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Search Results: 1 - 10 of 80662 matches for " Hongde Liu "
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Metabolomics Analysis of the Responses to Partial Hepatectomy in Hepatocellular Carcinoma Patients  [PDF]
Wan Chan, Shuhai Lin, Stella Sun, Hongde Liu, John M. Luk, Zongwei Cai
American Journal of Analytical Chemistry (AJAC) , 2011, DOI: 10.4236/ajac.2011.22016
Abstract: In this study, liquid chromatography/quadrupole time of flight mass spectrometry (LC/QTOFMS) was employed for investigating the metabolome of the sera collected from hepatocellular carcinoma (HCC) patients before and 3 to 5 months after partial hepatectomy. To investigate the changes in metabolic phenotypes after the hepatic resection, principal components analysis (PCA) and support vector machine (SVM) were performed for the data grouping and classification. Based on the obtained SVM model, mass spectrometry spectra, database searching as well as the confirmation from authentic standards, several differentiating metabolites were tentatively identified. To improve visualization, z-score plot and heat map display were performed, which exhibited the changes in concentration of the metabolites. As a result, depletion of circulating carnitine, reduced amino acid biosynthesis and increased rate of lipid peroxidation were observed. Meanwhile, up-regulation of hypoxanthine indicated that purine metabolism might serve as the salvage pathway. Collectively, the results reflected metabolic responses to surgical operation in HCC patients, suggesting perturbation of energy metabolism may occur in 3 to 5 months after the partial hepatectomy.
The Patterns of Histone Modifications in the Vicinity of Transcription Factor Binding Sites in Human Lymphoblastoid Cell Lines
Yumin Nie, Hongde Liu, Xiao Sun
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0060002
Abstract: Transcription factor (TF) binding at specific DNA sequences is the fundamental step in transcriptional regulation and is highly dependent on the chromatin structure context, which may be affected by specific histone modifications and variants, known as histone marks. The lack of a global binding map for hundreds of TFs means that previous studies have focused mainly on histone marks at binding sites for several specific TFs. We therefore studied 11 histone marks around computationally-inferred and experimentally-determined TF binding sites (TFBSs), based on 164 and 34 TFs, respectively, in human lymphoblastoid cell lines. For H2A.Z, methylation of H3K4, and acetylation of H3K27 and H3K9, the mark patterns exhibited bimodal distributions and strong pairwise correlations in the 600-bp region around enriched TFBSs, suggesting that these marks mainly coexist within the two nucleosomes proximal to the TF sites. TFs competing with nucleosomes to access DNA at most binding sites, contributes to the bimodal distribution, which is a common feature of histone marks for TF binding. Mark H3K79me2 showed a unimodal distribution on one side of TFBSs and the signals extended up to 4000 bp, indicating a longer-distance pattern. Interestingly, H4K20me1, H3K27me3, H3K36me3 and H3K9me3, which were more diffuse and less enriched surrounding TFBSs, showed unimodal distributions around the enriched TFBSs, suggesting that some TFs may bind to nucleosomal DNA. Besides, asymmetrical distributions of H3K36me3 and H3K9me3 indicated that repressors might establish a repressive chromatin structure in one direction to repress gene expression. In conclusion, this study demonstrated the ranges of histone marks associated with TF binding, and the common features of these marks around the binding sites. These findings have epigenetic implications for future analysis of regulatory elements.
MicroRNA Genes Derived from Repetitive Elements and Expanded by Segmental Duplication Events in Mammalian Genomes
Zhidong Yuan,Xiao Sun,Hongde Liu,Jianming Xie
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0017666
Abstract: MicroRNAs (miRNAs) are a class of small noncoding RNAs that regulate gene expression by targeting mRNAs for translation repression or mRNA degradation. Many miRNAs are being discovered and studied, but in most cases their origin, evolution and function remain unclear. Here, we characterized miRNAs derived from repetitive elements and miRNA families expanded by segmental duplication events in the human, rhesus and mouse genomes. We applied a comparative genomics approach combined with identifying miRNA paralogs in segmental duplication pair data in a genome-wide study to identify new homologs of human miRNAs in the rhesus and mouse genomes. Interestingly, using segmental duplication pair data, we provided credible computational evidence that two miRNA genes are located in the pseudoautosomal region of the human Y chromosome. We characterized all the miRNAs whether they were derived from repetitive elements or not and identified significant differences between the repeat-related miRNAs (RrmiRs) and non-repeat-derived miRNAs in (1) their location in protein-coding and intergenic regions in genomes, (2) the minimum free energy of their hairpin structures, and (3) their conservation in vertebrate genomes. We found some lineage-specific RrmiR families and three lineage-specific expansion families, and provided evidence indicating that some RrmiR families formed and expanded during evolutionary segmental duplication events. We also provided computational and experimental evidence for the functions of the conservative RrmiR families in the three species. Together, our results indicate that repetitive elements contribute to the origin of miRNAs, and large segmental duplication events could prompt the expansion of some miRNA families, including RrmiR families. Our study is a valuable contribution to the knowledge of evolution and function of non-coding region in genome.
Analysis of nucleosome positioning determined by DNA helix curvature in the human genome
Hongde Liu, Xueye Duan, Shuangxin Yu, Xiao Sun
BMC Genomics , 2011, DOI: 10.1186/1471-2164-12-72
Abstract: Curvature profiling revealed that in the vicinity of a transcription start site, there is also a nucleosome-free region. Near transcription factor binding sites, curvature profiling showed a trough, indicating nucleosome depletion. The trough of the curvature profile corresponds well to the high binding scores of transcription factors. Moreover, our analysis suggests that nucleosome positioning has a selective protection role. Target sites of miRNAs are occupied by nucleosomes, while single nucleotide polymorphism sites are depleted of nucleosomes.The results indicate that DNA sequences play an important role in nucleosome positioning, and the positioning is important not only in gene regulation, but also in genetic variation and miRNA functions.Nucleosome positioning refers to the position of a DNA helix with respect to the histone core [1]. Positioning has important roles in gene regulation, because packing DNA into nucleosomes can limit the accessibility of the sequences [2-4]. High-resolution genome-wide nucleosome maps are now available for the genomes of yeast, worms, flies, and humans [2,5-7]. Studies of these nucleosome position datasets have revealed some interesting characteristics, especially for promoter sequences. A typical nucleosome-free region (NFR) is near the transcription start site (TSS) and is followed by a well-positioned nucleosome [4]. Low nucleosome occupancy is a significant feature of a functional transcription factor binding site (TFBS) [8].At the same time, computational predictions using DNA sequence information have also advanced. Since the report of the nucleosome positioning code (an ~10 bp repeating pattern of dinucleotides AA-TT-TA/GC) in yeast [9], some models for predicting nucleosomes have been developed using DNA sequence properties, such as dinucleotide periodicity, and structural information of the DNA helix [5,7,10-13]. The successful predictions suggest that DNA sequences partly encode nucleosomes themselves, although some
Connecting Chromatin Modifying Factors to DNA Damage Response
Weiwei Lai,Hongde Li,Shuang Liu,Yongguang Tao
International Journal of Molecular Sciences , 2013, DOI: 10.3390/ijms14022355
Abstract: Cells are constantly damaged by factors that can induce DNA damage. Eukaryotic cells must rapidly load DNA repair proteins onto damaged chromatin during the DNA damage response (DDR). Chromatin-remodeling complexes use the energy from ATP hydrolysis to remodel nucleosomes and have well-established functions in transcription. Emerging lines of evidence indicate that chromatin-remodeling complexes are important and may remodel nucleosomes during DNA damage repair. New studies also reveal that ATP-dependent chromatin remodeling is involved in cell cycle progression, signal transduction pathways, and interaction and modification of DDR-related proteins that are specifically and intimately connected with the process of DNA damage. This article summarizes the recent advances in our understanding of the interplay between chromatin remodeling and DNA damage response.
Combined Preconditioning and Postconditioning Provides Synergistic Protection against Liver Ischemic Reperfusion Injury
Xiaoyu Song, Ning Zhang, Hongde XU, Liu Cao, Haipeng Zhang
International Journal of Biological Sciences , 2012,
Abstract: Hepatic Ischemia and Reperfusion Injury (IRI) is a major cause of liver damage during liver surgery and transplantation. Ischemic preconditioning and postconditioning are strategies that can reduce IRI. In this study, different combined types of pre- and postconditioning procedures were tested in a murine warm hepatic IRI model to evaluate their protective effects. Proanthocyanidins derived from grape seed was used before ischemia process as pharmacological preconditioning to combine with technical preconditioning and postconditioning. Three pathways related to IRI, including reactive oxygen species (ROS) generation, pro-inflammatory cytokines release and hypoxia responses were examined in hepatic IRI model. Individual and combined pre- and postconditioning protocols significantly reduce liver injury by decreasing the liver ROS and cytokine levels, as well as enhancing the hypoxia tolerance response. Our data also suggested that in addition to individual preconditioning or postconditioning, the combination of these two treatments could reduce liver ischemia/reperfusion injury more effectively by increasing the activity of ROS scavengers and antioxidants. The utilization of grape seed proanthocyanidins (GSP) could improve the oxidation resistance in combined pre- and postconditioning groups. The combined protocol also further increased the liver HIF-1 alpha protein level, but had no effect on pro-inflammatory cytokines release compared to solo treatment.
A new approach to the prediction of transmembrane structures
HongDe Liu,Rui Wang,XiaoQuan Lu,Jing Chen,Xiuhui Liu,Lan Ding
Chinese Science Bulletin , 2008, DOI: 10.1007/s11434-008-0055-5
Abstract: About 20%–30% of genome products have been predicted as membrane proteins, which have significant biological functions. The prediction of the amount and position for the transmembrane protein helical segments (TMHs) is the hot spot in bioinformatics. In this paper, a new approach, maximum spectrum of continuous wavelet transform (MSCWT), is proposed to predict TMHs. The predictions for eight SARS-CoV membrane proteins indicate that MSCWT has the same capacity with software TMpred. Moreover, the test on a dataset of 131 structure-known proteins with 548 TMHs shows that the prediction accuracy of MSCWT for TMHs is 91.6% and that for membrane protein is 89.3%.
A new approach to the prediction of transmembrane structures
HongDe Liu,Rui Wang,XiaoQuan Lu,Jing Chen,Xiuhui Liu,Lan Ding,

科学通报(英文版) , 2008,
Abstract: About 20%-30% of genome products have been predicted as membrane proteins, which have sig-nificant biological functions. The prediction of the amount and position for the transmembrane protein helical segments (TMHs) is the hot spot in bioinformatics. In this paper, a new approach, maximum spectrum of continuous wavelet transform (MSCWT), is proposed to predict TMHs. The predictions for eight SARS-CoV membrane proteins indicate that MSCWT has the same capacity with software TMpred. Moreover, the test on a dataset of 131 structure-known proteins with 548 TMHs shows that the predic-tion accuracy of MSCWT for TMHs is 91.6% and that for membrane protein is 89.3%.
Origin and evolution of a placental-specific microRNA family in the human genome
Zhidong Yuan, Xiao Sun, Dongke Jiang, Yan Ding, Zhiyuan Lu, Lejun Gong, Hongde Liu, Jianming Xie
BMC Evolutionary Biology , 2010, DOI: 10.1186/1471-2148-10-346
Abstract: We have shown that all members of the miR-1302 family are derived from MER53 elements. Although the conservation scores of the MER53-derived pre-miRNA sequences are low, we have identified 36 potential paralogs of MER53-derived miR-1302 genes in the human genome and 58 potential orthologs of the human miR-1302 family in placental mammals. We suggest that in placental species, this miRNA family has evolved following the birth-and-death model of evolution. Three possible mechanisms that can mediate miRNA duplication in evolutionary history have been proposed: the transposition of the MER53 element, segmental duplications and Alu-mediated recombination. Finally, we have found that the target genes of miR-1302 are over-represented in transportation, localization, and system development processes and in the positive regulation of cellular processes. Many of them are predicted to function in binding and transcription regulation.The members of miR-1302 family that are derived from MER53 elements are placental-specific miRNAs. They emerged at the early stage of the recent 180 million years since eutherian mammals diverged from marsupials. Under the birth-and-death model, the miR-1302 genes have experienced a complex expansion with some members evolving by segmental duplications and some by Alu-mediated recombination events.MiRNAs are endogenously expressed, single-stranded RNAs ~22 nucleotides (nt) in length [1]. In animals, miRNAs are transcribed as long primary miRNA (pri-miRNA) sequences that are processed in the nucleus to give precursor sequences of miRNA (pre-miRNAs). The pre-miRNA sequences are exported to the cytoplasm where they are cleaved to produce mature miRNAs. The miRNAs are then incorporated into RNA-induced silencing complexes where they function either to inhibit translation or to mediate the degradation of their target mRNAs commonly by binding to complementary regions in the 3' untranslated regions (UTRs) [2-4]. MiRNAs play a pivotal role in many cellula
Analysis of nucleosome positioning in promoters of miRNA genes and protein-coding genes
HongDe Liu,DeJin Zhang,JianMing Xie,ZhiDong Yuan,Xin Ma,ZhiYuan Lu,LeJun Gong,Xiaoauthor Sun
Chinese Science Bulletin , 2010, DOI: 10.1007/s11434-009-3730-2
Abstract: Nucleosome positioning in promoters is important for gene transcription regulation. In this paper, with a nucleosome prediction model, curvature profile, the characteristics of nucleosome positioning in promoters are analyzed for miRNA genes and protein-coding genes. In the vicinity of transcription start site (TSS), there is a nucleosome-free region (NFR) followed by a positioned nucleosome at ~200 bp downstream of TSS. A similar characteristic is observed in independent intronic promoters and intergenic promoters, namely, both types of promoters have a longer NFR in 0– 400 bp upstream of TSS. Moreover, transcription factor binding sites (TFBSs) locate in the NFR with a high concentration. However, nucleosome pattern in dependent intronic promoters are like that in protein-coding promoters, with two nucleosomes positioned at 200– 400 bp and 400– 600 bp upstream of TSS. The results indicate nucleosome positioning is probably different in independent miRNA promoters and protein-coding promoters; and positioning seems to be an important factor not only in regulation of protein-coding gene, but also in that of miRNA gene.
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