oalib

Publish in OALib Journal

ISSN: 2333-9721

APC: Only $99

Submit

Any time

2019 ( 66 )

2018 ( 1896 )

2017 ( 1791 )

2016 ( 1848 )

Custom range...

Search Results: 1 - 10 of 119839 matches for " Hongda Wang "
All listed articles are free for downloading (OA Articles)
Page 1 /119839
Display every page Item
Tetrameric Structure of Centromeric Nucleosomes in Interphase Drosophila Cells
Yamini Dalal,Hongda Wang,Stuart Lindsay,Steven Henikoff
PLOS Biology , 2012, DOI: 10.1371/journal.pbio.0050218
Abstract: Centromeres, the specialized chromatin structures that are responsible for equal segregation of chromosomes at mitosis, are epigenetically maintained by a centromere-specific histone H3 variant (CenH3). However, the mechanistic basis for centromere maintenance is unknown. We investigated biochemical properties of CenH3 nucleosomes from Drosophila melanogaster cells. Cross-linking of CenH3 nucleosomes identifies heterotypic tetramers containing one copy of CenH3, H2A, H2B, and H4 each. Interphase CenH3 particles display a stable association of approximately 120 DNA base pairs. Purified centromeric nucleosomal arrays have typical “beads-on-a-string” appearance by electron microscopy but appear to resist condensation under physiological conditions. Atomic force microscopy reveals that native CenH3-containing nucleosomes are only half as high as canonical octameric nucleosomes are, confirming that the tetrameric structure detected by cross-linking comprises the entire interphase nucleosome particle. This demonstration of stable half-nucleosomes in vivo provides a possible basis for the instability of centromeric nucleosomes that are deposited in euchromatic regions, which might help maintain centromere identity.
Single-epitope recognition imaging of native chromatin
Hongda Wang, Yamini Dalal, Steven Henikoff, Stuart Lindsay
Epigenetics & Chromatin , 2008, DOI: 10.1186/1756-8935-1-10
Abstract: Here we apply a recognition mode of AFM imaging to directly identify CenH3 within histone core particles released from native centromeric chromatin. More than 90% of these particles were found to be tetrameric in height. The specificity of recognition was confirmed by blocking with a CenH3 peptide, and the strength of the interaction was quantified by force measurements. These results imply that the particles imaged by AFM are indeed mature CenH3-containing hemisomes.Efficient and highly specific recognition of CenH3 in histone core particles isolated from native centromeric chromatin demonstrates that tetramers are the predominant form of centromeric nucleosomes in mature tetramers. Our findings provide proof of principle that this approach can yield insights into chromatin biology using direct and rapid detection of native nucleosomes in physiological salt concentrations.Eukaryotic genomes are packaged with octameric protein particles, consisting of two copies each of histones H2A, H2B, H3 and H4, which wrap nearly two turns of DNA to form nucleosomes [1]. Since the discovery of nucleosomes in the early 1970s, a variety of techniques have been applied to their study. However, both ultrastructural technologies (e.g. crystallography and electron microscopy) and biochemical analyses (e.g. nuclease assays and sedimentation) have been limited in their scope, because they cannot simultaneously assay structure and dynamics. In recent years, progress has been made in applying new technologies that have the potential to bridge the gap between static ultrastructural features and dynamic physiological processes in the study of chromatin. These technologies, which include scanning confocal fluorescence microscopy [2], molecular tweezers [3,4] and atomic force microscopy (AFM) [5,6], have provided remarkable insights into the behavior of individual nucleosomes. The combination of single-molecule resolution, solution biochemistry and observation of native macromolecular complex
Tetrameric Structure of Centromeric Nucleosomes in Interphase Drosophila Cells
Yamini Dalal,Hongda Wang,Stuart Lindsay,Steven Henikoff
PLOS Biology , 2007, DOI: 10.1371/journal.pbio.0050218
Abstract: Centromeres, the specialized chromatin structures that are responsible for equal segregation of chromosomes at mitosis, are epigenetically maintained by a centromere-specific histone H3 variant (CenH3). However, the mechanistic basis for centromere maintenance is unknown. We investigated biochemical properties of CenH3 nucleosomes from Drosophila melanogaster cells. Cross-linking of CenH3 nucleosomes identifies heterotypic tetramers containing one copy of CenH3, H2A, H2B, and H4 each. Interphase CenH3 particles display a stable association of approximately 120 DNA base pairs. Purified centromeric nucleosomal arrays have typical “beads-on-a-string” appearance by electron microscopy but appear to resist condensation under physiological conditions. Atomic force microscopy reveals that native CenH3-containing nucleosomes are only half as high as canonical octameric nucleosomes are, confirming that the tetrameric structure detected by cross-linking comprises the entire interphase nucleosome particle. This demonstration of stable half-nucleosomes in vivo provides a possible basis for the instability of centromeric nucleosomes that are deposited in euchromatic regions, which might help maintain centromere identity.
Single Nucleotide Polymorphisms in the Tumor Necrosis Factor-Alpha Gene Promoter Region Alter the Risk of Psoriasis Vulgaris and Psoriatic Arthritis: A Meta-Analysis
Junqing Zhu, Hongda Qu, Xiaoguang Chen, Hao Wang, Juan Li
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0064376
Abstract: Background It has been confirmed that tumor necrosis factor-alpha (TNFα), a macrophage-derived pro-inflammatory cytokine, plays an important role in the pathogenesis of psoriasis vulgaris and psoriatic arthritis (PsV&PsA). In contrast, the reported association of TNFα gene promoter region single nucleotide polymorphisms (SNPs) and PsV&PsA has remained controversial. Accordingly, we performed a meta-analysis to provide new evidence that SNPs in the TNFα gene promoter region alter not only the risk of psoriasis vulgaris (PsV) or psoriatic arthritis (PsA) but also of PsV&PsA. Methods Interrelated literature dated to October 2012 was acquired from the PubMed, ScienceDirect, and SpringerLink databases. The number of the genotypes and/or alleles for the TNFα promoter in the PsV and PsA and control subjects was obtained. Odds ratios (ORs) and 95% confidence intervals (CIs) were used to calculate the risk of PsV and/or PsA with TNFα promoter SNPs. Results A total of 26 papers of 2159 for PsV (2129 normal controls) and 2360 for PsA (2997 normal controls) were included in our meta-analysis. The results showed that the variant genotype and allele of TNFα -308A/G was protective in pooled groups of patients with PsV&PsA (OR = 0.682, 0.750; 95% CI, 0.596-0.779, 0.653-0.861). However, the variant genotypes and alleles of TNFα -238A/G and -857T/C had an increased risk of PsV&PsA (OR = 2.493, 2.228, 1.536, 1.486, 95% CI, 1.777-3.498, 1.628-3.049, 1.336-1.767, 1.309-1.685). Moreover, the meta-analysis revealed a significant association between TNFα -238A/G and -857T/C polymorphism and PsA susceptibility (OR = 2.242, 2.052, 1.419, 1.465; 95% CI, 1.710-2.941, 1.614-2.610, 1.214-1.658, 1.277-1.681). In contrast, the variant genotypes and alleles of TNFα -308A/G proved to be protective against PsV (OR = 0.574, 0.650, 95% CI, 0.478-0.690, 0.556-0.759), whereas TNFα -238A/G was found to have a risk association (OR = 2.636, 2.223, 95% CI, 1.523-4.561, 1.317-3.751). Conclusions SNPs in the TNFα gene promoter region alter the risk of PsV and/or PsA.
Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails
Hongda Huang, Jiahai Zhang, Weiqun Shen, Xingsheng Wang, Jiawen Wu, Jihui Wu, Yunyu Shi
BMC Structural Biology , 2007, DOI: 10.1186/1472-6807-7-57
Abstract: Here we report the solution structure of human Brd2 BD2 determined by NMR. Although the overall fold resembles the bromodomains from other proteins, significant differences can be found in loop regions, especially in the ZA loop in which a two amino acids insertion is involved in an uncommon π-helix, termed πD. The helix πD forms a portion of the acetyl-lysine binding site, which could be a structural characteristic of Brd2 BD2 and other BET bromodomains. Unlike Brd2 BD1, BD2 is monomeric in solution. With NMR perturbation studies, we have mapped the H4-AcK12 peptide binding interface on Brd2 BD2 and shown that the binding was with low affinity (2.9 mM) and in fast exchange. Using NMR and mutational analysis, we identified several residues important for the Brd2 BD2-H4-AcK12 peptide interaction and probed the potential mechanism for the specific recognition of acetylated histone codes by Brd2 BD2.Brd2 BD2 is monomeric in solution and dynamically interacts with H4-AcK12. The additional secondary elements in the long ZA loop may be a common characteristic of BET bromodomains. Surrounding the ligand-binding cavity, five aspartate residues form a negatively charged collar that serves as a secondary binding site for H4-AcK12. We suggest that Brd2 BD1 and BD2 may possess distinctive roles and cooperate to regulate Brd2 functions. The structure basis of Brd2 BD2 will help to further characterize the functions of Brd2 and its BET members.Eukaryotic transcription is a highly regulated process. Transcription activation in eukaryotes requires the modification of histones on enhancers and promoters [1,2]. Histone acetylation plays a major role in this modification, and forms histone codes in combination with methylation, phosphorylation and ubiquitination [3-5]. One potential postulate of histone codes is that defined patterns of modification in histones can be recognized by specific factors. Bromodomain, a conserved ~110 amino acid module that is originally identified by seque
A STUDY ON CHEMICAL CONSTITUENTS OF ESSENTIAL OIL FROM CEPHALOTAXUS FORTUNEI LEAVES
三尖杉叶精油化学成分的研究

Su Yingjuan,Wang Ting,Zhang Hongda,
苏应娟
,王艇,张宏达

植物科学学报 , 1995,
Abstract: 三尖杉叶精油化学成分的研究苏应娟,王艇,张宏达(中国科学院武汉植物研究所武汉430074)(中山大学生命科学学院广州510275)关键词三尖杉,精油,化学分类ASTUDYONCHEMICALCONSTITUENTSOFESSENTIALOILFROM...
A STUDY ON CHEMICAL CONSTITUENTS OF ESSENTIAL OIL FROM PODOCARPUS MACROPHYLLUS
罗汉松叶精油化学成分的研究

Su Yingjuan,Wang Ting,Zhang Hongda,
苏应娟
,王艇,张宏达

植物科学学报 , 1995,
Abstract: 罗汉松叶精油化学成分的研究苏应娟,王艇,张宏达(中国科学院武汉植物研究所武汉430074)(广州中山大学生命科学学院510275)关键词罗汉松,精油,化学分类ASTUDYONCHEMICALCONSTITUENTSOFESSENTIALOILFROM...
The Asymmetrical Structure of Golgi Apparatus Membranes Revealed by In situ Atomic Force Microscope
Haijiao Xu, Weiheng Su, Mingjun Cai, Junguang Jiang, Xianlu Zeng, Hongda Wang
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0061596
Abstract: The Golgi apparatus has attracted intense attentions due to its fascinating morphology and vital role as the pivot of cellular secretory pathway since its discovery. However, its complex structure at the molecular level remains elusive due to limited approaches. In this study, the structure of Golgi apparatus, including the Golgi stack, cisternal structure, relevant tubules and vesicles, were directly visualized by high-resolution atomic force microscope. We imaged both sides of Golgi apparatus membranes and revealed that the outer leaflet of Golgi membranes is relatively smooth while the inner membrane leaflet is rough and covered by dense proteins. With the treatment of methyl-β-cyclodextrin and Triton X-100, we confirmed the existence of lipid rafts in Golgi apparatus membrane, which are mostly in the size of 20 nm –200 nm and appear irregular in shape. Our results may be of significance to reveal the structure-function relationship of the Golgi complex and pave the way for visualizing the endomembrane system in mammalian cells at the molecular level.
A Comparative Study of Amplitude and Timing Estimation in Experimental Particle Physics using Monte Carlo Simulation  [PDF]
Hongda Xu, Datao Gong, Yun Chiu
Journal of Modern Physics (JMP) , 2013, DOI: 10.4236/jmp.2013.45B009
Abstract:

Optimal detection of liquid ionization calorimeter signal in experimental particle physics is considered. A few linear and nonlinear approaches for amplitude and arrival time estimation based on the χ2 function are compared in simulation considering the noise sample correlation introduced by the analog pulse shaper. The estimation bias of the first-order approximation, a.k.a linear optimal filtering, is studied and contrasted to those of the second-order as well as the exhaustive search. A gradient-descent technique is presented as an alternative to the exhaustive search with significantly reduced search time and computation complexity. Results from various pulse shapers including the CR-RC2, CR-RC3, and CR2-RC2 are also compared.

Studying the Nucleated Mammalian Cell Membrane by Single Molecule Approaches
Weidong Zhao, Yongmei Tian, Mingjun Cai, Feng Wang, Jiazhen Wu, Jing Gao, Shuheng Liu, Junguang Jiang, Shibo Jiang, Hongda Wang
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0091595
Abstract: The cell membrane plays a key role in compartmentalization, nutrient transportation and signal transduction, while the pattern of protein distribution at both cytoplasmic and ectoplasmic sides of the cell membrane remains elusive. Using a combination of single-molecule techniques, including atomic force microscopy (AFM), single molecule force spectroscopy (SMFS) and stochastic optical reconstruction microscopy (STORM), to study the structure of nucleated cell membranes, we found that (1) proteins at the ectoplasmic side of the cell membrane form a dense protein layer (4 nm) on top of a lipid bilayer; (2) proteins aggregate to form islands evenly dispersed at the cytoplasmic side of the cell membrane with a height of about 10–12 nm; (3) cholesterol-enriched domains exist within the cell membrane; (4) carbohydrates stay in microdomains at the ectoplasmic side; and (5) exposed amino groups are asymmetrically distributed on both sides. Based on these observations, we proposed a Protein Layer-Lipid-Protein Island (PLLPI) model, to provide a better understanding of cell membrane structure, membrane trafficking and viral fusion mechanisms.
Page 1 /119839
Display every page Item


Home
Copyright © 2008-2017 Open Access Library. All rights reserved.