分类: 计算机科学 >> 计算机科学的集成理论 提交时间: 2022-11-18 合作期刊: 《数据智能(英文)》
摘要: With the rapid growth of the linked data on the Web, the quality assessment of the RDF data set becomes particularly important, especially for the quality and accessibility of the linked data. In most cases, RDF data sets are shared online, leading to a high maintenance cost for the quality assessment. This also potentially pollutes Internet data. Recently blockchain technology has shown the potential in many applications. Using the blockchain storage quality assessment results can reduce the centralization of the authority, and the quality assessment results have characteristics such as non-tampering. To this end, we propose an RDF data quality assessment model in a decentralized environment, pointing out a new dimension of RDF data quality. We use the blockchain to record the data quality assessment results and design a detailed update strategy for the quality assessment results. We have implemented a system DCQA to test and verify the feasibility of the quality assessment model. The proposed method can provide users with better cost-effective results when knowledge is independently protected.
分类: 生物学 >> 生物物理学 >> 生物物理、生物化学与分子生物学 提交时间: 2016-05-12
摘要: Sulfolobus synthesizes large amounts of small chromatin proteins Cren7 and Sul7d. The two proteins share overall structural similarity, but differ distinctly in the DNA-binding region between beta 3- and beta 4-strands. While Sul7d possesses a hinge of two amino acid residues, Cren7 contains a flexible seven-residue loop (loop beta 3-beta 4) in the region. Here, we report the role of loop beta 3-beta 4 in the interaction of Cren7 with duplex DNA. We show that all residues with a large side chain on the loop, i.e., Pro30, Lys31, Arg33 and Lys34, contributed significantly to the binding of Cren7 to DNA. The three basic amino acids affected the ability of Cren7 to constrain negative DNA supercoils in a residue number-dependent manner. The crystal structure of a complex between a mutant Cren7 protein (GR) with loop beta 3-beta 4 replaced by two residues (Gly and Arg) to mimic the hinge at the corresponding position in Sul7d and an 8-bp dsDNA has been determined. Structural comparison between the GR-DNA and Cren7-DNA complexes shows that GR resembles Sul7d more than Cren7 in DNA-binding size and in the effect on the width of the major groove of DNA and the pattern of DNA bending. However, GR induces smaller DNA curvature than Sul7d. Our results suggest that Cren7 and Sul7d package chromosomal DNA in a slightly different fashion, presumably permitting different chromosomal accessibility by proteins functioning in DNA transactions.
分类: 生物学 >> 生物物理学 >> 细胞生物学 提交时间: 2016-05-12
摘要: Specific recognition of centromere-specific histone variant CENP-A-containing chromatin by CENP-N is an essential process in the assembly of the kinetochore complex at centromeres prior to mammalian cell division. However, the mechanisms of CENP-N recruitment to centromeres/kinetochores remain unknown. Here, we show that a CENP-A-specific RG loop (Arg80/Gly81) plays an essential and dual regulatory role in this process. The RG loop assists the formation of a compact "ladder-like" structure of CENP-A chromatin, concealing the loop and thus impairing its role in recruiting CENP-N. Upon G1/S-phase transition, however, centromeric chromatin switches from the compact to an open state, enabling the now exposed RG loop to recruit CENP-N prior to cell division. Our results provide the first insights into the mechanisms by which the recruitment of CENP-N is regulated by the structural transitions between compaction and relaxation of centromeric chromatin during the cell cycle.
分类: 生物学 >> 生物物理学 >> 神经科学 提交时间: 2016-05-11
摘要: All neurodegenerative diseases are associated with oxidative stress-induced neuronal death. Forkhead box O3a (FOXO3a) is a key transcription factor involved in neuronal apoptosis. However, how FOXO3a forms complexes and functions in oxidative stress processing remains largely unknown. In the present study, we show that histone deacetylase 2 (HDAC2) forms a physical complex with FOXO3a, which plays an important role in FOXO3a-dependent gene transcription and oxidative stress-induced mouse cerebellar granule neuron (CGN) apoptosis. Interestingly, we also found that HDAC2 became selectively enriched in the promoter region of the p21 gene, but not those of other target genes, and inhibited FOXO3a-mediated p21 transcription. Furthermore, we found that oxidative stress reduced the interaction between FOXO3a and HDAC2, leading to an increased histone H4K16 acetylation level in the p21 promoter region and upregulated p21 expression in a manner independent of p53 or E2F1. Phosphorylation of HDAC2 at Ser 394 is important for the HDAC2-FOXO3a interaction, and we found that cerebral ischemia/reperfusion reduced phosphorylation of HDAC2 at Ser 394 and mitigated the HDAC2-FOXO3a interaction in mouse brain tissue. Our study reveals the novel regulation of FOXO3a-mediated selective gene transcription via epigenetic modification in the process of oxidative stress-induced cell death, which could be exploited therapeutically.