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Search Results: 1 - 10 of 119856 matches for " Wang Xiaochen "
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Templated J-Aggregate Nanotubes for the Detection of Dopamine  [PDF]
Samuel Rhodes, Xiaochen Wang, Wenlang Liang, Hyoung Jin Cho, Jiyu Fang
Journal of Materials Science and Chemical Engineering (MSCE) , 2017, DOI: 10.4236/msce.2017.51018
Abstract: J-aggregates of dye molecules are a unique supramolecular structure, which shows great promise in photoelectric devices due to its remarkable optical and transport properties. In this paper, we report the templated formation of J-aggregate nanotubes by the adsorption of 3,3’-diethylthiacarbocyanine iodide on the self-assembled nanotubes of lithocholic acid. The optical and electronic properties of the templated J-aggregate nanotubes are studied. A sensor platform is fabricated by depositing the J-aggregate nanotubes on interdigitated gold electrodes for the detection of dopamine (DA). We find that the current change of the J-aggregate nanotube-based sensor platform in response to DA is linear in the concentration range from 10 nM to 70 nM, giving the detection limit of 0.27 nM.
Xuesaitong Soft Capsule (Chinese Patent Medicine) for the Treatment of Unstable Angina Pectoris: A Meta-Analysis and Systematic Review
Xiaochen Yang,Xingjiang Xiong,Heran Wang,Guoyan Yang,Jie Wang
Evidence-Based Complementary and Alternative Medicine , 2013, DOI: 10.1155/2013/948319
Abstract: Objective. To provide a systematic review to evaluate the effectiveness and safety of Xuesaitong soft capsule (XST) in treating unstable angina (UA). Methods. An extensive search of 6 medical databases was performed up to August 2013. Randomized controlled trials (RCTs) involving XST alone or combined with conventional drugs versus conventional drugs were included. A meta-analysis of reduction of angina symptoms and electrocardiogram (ECG) improvement was performed to evaluate the effects of XST on UA. Results. After researching, a total of 6 RCTs with 716 participants were included. Our review showed that XST combined with conventional drugs had significant effect on relieving angina symptoms (RR: ; ) and improving ECG (RR: ; ) compared with conventional drugs alone. Conclusions. XST appears to have beneficial effects on improvement of ECG, reduction of angina symptoms, and decreasing the frequency and duration of angina attack in participants with UA. However, the findings should be interpreted with caution due to the poor methodological quality of the included trials. 1. Introduction Coronary artery disease (CHD) is one of the leading causes of death in most developed and some developing countries [1, 2]. Antiplatelet agents and anticoagulants have demonstrated variable clinical effects in coronary heart disease (CHD), including unstable angina pectoris (UA) and acute myocardial infarction (AMI) [3, 4]. Among the antiplatelet agents, aspirin has been shown to reduce the risk for thrombosis and ischemic events. However, the possibility of aspirin resistance, which has been described as a number of phenomena, including antithrombotic complications, prolongation of the bleeding time, and inhibition of thromboxane biosynthesis, provides an impetus for researching new medicine with high effectiveness and fewer adverse effects [5]. Sanqi, also known as radix notoginseng, is a hemostatic herbal medicine that may have protective effect in patients with UA [6] and has been used for cardiovascular diseases for hundreds of years in China. Recently, with the growing and sustained interest in the benefits of Chinese herbal medicine (CHM) and potential drug interactions with western medications, Sanqi called much attention for its good cardiovascular effects, including inhibition of platelet aggregation, increasing blood flow, improving left ventricular diastolic function in hypertensive patients, and anti-inflammatory effect [7, 8]. Radix notoginseng consists of complex compounds, including saponin, dencichine, polysaccharides, amino acids, flavonoids,
Phospho-Tyrosine(s) vs. Phosphatidylinositol Binding in Shc Mediated Integrin Signaling  [PDF]
Xiaochen Lin, Olga Vinogradova
American Journal of Molecular Biology (AJMB) , 2015, DOI: 10.4236/ajmb.2015.52003
Abstract: The Shc adaptor protein, particularly its p52 isoform, has been identified as a primary signaling partner for the tyrosine(s)-phosphorylated cytoplasmic tails of activated β3 integrins. Inspired by our recent structure of the Shc PTB domain in complex with a bi-phosphorylated peptide derived from β3 cytoplasmic tail, we have initiated the investigation of Shc interaction with phospholipids of the membrane. We are particularly focused on PtdIns and their effects on Shc mediated integrin signaling in vitro. Here we present thermodynamic profiles and molecular details of the interactions between Shc, integrin, and PtdIns, all of which have been studied by ITC and solution NMR methods. A model of p52 Shc interaction with phosphorylated β3 integrin cytoplasmic tail at the cytosolic face of the plasma membrane is proposed based on these data.
Comprehensive Identification and Annotation of Cell Type-Specific and Ubiquitous CTCF-Binding Sites in the Human Genome
Hebing Chen, Yao Tian, Wenjie Shu, Xiaochen Bo, Shengqi Wang
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0041374
Abstract: Chromatin insulators are DNA elements that regulate the level of gene expression either by preventing gene silencing through the maintenance of heterochromatin boundaries or by preventing gene activation by blocking interactions between enhancers and promoters. CCCTC-binding factor (CTCF), a ubiquitously expressed 11-zinc-finger DNA-binding protein, is the only protein implicated in the establishment of insulators in vertebrates. While CTCF has been implicated in diverse regulatory functions, CTCF has only been studied in a limited number of cell types across human genome. Thus, it is not clear whether the identified cell type-specific differences in CTCF-binding sites are functionally significant. Here, we identify and characterize cell type-specific and ubiquitous CTCF-binding sites in the human genome across 38 cell types designated by the Encyclopedia of DNA Elements (ENCODE) consortium. These cell type-specific and ubiquitous CTCF-binding sites show uniquely versatile transcriptional functions and characteristic chromatin features. In addition, we confirm the insulator barrier function of CTCF-binding and explore the novel function of CTCF in DNA replication. These results represent a critical step toward the comprehensive and systematic understanding of CTCF-dependent insulators and their versatile roles in the human genome.
A novel representation of RNA secondary structure based on element-contact graphs
Wenjie Shu, Xiaochen Bo, Zhiqiang Zheng, Shengqi Wang
BMC Bioinformatics , 2008, DOI: 10.1186/1471-2105-9-188
Abstract: In this study, we present a complete and fine scheme for RNA graph representation as a new basis for constructing RNA topological indices. We propose a combination of three vertex-weighted element-contact graphs (ECGs) to describe the RNA element details and their adjacent patterns in RNA secondary structure. Both the stem and loop topologies are encoded completely in the ECGs. The relationship among the three typical topological index families defined by their ECGs and RNA secondary structures was investigated from a dataset of 6,305 ncRNAs. The applicability of topological indices is illustrated by three application case studies. Based on the applied small dataset, we find that the topological indices can distinguish true pre-miRNAs from pseudo pre-miRNAs with about 96% accuracy, and can cluster known types of ncRNAs with about 98% accuracy, respectively.The results indicate that the topological indices can characterize the details of RNA structures and may have a potential role in identifying and classifying ncRNAs. Moreover, these indices may lead to a new approach for discovering novel ncRNAs. However, further research is needed to fully resolve the challenging problem of predicting and classifying noncoding RNAs.Recent years have witnessed an explosive growth in RNA research, as numerous new noncoding RNAs (ncRNAs) have been discovered [1,2], and rich information has been revealed in the various relationships between their structures and cellular functions [3]. It is increasingly evident that RNAs play important roles, far beyond transferring genetic information from DNA to protein. Exploring the structural diversity of the RNA population constitutes a central goal in RNomics [4], which requires new computational methods for the comparison, identification and classification of RNA.As there remain many difficulties in predicting three-dimensional RNA structure, secondary structures are typically used as a basis for researching RNA conformation. RNA secondary st
EvoRSR: an integrated system for exploring evolution of RNA structural robustness
Wenjie Shu, Ming Ni, Xiaochen Bo, Zhiqiang Zheng, Shengqi Wang
BMC Bioinformatics , 2009, DOI: 10.1186/1471-2105-10-249
Abstract: In this study, we developed the open-source integrated system EvoRSR (Evolution of RNA Structural Robustness) to explore the evolution of robustness based on biologically important landscapes induced by RNA folding. EvoRSR is object-oriented, modular, and freely available at http://biotech.bmi.ac.cn/EvoRSR webcite under the GNU/GPL license. We present an overview of EvoRSR package and illustrate its features with the miRNA gene cel-mir-357.EvoRSR is a novel and flexible package for exploring the evolution of robustness. Accordingly, EvoRSR can be used for future studies to investigate the evolution and origin of robustness and to address other common questions about robustness. While the current EvoRSR environment is a versatile analysis framework, future versions can include features to enhance evolutionary studies of robustness.Robustness is a fundamental and ubiquitous phenomenon in biological systems, in which phenotypes are resistant to change in the presence of various perturbations. When these perturbations are inherited, such as genetic mutations, the phenomenon is known as genetic robustness. Alternatively, when the perturbations are due to environmental factors, the phenomenon is called environmental robustness [1]. Both types of robustness appear at various levels of biological organization, affecting gene expression, protein folding, metabolic flux, physiological homeostasis, development, and organism fitness [2]. Biologists' long-standing interest in robustness has roots in Fisher's work on dominance [3-5] and Waddington's developmental canalization research [6,7]. Despite being found throughout nature, the evolutionary origins of robustness remain unclear. Current competing explanations for the origins of robustness include that it evolves as a direct consequence of natural selection, as an intrinsic property of adaptations, or as congruent correlate of environment robustness. Additionally, it is unknown how robustness evolves and how the robustness va
Correlation between sequence conservation and structural thermodynamics of microRNA precursors from human, mouse, and chicken genomes
Ming Ni, Wenjie Shu, Xiaochen Bo, Shengqi Wang, Songgang Li
BMC Evolutionary Biology , 2010, DOI: 10.1186/1471-2148-10-329
Abstract: We investigated the correlation between pre-miRNA sequence conservation and structural stability as measured by adjusted minimum folding free energies in pre-miRNAs isolated from human, mouse, and chicken. The analysis revealed that conserved and non-conserved pre-miRNA sequences had structures with similar average stabilities. However, the relatively ultra stable and unstable pre-miRNAs were more likely to be non-conserved than pre-miRNAs with moderate stability. Non-conserved pre-miRNAs had more G+C than A+U nucleotides, while conserved pre-miRNAs contained more A+U nucleotides. Notably, the U content of conserved pre-miRNAs was especially higher than that of non-conserved pre-miRNAs. Further investigations showed that conserved and non-conserved pre-miRNAs exhibited different structural element features, even though they had comparable levels of stability.We proposed that there is a correlation between structural thermodynamic stability and sequence conservation for pre-miRNAs from human, mouse, and chicken genomes. Our analyses suggested that pre-miRNAs with relatively ultra stable or unstable structures were less favoured by natural selection than those with moderately stable structures. Comparison of nucleotide compositions between non-conserved and conserved pre-miRNAs indicated the importance of U nucleotides in the pre-miRNA evolutionary process. Several characteristic structural elements were also detected in conserved pre-miRNAs.MicroRNAs (miRNAs) are small endogenous non-coding RNAs that regulate expression at the post-transcriptional level in animals and plants [1]. Both plant and animal miRNAs are cleaved from one arm of foldback precursors (pre-miRNAs). It is generally accepted that pre-miRNA secondary and/or tertiary structures are critical in miRNA biogenesis [2-5]. The thermodynamic stability of pre-miRNA hairpin secondary structures, hereafter called pre-miRNA stability, is a fundamental property of RNA structure and has been systematically studie
In silico genetic robustness analysis of microRNA secondary structures: potential evidence of congruent evolution in microRNA
Wenjie Shu, Xiaochen Bo, Ming Ni, Zhiqiang Zheng, Shengqi Wang
BMC Evolutionary Biology , 2007, DOI: 10.1186/1471-2148-7-223
Abstract: We examine the robustness of 1,082 miRNA genes covering six species. Our data suggest the stem-loop structures of miRNA precursors exhibit a significantly higher level of genetic robustness, which goes beyond the intrinsic robustness of the stem-loop structure and is not a byproduct of the base composition bias. Furthermore, we demonstrate that the phenotype of miRNA buffers against genetic perturbations, and at the same time is also insensitive to environmental perturbations.The results suggest that the increased robustness of miRNA stem-loops may result from congruent evolution for environment robustness. Potential applications of our findings are also discussed.Robustness, a fundamental and ubiquitously observed phenomenon in biological systems, is defined as the ability to maintain stable functioning in the face of various perturbations, and is characterized as genetic or environmental robustness, depending on whether the perturbations are inheritable or not [1]. Genetic robustness describes insensitivity of a phenotype facing genetic mutations, and the insensitivity to environmental factors is called environmental robustness. Phenotype robustness appears at various levels of biological systems, including gene expression, protein folding, metabolic flux, physiological homeostasis, development, and even organism fitness [2]. It is consequently not surprising that biologists have a long-standing interest in robustness, going back to Fisher's work on dominance [3-5], and to Waddington's developmental canalization research [6,7]. Hiroaki Kitano argues that the requirements for robustness and evolvability are similar, since robustness facilitates evolution and evolution favours robust traits [8]. A proper understanding of the origin of robustness in biological systems will catalyze our understanding of evolution [9].The evolution of mechanism underlying the buffering of the phenotype against genetic and environmental influences has received much theoretical and exper
Association of mutation patterns in gyrA/B genes and ofloxacin resistance levels in Mycobacterium tuberculosis isolates from East China in 2009
Zhenling Cui, Jie Wang, Junmei Lu, Xiaochen Huang, Zhongyi Hu
BMC Infectious Diseases , 2011, DOI: 10.1186/1471-2334-11-78
Abstract: The quinolone resistance-determining region of gyrA/B were sequenced in 192 M. tuberculosis clinical isolates and the minimal inhibitory concentrations (MICs) of 95 ofloxacin-resistant M. tuberculosis isolates were determined by using microplate nitrate reductase assays.Mutations in gyrA (codons 90, 91 and 94) and in gyrB (G551R, D500N, T539N, R485C/L) were observed in 89.5% (85/95) and 11.6% (11/95) of ofloxacin-resistant strains, respectively. The gyrB mutations G551R and G549D were observed in 4.1% (4/97) of ofloxacin-susceptible strains and no mutation was found in gyrA in ofloxacin-susceptible strains. The MICs of all ofloxacin-resistant strains showed no significant difference among strains with mutations at codons 90, 91 or 94 in gyrA (F = 1.268, p = 0.287). No differences were detected among strains with different amino acid mutations in the quinolone resistance-determining region of gyrA (F = 1.877, p = 0.123). The difference in MICs between ofloxacin-resistant strains with mutations in gyrA only and ofloxacin-resistant strains with mutations in both gyrA and gyrB genes was not statistically significant (F = 0.549, p = 0.461).Although gyrA/B mutations can lead to ofloxacin resistance in M. tuberculosis, there were no associations of different mutation patterns in gyrA/B and the level of ofloxacin resistance in M. tuberculosis isolates from East China in 2009.Fluoroquinolones (FQs), such as ofloxacin (OFX), levofloxacin and moxifloxacin, are widely used anti-tubercular therapeutic agents for the treatment of multidrug-resistant tuberculosis (MTB) [1]. In mycobacteria, FQs bind to DNA gyrase and inhibit DNA replication [2]. This mechanism has been verified by the structural analysis and functional analysis of enzymes of M. tuberculosis (MTB), including DNA gyrase [3,4]. These studies showed that the MTB strains with wild-type gyrA/B genes were highly susceptible to FQs. Moreover, a murine model study showed that low-level FQ resistance could be overcome with
Pb2+, Cu2+, Zn2+, Mg2+ and Mn2+ reduce the affinities of flavone, genistein and kaempferol for human serum albumin in vitro
Yang Fan,Wang Jie,Liu Chunxi,Xiaochen Xu
Archives of Biological Sciences , 2011, DOI: 10.2298/abs1103623y
Abstract: Flavone (Fl), genistein (Gen) and kaempferol (Kol) were studied for their affinities towards human serum albumin (HSA) in the presence and absence of Pb2+,Cu2+,Zn2+,Mg2+ and Mn2+. The fluorescence intensities of HSA decreased with increasing concentration of the three flavonoids. Kaempferol resulted in a blue-shift of the λem of HSA from 336 to 330 nm; flavone showed an obvious red-shift of the λem of HSA from 336 to 342 nm; genistein did not cause an obvious blue-shift or red-shift of the λem of HSA. However, the extents of λem-shifts induced by the flavonoids in the presence of metal ions were much bigger than that in the absence of mental ions. Pb2+,Cu2+,Zn2+,Mg2+ and Mn2+ reduced the quenching constants of the flavonoids for HSA by 14.6% to 60.7% , 28% to 67.9%,3.5% to 59.4%, 23.2% to 63.7% and 14% to 65%, respectively. The affinities of flavone, genistein and kaempferol for HSA decreased about 10.84%, 10.05%and 3.56% in the presence of Pb2+, respectively. Cu2+ decreased the affinities of flavone, genistein and kaempferol for HSA about 14.04%, 5.14%and 8.89%, respectively. Zn2+ decreased the affinities of flavone, genistein and kaempferol for HSA about 3.79%, 0.55% and 3.58%, respectively. Mg2+ decreased the affinities of flavone, genistein and kaempferol for HSA about 16.94%, 2.94%and 7.04%, respectively. Mn2+ decreased the affinities of flavone, genistein and kaempferol for HSA about 14.24%, 3.66% and 4.78%, respectively.
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