility/protective effects. Finally, we determined the relationship of HLA-DRB1*04 population carrier frequency and latitude to GCA incidence reported in different countries.ResultsIn our UK data (225 cases and 1378 controls), HLA-DRB1*04 carriage was associated with GCA susceptibility (odds ratio (OR) = 2.69, P = 1.5×10−11), but HLA-DRB1*01 was protective (adjusted OR = 0.55, P = 0.0046). In meta-analysis combined with 14 published studies (an additional 691 cases and 4038 controls), protective effects were seen from HLA-DR2, which comprises HLA-DRB1*15 and HLA-DRB1*16 (OR = 0.65, P = 8.2×10−6) and possibly from HLA-DRB1*01 (OR = 0.73, P = 0.037). GCA incidence (n = 17 countries) was associated with population HLA-DRB1*04 allele frequency (P = 0.008; adjusted R2 = 0.51 on univariable analysis, adjusted R2 = 0.62 after also including latitude); latitude also made an independent contribution.ConclusionsWe confirm that HLA-DRB1*04 is a GCA susceptibility allele. The susceptibility data are best explained by amino acid risk residues V, H, and H at positions 11, 13, and 33, contrary to previous suggestions of amino acids in the second hypervariable region. Worldwide, GCA incidence was independently associated both with population frequency of HLA-DRB1*04 and with latitude itself. We conclude that variation in population HLA-DRB1*04 frequency may partly explain variations in GCA incidence and that HLA-DRB1*04 may warrant investigation as a potential prognostic or predictive biomarker.
Electronic supplementary material
The online version of this article (doi:10.1186/s13075-015-0692-4) contains supplementary material, which is available to authorized users. 相似文献579.
The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration 总被引:6,自引:0,他引:6
Smith B Ashburner M Rosse C Bard J Bug W Ceusters W Goldberg LJ Eilbeck K Ireland A Mungall CJ;OBI Consortium Leontis N Rocca-Serra P Ruttenberg A Sansone SA Scheuermann RH Shah N Whetzel PL Lewis S 《Nature biotechnology》2007,25(11):1251-1255
The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or 'ontologies'. Unfortunately, the very success of this approach has led to a proliferation of ontologies, which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium is pursuing a strategy to overcome this problem. Existing OBO ontologies, including the Gene Ontology, are undergoing coordinated reform, and new ontologies are being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable and logically well formed and to incorporate accurate representations of biological reality. We describe this OBO Foundry initiative and provide guidelines for those who might wish to become involved. 相似文献
580.
Genetic consequences of Pleistocene range shifts: contrast between the Arctic, the Alps and the East African mountains 总被引:5,自引:2,他引:3
Ehrich D Gaudeul M Assefa A Koch MA Mummenhoff K Nemomissa S;Intrabiodiv Consortium Brochmann C 《Molecular ecology》2007,16(12):2542-2559
In wide-ranging species, the genetic consequences of range shifts in response to climate change during the Pleistocene can be predicted to differ among different parts of the distribution area. We used amplified fragment length polymorphism data to compare the genetic structure of Arabis alpina, a widespread arctic-alpine and afro-alpine plant, in three distinct parts of its range: the North Atlantic region, which was recolonized after the last ice age, the European Alps, where range shifts were probably primarily altitudinal, and the high mountains of East Africa, where the contemporary mountain top populations result from range contraction. Genetic structure was inferred using clustering analyses and estimates of genetic diversity within and between populations. There was virtually no diversity in the vast North Atlantic region, which was probably recolonized from a single refugial population, possibly located between the Alps and the northern ice sheets. In the European mountains, genetic diversity was high and distinct genetic groups had a patchy and sometimes disjunct distribution. In the African mountains, genetic diversity was high, clearly structured and partially in accordance with a previous chloroplast phylogeography. The fragmented structure in the European and African mountains indicated that A. alpina disperses little among established populations. Occasional long-distance dispersal events were, however, suggested in all regions. The lack of genetic diversity in the north may be explained by leading-edge colonization by this pioneer plant in glacier forelands, closely following the retracting glaciers. Overall, the genetic structure observed corresponded to the expectations based on the environmental history of the different regions. 相似文献