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Träfflista för sökning "WFRF:(Tian Chao) "

Sökning: WFRF:(Tian Chao)

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1.
  • Klionsky, Daniel J., et al. (författare)
  • Guidelines for the use and interpretation of assays for monitoring autophagy
  • 2012
  • Ingår i: Autophagy. - : Landes Bioscience. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
  • Forskningsöversikt (refereegranskat)abstract
    • In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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3.
  • Cheng, Shi-Ping, et al. (författare)
  • Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger
  • 2021
  • Ingår i: Horticulture Research. - : Springer Nature. - 2052-7276. ; 8:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Ginger (Zingiber officinale) is one of the most valued spice plants worldwide; it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance. Here, we present a haplotype-resolved, chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb. Remarkable structural variation was identified between haplotypes, and two inversions larger than 15 Mb on chromosome 4 may be associated with ginger infertility. We performed a comprehensive, spatiotemporal, genome-wide analysis of allelic expression patterns, revealing that most alleles are coordinately expressed. The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements, greater coding sequence divergence, more relaxed selection pressure, and more transcription factor binding site differences. We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis. Our allele-aware assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in ginger.
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4.
  • Hom, Geoffrey, et al. (författare)
  • Association of systemic lupus erythematosus with C8orf13-BLK and ITGAM-ITGAX.
  • 2008
  • Ingår i: New England Journal of Medicine. - : Massachusetts Medical Society. - 0028-4793 .- 1533-4406. ; 358:9, s. 900-909
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND: Systemic lupus erythematosus (SLE) is a clinically heterogeneous disease in which the risk of disease is influenced by complex genetic and environmental contributions. Alleles of HLA-DRB1, IRF5, and STAT4are established susceptibility genes; there is strong evidence for the existence of additional risk loci.METHODS: We genotyped more than 500,000 single-nucleotide polymorphisms (SNPs) in DNA samples from 1311 case subjects with SLE and 1783 control subjects; all subjects were North Americans of European descent. Genotypes from 1557 additional control subjects were obtained from public data repositories. We measured the association between the SNPs and SLE after applying strict quality-control filters to reduce technical artifacts and to correct for the presence of population stratification. Replication of the top loci was performed in 793 case subjects and 857 control subjects from Sweden.RESULTS: Genetic variation in the region upstream from the transcription initiation site of the gene encoding B lymphoid tyrosine kinase (BLK) and C8orf13 (chromosome 8p23.1) was associated with disease risk in both the U.S. and Swedish case–control series (rs13277113; odds ratio, 1.39; P=1×10−10) and also with altered levels of messenger RNA in B-cell lines. In addition, variants on chromosome 16p11.22, near the genes encoding integrin alpha M (ITGAM, or CD11b) and integrin alpha X (ITGAX), were associated with SLE in the combined sample (rs11574637; odds ratio, 1.33; P=3×10−11).
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5.
  • Jia, Kai-Hua, et al. (författare)
  • Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome
  • 2021
  • Ingår i: Horticulture Research. - 2052-7276. ; 8:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Polyploidization plays a key role in plant evolution, but the forces driving the fate of homoeologs in polyploid genomes, i.e., paralogs resulting from a whole-genome duplication (WGD) event, remain to be elucidated. Here, we present a chromosome-scale genome assembly of tetraploid scarlet sage (Salvia splendens), one of the most diverse ornamental plants. We found evidence for three WGD events following an older WGD event shared by most eudicots (the γ event). A comprehensive, spatiotemporal, genome-wide analysis of homoeologs from the most recent WGD unveiled expression asymmetries, which could be associated with genomic rearrangements, transposable element proximity discrepancies, coding sequence variation, selection pressure, and transcription factor binding site differences. The observed differences between homoeologs may reflect the first step toward sub- and/or neofunctionalization. This assembly provides a powerful tool for understanding WGD and gene and genome evolution and is useful in developing functional genomics and genetic engineering strategies for scarlet sage and other Lamiaceae species.
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6.
  • Sampson, Joshua N., et al. (författare)
  • Analysis of Heritability and Shared Heritability Based on Genome-Wide Association Studies for 13 Cancer Types
  • 2015
  • Ingår i: Journal of the National Cancer Institute. - 0027-8874 .- 1460-2105. ; 107:12
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Studies of related individuals have consistently demonstrated notable familial aggregation of cancer. We aim to estimate the heritability and genetic correlation attributable to the additive effects of common single-nucleotide polymorphisms (SNPs) for cancer at 13 anatomical sites.Methods: Between 2007 and 2014, the US National Cancer Institute has generated data from genome-wide association studies (GWAS) for 49 492 cancer case patients and 34 131 control patients. We apply novel mixed model methodology (GCTA) to this GWAS data to estimate the heritability of individual cancers, as well as the proportion of heritability attributable to cigarette smoking in smoking-related cancers, and the genetic correlation between pairs of cancers.Results: GWAS heritability was statistically significant at nearly all sites, with the estimates of array-based heritability, h(l)(2), on the liability threshold (LT) scale ranging from 0.05 to 0.38. Estimating the combined heritability of multiple smoking characteristics, we calculate that at least 24% (95% confidence interval [CI] = 14% to 37%) and 7% (95% CI = 4% to 11%) of the heritability for lung and bladder cancer, respectively, can be attributed to genetic determinants of smoking. Most pairs of cancers studied did not show evidence of strong genetic correlation. We found only four pairs of cancers with marginally statistically significant correlations, specifically kidney and testes (rho = 0.73, SE = 0.28), diffuse large B-cell lymphoma (DLBCL) and pediatric osteosarcoma (rho = 0.53, SE = 0.21), DLBCL and chronic lymphocytic leukemia (CLL) (rho = 0.51, SE = 0.18), and bladder and lung (rho = 0.35, SE = 0.14). Correlation analysis also indicates that the genetic architecture of lung cancer differs between a smoking population of European ancestry and a nonsmoking Asian population, allowing for the possibility that the genetic etiology for the same disease can vary by population and environmental exposures.Conclusion: Our results provide important insights into the genetic architecture of cancers and suggest new avenues for investigation.
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7.
  • Teng, Chao, et al. (författare)
  • Influence of Triple Bonds as pi-Spacer Units in Metal-Free Organic Dyes for Dye-Sensitized Solar Cells
  • 2010
  • Ingår i: The Journal of Physical Chemistry C. - 1932-7447 .- 1932-7455. ; 114:25, s. 11305-11313
  • Tidskriftsartikel (refereegranskat)abstract
    • Four metal-free organic sensitizers (TC101-TC104) with triple bonds in pi-spacers and five reference dyes (TC, TC105, TPC1, D5, and TH208) without triple bonds were applied in dye-sensitized solar cells to study the influence of triple bonds as pi-spacer units on their photoelectrochemical properties and dye-sensitized solar cells (DSCs) performance. Results show that the introduction of triple bond could red-shift the dye's absorption spectrum due to the enhancement of the pi-spacer. However, the spectrum red-shift is much less than that of the introduction of double bond because of more electronegativity of triple bond. The incident photon-to-current conversion efficiency reveals that the electron transfer yield (Phi(nu)(ET)) of DSCs becomes larger with the introduction of triple bond. Electrochemical impedance spectroscopy analysis reveals that the introduction of triple bond almost does not change the electron lifetimes in TiO2 films but decreases the effective diffusion lengths.
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8.
  • Teng, Chao, et al. (författare)
  • Influence of triple bonds as π-spacer units in metal-free organic dyes for dye-sensitized solar cells.
  • 2010
  • Ingår i: The Journal of Physical Chemistry C. - 1932-7447 .- 1932-7455. ; 114:25, s. 11305-11313
  • Tidskriftsartikel (refereegranskat)abstract
    • Four metal-free org. sensitizers (TC101-TC104) with triple bonds in π-spacers and 5 ref. dyes (TC, TC105, TPC1, D5, and TH208) without triple bonds were applied in dye-sensitized solar cells to study the influence of triple bonds as π-spacer units on their photoelectrochem. properties and dye-sensitized solar cells (DSCs) performance. The introduction of triple bond could red shift the dye's absorption spectrum due to the enhancement of the π-spacer. However, the spectrum red shift is much less than that of the introduction of double bond because of more electronegativity of triple bond. The incident photon-to-current conversion efficiency reveals that the electron transfer yield (Φ(ν)ET) of DSCs becomes larger with the introduction of triple bond. Electrochem. impedance spectroscopy anal. reveals that the introduction of triple bond almost does not change the electron lifetimes in TiO2 films but decreases the effective diffusion lengths. [on SciFinder(R)]
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9.
  • Teng, Chao, et al. (författare)
  • Influence of Triple Bonds as π-Spacer Units in Metal-Free Organic Dyes for Dye-SensitizedSolar Cells
  • 2010
  • Ingår i: The Journal of Physical Chemistry C. - 1932-7447 .- 1932-7455. ; 114:25, s. 11305-11313
  • Tidskriftsartikel (refereegranskat)abstract
    • Four metal-free organic sensitizers (TC101-TC104) with triple bonds in pi-spacers and five reference dyes (TC, TC105, TPC1, D5, and TH208) without triple bonds were applied in dye-sensitized solar cells to study the influence of triple bonds as pi-spacer units on their photoelectrochemical properties and dye-sensitized solar cells (DSCs) performance. Results show that the introduction of triple bond could red-shift the dye's absorption spectrum due to the enhancement of the pi-spacer. However, the spectrum red-shift is much less than that of the introduction of double bond because of more electronegativity of triple bond. The incident photon-to-current conversion efficiency reveals that the electron transfer yield (Phi(nu)(ET)) of DSCs becomes larger with the introduction of triple bond. Electrochemical impedance spectroscopy analysis reveals that the introduction of triple bond almost does not change the electron lifetimes in TiO2 films but decreases the effective diffusion lengths.
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10.
  • Chung, Sharon A, et al. (författare)
  • European population substructure is associated with mucocutaneous manifestations and autoantibody production in systemic lupus erythematosus
  • 2009
  • Ingår i: Arthritis and Rheumatism. - 0004-3591 .- 1529-0131. ; 60:8, s. 2448-2456
  • Tidskriftsartikel (refereegranskat)abstract
    • OBJECTIVE: To determine whether genetic substructure in European-derived populations is associated with specific manifestations of systemic lupus erythematosus (SLE), including mucocutaneous phenotypes, autoantibody production, and renal disease. METHODS: SLE patients of European descent (n=1,754) from 8 case collections were genotyped for >1,400 ancestry informative markers that define a north-south gradient of European substructure. Using the Structure program, each SLE patient was characterized in terms of percent Northern (versus percent Southern) European ancestry based on these genetic markers. Nonparametric methods, including tests for trend, were used to identify associations between Northern European ancestry and specific SLE manifestations. RESULTS: In multivariate analyses, increasing levels of Northern European ancestry were significantly associated with photosensitivity (Ptrend=0.0021, odds ratio for highest quartile of Northern European ancestry versus lowest quartile [ORhigh-low] 1.64, 95% confidence interval [95% CI] 1.13-2.35) and discoid rash (Ptrend=0.014, ORhigh-low 1.93, 95% CI 0.98-3.83). In contrast, increasing levels of Northern European ancestry had a protective effect against the production of anticardiolipin autoantibodies (Ptrend=1.6x10(-4), ORhigh-low 0.46, 95% CI 0.30-0.69) and anti-double-stranded DNA autoantibodies (Ptrend=0.017, ORhigh-low 0.67, 95% CI 0.46-0.96). CONCLUSION: This study demonstrates that specific SLE manifestations vary according to Northern versus Southern European ancestry. Thus, genetic ancestry may contribute to the clinical heterogeneity and variation in disease outcomes among SLE patients of European descent. Moreover, these results suggest that genetic studies of SLE subphenotypes will need to carefully address issues of population substructure based on genetic ancestry.
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