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91.
Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment 总被引:2,自引:0,他引:2
Moran MA Buchan A González JM Heidelberg JF Whitman WB Kiene RP Henriksen JR King GM Belas R Fuqua C Brinkac L Lewis M Johri S Weaver B Pai G Eisen JA Rahe E Sheldon WM Ye W Miller TR Carlton J Rasko DA Paulsen IT Ren Q Daugherty SC Deboy RT Dodson RJ Durkin AS Madupu R Nelson WC Sullivan SA Rosovitz MJ Haft DH Selengut J Ward N 《Nature》2004,432(7019):910-913
Since the recognition of prokaryotes as essential components of the oceanic food web, bacterioplankton have been acknowledged as catalysts of most major biogeochemical processes in the sea. Studying heterotrophic bacterioplankton has been challenging, however, as most major clades have never been cultured or have only been grown to low densities in sea water. Here we describe the genome sequence of Silicibacter pomeroyi, a member of the marine Roseobacter clade (Fig. 1), the relatives of which comprise approximately 10-20% of coastal and oceanic mixed-layer bacterioplankton. This first genome sequence from any major heterotrophic clade consists of a chromosome (4,109,442 base pairs) and megaplasmid (491,611 base pairs). Genome analysis indicates that this organism relies upon a lithoheterotrophic strategy that uses inorganic compounds (carbon monoxide and sulphide) to supplement heterotrophy. Silicibacter pomeroyi also has genes advantageous for associations with plankton and suspended particles, including genes for uptake of algal-derived compounds, use of metabolites from reducing microzones, rapid growth and cell-density-dependent regulation. This bacterium has a physiology distinct from that of marine oligotrophs, adding a new strategy to the recognized repertoire for coping with a nutrient-poor ocean. 相似文献
92.
93.
Nejentsev S Howson JM Walker NM Szeszko J Field SF Stevens HE Reynolds P Hardy M King E Masters J Hulme J Maier LM Smyth D Bailey R Cooper JD Ribas G Campbell RD Clayton DG Todd JA;Wellcome Trust Case Control Consortium 《Nature》2007,450(7171):887-892
The major histocompatibility complex (MHC) on chromosome 6 is associated with susceptibility to more common diseases than any other region of the human genome, including almost all disorders classified as autoimmune. In type 1 diabetes the major genetic susceptibility determinants have been mapped to the MHC class II genes HLA-DQB1 and HLA-DRB1 (refs 1-3), but these genes cannot completely explain the association between type 1 diabetes and the MHC region. Owing to the region's extreme gene density, the multiplicity of disease-associated alleles, strong associations between alleles, limited genotyping capability, and inadequate statistical approaches and sample sizes, which, and how many, loci within the MHC determine susceptibility remains unclear. Here, in several large type 1 diabetes data sets, we analyse a combined total of 1,729 polymorphisms, and apply statistical methods-recursive partitioning and regression-to pinpoint disease susceptibility to the MHC class I genes HLA-B and HLA-A (risk ratios >1.5; P(combined) = 2.01 x 10(-19) and 2.35 x 10(-13), respectively) in addition to the established associations of the MHC class II genes. Other loci with smaller and/or rarer effects might also be involved, but to find these, future searches must take into account both the HLA class II and class I genes and use even larger samples. Taken together with previous studies, we conclude that MHC-class-I-mediated events, principally involving HLA-B*39, contribute to the aetiology of type 1 diabetes. 相似文献
94.
95.
Todd E. Clark 《Journal of forecasting》1999,18(7):489-504
This study examines the small‐sample properties of some commonly used tests of equal forecast accuracy. The paper considers the size and power of different tests and the performance of different heteroscedasticity and autocorrelation‐consistent (HAC) variance estimators. Monte Carlo experiments show that the tests all suffer some size distortions in small samples, with the distortions varying across tests. The experiments also show that, adjusted for size distortions, the tests have broadly similar power, although some small differences exist. Finally, the experiments indicate that the size and power performances of HAC estimators vary with the features of the data. Copyright © 1999 John Wiley & Sons, Ltd. 相似文献
96.
Todd E. Clark 《Journal of forecasting》2000,19(1):1-21
This study examines the problem of forecasting an aggregate of cointegrated disaggregates. It first establishes conditions under which forecasts of an aggregate variable obtained from a disaggregate VECM will be equal to those from an aggregate, univariate time series model, and develops a simple procedure for testing those conditions. The paper then uses Monte Carlo simulations to show, for a finite sample, that the proposed test has good size and power properties and that whether a model satisfies the aggregation conditions is closely related to out‐of‐sample forecast performance. The paper then shows that ignoring cointegration and specifying the disaggregate model as a VAR in differences can significantly affect analyses of aggregation, with the VAR‐based test for aggregation possibly leading to faulty inference and the differenced VAR forecasts potentially understating the benefits of disaggregate information. Finally, analysis of an empirical problem confirms the basic results. Copyright © 2000 John Wiley & Sons, Ltd. 相似文献
97.
The genome of woodland strawberry (Fragaria vesca) 总被引:3,自引:0,他引:3
Shulaev V Sargent DJ Crowhurst RN Mockler TC Folkerts O Delcher AL Jaiswal P Mockaitis K Liston A Mane SP Burns P Davis TM Slovin JP Bassil N Hellens RP Evans C Harkins T Kodira C Desany B Crasta OR Jensen RV Allan AC Michael TP Setubal JC Celton JM Rees DJ Williams KP Holt SH Ruiz Rojas JJ Chatterjee M Liu B Silva H Meisel L Adato A Filichkin SA Troggio M Viola R Ashman TL Wang H Dharmawardhana P Elser J Raja R Priest HD Bryant DW Fox SE Givan SA Wilhelm LJ Naithani S Christoffels A Salama DY 《Nature genetics》2011,43(2):109-116
98.
Twenty-three study sites were established in the sagebrush communities bordering Utah Lake. Relic (ungrazed) and grazed stands were represented in the sample. Differences in species composition, vegetation, and soil characteristics were assessed. Major differences in species composition and vegetative characteristics were due to the influence of grazing. Major changes were loss of native perennial grass cover, and increases in cover from introduced annual species. Differences in the soil characteristics were due to habitat rather than grazing influences. 相似文献
99.
de Bakker PI Burtt NP Graham RR Guiducci C Yelensky R Drake JA Bersaglieri T Penney KL Butler J Young S Onofrio RC Lyon HN Stram DO Haiman CA Freedman ML Zhu X Cooper R Groop L Kolonel LN Henderson BE Daly MJ Hirschhorn JN Altshuler D 《Nature genetics》2006,38(11):1298-1303
A general question for linkage disequilibrium-based association studies is how power to detect an association is compromised when tag SNPs are chosen from data in one population sample and then deployed in another sample. Specifically, it is important to know how well tags picked from the HapMap DNA samples capture the variation in other samples. To address this, we collected dense data uniformly across the four HapMap population samples and eleven other population samples. We picked tag SNPs using genotype data we collected in the HapMap samples and then evaluated the effective coverage of these tags in comparison to the entire set of common variants observed in the other samples. We simulated case-control association studies in the non-HapMap samples under a disease model of modest risk, and we observed little loss in power. These results demonstrate that the HapMap DNA samples can be used to select tags for genome-wide association studies in many samples around the world. 相似文献
100.
Yamanouchi J Rainbow D Serra P Howlett S Hunter K Garner VE Gonzalez-Munoz A Clark J Veijola R Cubbon R Chen SL Rosa R Cumiskey AM Serreze DV Gregory S Rogers J Lyons PA Healy B Smink LJ Todd JA Peterson LB Wicker LS Santamaria P 《Nature genetics》2007,39(3):329-337
Autoimmune diseases are thought to result from imbalances in normal immune physiology and regulation. Here, we show that autoimmune disease susceptibility and resistance alleles on mouse chromosome 3 (Idd3) correlate with differential expression of the key immunoregulatory cytokine interleukin-2 (IL-2). In order to test directly that an approximately twofold reduction in IL-2 underpins the Idd3-linked destabilization of immune homeostasis, we show that engineered haplodeficiency of Il2 gene expression not only reduces T cell IL-2 production by twofold but also mimics the autoimmune dysregulatory effects of the naturally occurring susceptibility alleles of Il2. Reduced IL-2 production achieved by either genetic mechanism correlates with reduced function of CD4(+) CD25(+) regulatory T cells, which are critical for maintaining immune homeostasis. 相似文献