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Search Results: 1 - 10 of 10671 matches for " Linfang Du "
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Evaluation of GO-based functional similarity measures using S. cerevisiae protein interaction and expression profile data
Tao Xu, LinFang Du, Yan Zhou
BMC Bioinformatics , 2008, DOI: 10.1186/1471-2105-9-472
Abstract: In this study, we evaluated five functional similarity methods using both protein-protein interaction (PPI) and expression data of S. cerevisiae. The receiver operating characteristics (ROC) and correlation coefficient analysis of these methods showed that the maximum method outperformed the other methods. Statistical comparison of multiple- and single-term annotated proteins in biological process ontology indicated that genes with multiple GO terms may be more reliable for separating true positives from noise.This study demonstrated the reliability of current approaches that elevate the similarity of GO terms to the similarity of proteins. Suggestions for further improvements in functional similarity analysis are also provided.Gene ontology (GO) [1] describes gene products based on their functions and is a structured and controlled vocabulary that has become quite popular among the known taxonomies. The root ontology (ALL) of GO consists of three independent terms: biological process (BP), molecular function (MF), and cellular component (CC). GO data provides a novel way to measure the functional relationship between gene products, which is the basis of most gene correlation studies [2]. Researchers interested in functionally related genes always hope to improve the accuracy of the results beyond the boundaries of currently available experimental data. Addition of knowledge data, for example, by computing the semantic similarity between genes may partially address this problem. Most semantic-based applications follow a three-step approach that includes semantic similarity calculations of paired GO terms, functional similarity calculations of all possible combinations of related GO terms, and further studies such as clustering analysis [3-6]. However, optimization of the methods for elevating the similarity of GO terms to the similarity of proteins is still required.In semantic-based applications, it is necessary to compute the similarity among GO terms before inves
Improving detection of differentially expressed gene sets by applying cluster enrichment analysis to Gene Ontology
Tao Xu, JianLei Gu, Yan Zhou, LinFang Du
BMC Bioinformatics , 2009, DOI: 10.1186/1471-2105-10-240
Abstract: We proposed a method for enriching clustered GO terms based on semantic similarity, namely cluster enrichment analysis based on GO (CeaGO), to extend the individual term analysis method. Using an Affymetrix HGU95aV2 chip dataset with simulated gene sets, we illustrated that CeaGO was sensitive enough to detect moderate expression changes. When compared to parent-based individual term analysis methods, the results showed that CeaGO may provide more accurate differentiation of gene expression results. When used with two acute leukemia (ALL and ALL/AML) microarray expression datasets, CeaGO correctly identified specifically enriched GO groups that were overlooked by other individual test methods.By applying CeaGO to both simulated and real microarray data, we showed that this approach could enhance the interpretation of microarray experiments. CeaGO is currently available at http://chgc.sh.cn/en/software/CeaGO/ webcite.Identifying differentially expressed genes (DEGs) from microarray experiments enables researchers to elucidate related biological processes. In addition to studies focused on individual genes such as SAM[1], statistical techniques have been successfully employed to determine whether predefined groups, for example those in Gene Ontology (GO) [2], or in a metabolic pathway, are differentially expressed. There are two main statistical testing approaches: individual gene analysis (IGA) [3,4] and Gene Set Analysis (GSA) [5]. IGA is performed in two steps: first, genes of interest are selected using a cutoff threshold, and the enriched biological categories are gained by statistically testing these genes against the background: typically all genes in the category (e.g., Fisher's exact test). The major limitation of IGA is that the result is significantly affected by an arbitrarily chosen cutoff in the first step. Hence, the GSA approach was developed to address this issue. GSA methods calculate a score based on all the genes within the gene set. Since it is fr
Studies on the relationship between cyanide-resistant respiration and expression of alternative oxidase in mung bean using antibodies prepared by synthetic polypeptide
Chijun Li,Houguo Liang,Linfang Du,Rui Wang
Science China Life Sciences , 2001, DOI: 10.1007/BF02882074
Abstract: Twelve peptides, including eight conservative amino acid residues in the amino acid sequence of hydrophilic S helix of the alternative oxidase (AOX), were synthesized by solid-phase method. The polypeptide was coupled with α-chymotrypsinogen, and the antibodies were obtained through immunizing domestic rabbit by injecting this complex. By using these antibodies, which were raised to immunoreact with total proteins of purified mitochondria from different organs of mung bean seedlings, we find that there are two hybridizable AOX bands in mitochondria. Their molecular weights are about 35 and 38 ku, respectively. Moreover, the respiratory parameters of hypocotyl, true leaf and cotyledon of mung bean seedlings show that true leaf has the highest total respiration (Vt), alternative pathway (AP) capacity (Valt) and the activity of AP (ρValt) among the three organs. Vt andρV alt of cotyledon ranked the second. Hypocotyl has the lowest Vt andρV alt, but its Valt is higher than that of cotyledon. These results are consistent with the analysis of Western blotting of expression of AOX. The highest Vt andρV alt in true leaf are accompanied two hybridizable polypeptides of AOX protein, 35 ku and 38 ku respectively. The next is cotyledon Vt andρV alt with only one 38 ku hybridizable polypeptide of AOX protein. HypocotylV t andρV alt is the lowest and its immunoblotting band is similar to that of cotyledon, but the expressive amount of 38 ku protein is less than that of cotyledon. The results suggest that the 35 ku AOX may contribute mainly to true leafρV alt.
Effects of temperature on the expression of STN7 and phosphorylation of LHCII proteins in Arabidopsis thaliana
Yuan Hu,Xiu Gao,JiaHong Jiang,Yan Ran,LinFang Du
Chinese Science Bulletin , 2008, DOI: 10.1007/s11434-008-0354-x
Abstract: In Arabidopsis thaliana, STN7 kinase is required for phosphorylation of LHCII and for state transitions. In this paper, a hydrophilic polypeptide, derived from the amino acid sequence of STN7, was conjugated to a carrier protein, bovine serum albumin (BSA), to obtain the polyclonal antibody. Immunogenicity and specificity of the polyclonal antibody were evaluated by agar gel immunodiffusion (AGID) test and Western blot analysis. The results show that besides the phosphorylation of LHCII proteins, also the expression of STN7 was regulated by temperature conditions. In addition, the change tendency of LHCII proteins phosphorylation was not only coherent with expression of STN7 with respect to increasing temperature, but also closely related to state transitions. These results would provide useful information for studying regulatory mechanism of LHCII proteins phosphorylation and expression of STN7.
The presence of phosphorylation form of D1 protein in its cross-linked aggregates in high light treated spinach leaves in vivo
Huimin Wei,Junwei Guo,Shuang Zhang,Bo Huang,Yinqiu Liu,Linfang Du,
WEI
,Huimin,GUO,Junwei,ZHANG,Shuang,HUANG,Bo,LIU,Yinqiu,DU,Linfang

科学通报(英文版) , 2006,
Abstract: In the present study, using specific antibody against D1 protein, we detected four aggregates of D1 protein in thylakoid membranes from spinach leaves illuminated at high light (800–2500 μmol photons·m 2·s 1) for 3 h. Their accumulations were dependent on the light intensity to which the leaves had been subjected. Further immunoblot analysis indicated that 70 kD aggregate was a product of D1 protein cross-linked with CP43, 65 and 60 kD aggregate were two cross-linked products between D1 and D2 proteins, and 41 kD aggregate was one cross-linked D1 with α-subunit of cytochrome b 559 (Cyt b 559). This result provided the evidence for the existence of the aggregation of the D1 protein in vivo. The maximal level of D1/Cyt b 559 aggregate occurred at 1000 μmol photons·m 2·s 1 but drastically decreased with further increasing light intensity. Immunoblot analysis with phosphothreonine (Thr (P)) antibody indicated that D1/CP43 and D1/Cyt b 559 aggregates contained the phosphorylated protein(s). In vitro dephosphorylation experiment also showed that D1/Cyt b 559 and D1/CP43 aggregates lost the immunoreactivity with Thr (P) antibody after the phosphatase treatment of the membranes from high-light-illuminated leaves. Our results demonstrated that strong illumination of spinach leaves induced cross-linked products of D1 protein with its nearby polypeptides of PS, some of which co.n-tained the phosphorylated D1 protein.
The Amphiphilic Self-Assembling Peptide EAK16-I as a Potential Hydrophobic Drug Carrier
Jing Wang,Fushan Tang,Feng Li,Juan Lin,Yinghui Zhang,Linfang Du,Xiaojun Zhao
Journal of Nanomaterials , 2008, DOI: 10.1155/2008/516286
Abstract: It is crucial for hydrophobic drugs to be dissolved and stabilized by carriers in aqueous systems and then to be delivered into target cells. An amphiphilic self-assembling peptide EAK16-I (Ac-AEAKAEAKAEAKAEAK-NH2) is reported here to be able to stabilize a model hydrophobic compound, pyrene, in aqueous solution, resulting in the formation of colloidal suspensions. Egg phosphatidylcholine (EPC) vesicles are used as plasma membranes mimic. Fluorescence data shows that the pyrene is presented in the crystalline form when stabilized by EAK16-I and molecularly migrates from its peptide encapsulations into the membrane bilayers of EPC vesicles when the suspension is mixed with EPC vesicles. Furthermore, the release rate can be controlled by changing peptide-to-pyrene ratio, and the higher ratios lead to the slower release rates due to a thicker encapsulation on the pyrene microcrystals. This demonstrates that EAK16-I, as a promising nanobiomaterial, has the potential to be a hydrophobic compounds carrier.
The presence of phosphorylation form of D1 protein in its cross-linked aggregates in high light treated spinach leaves in vivo
Huimin Wei,Junwei Guo,Shuang Zhang,Bo Huang,Yinqiu Liu,Linfang Du
Chinese Science Bulletin , 2006, DOI: 10.1007/s11434-005-1529-3
Abstract: In the present study, using specific antibody against D1 protein, we detected four aggregates of D1 protein in thylakoid membranes from spinach leaves illuminated at high light (800–2500 μmol photons·m 2·s 1) for 3 h. Their accumulations were dependent on the light intensity to which the leaves had been subjected. Further immunoblot analysis indicated that 70 kD aggregate was a product of D1 protein cross-linked with CP43, 65 and 60 kD aggregate were two cross-linked products between D1 and D2 proteins, and 41 kD aggregate was one cross-linked D1 with α-subunit of cytochrome b 559 (Cyt b 559). This result provided the evidence for the existence of the aggregation of the D1 protein in vivo. The maximal level of D1/Cyt b 559 aggregate occurred at 1000 μmol photons·m 2·s 1 but drastically decreased with further increasing light intensity. Immunoblot analysis with phosphothreonine (Thr (P)) antibody indicated that D1/CP43 and D1/Cyt b 559 aggregates contained the phosphorylated protein(s). In vitro dephosphorylation experiment also showed that D1/Cyt b 559 and D1/CP43 aggregates lost the immunoreactivity with Thr (P) antibody after the phosphatase treatment of the membranes from high-light-illuminated leaves. Our results demonstrated that strong illumination of spinach leaves induced cross-linked products of D1 protein with its nearby polypeptides of PS, some of which co.n-tained the phosphorylated D1 protein.
Implementation of the No Packet Loss Network Communication in VxWorks
Linfang Zhang
Modern Applied Science , 2010, DOI: 10.5539/mas.v4n9p30
Abstract: By VxWorks, the real-time control system of certain equipment adopts the UDP/IP network communication, which requires that the control process has strong real-time character and complex task scheduling. In the work condition with frequently interactive network tasks, the control system is easy to lose packets, and to solve this problem, this article adopts the double-loop buffer structure processing mechanism to realize the no packet loss network communication method, which could largely enhance the reliability of the network communication and improve the stability of the control system. Based on the excellent multi-task scheduling ability of VxWorks, this method could essentially enhance the efficiency and reliability of software. By testing, this method is efficient and feasible.
Studies on the relationship between cyanide-resistant respiration and expression of alternative oxidase in mungbean using antibodies prepared by synthetic polypeptide
Studies on the relationship between cyanide-resistant respiration and expression of alternative oxidase in mung bean using antibodies prepared by synthetic polypeptide

LI Chijun,LIANG Houguo,DU Linfang,WANG Rui,
李驰峻
,梁厚果,杜林方,王锐

中国科学C辑(英文版) , 2001,
Abstract: Twelve peptides, including eight conservative amino acid residues in the amino acid sequence of hydrophilic S helix of the alternative oxidase (AOX), were synthesized by solid-phase method. The polypeptide was coupled with α-chymotrypsinogen, and the antibodies were obtained through immunizing domestic rabbit by injecting this complex. By using these antibodies, which were raised to immunoreact with total proteins of purified mitochondria from different organs of mung bean seedlings, we find that there are two hybridizable AOX bands in mitochondria. Their molecular weights are about 35 and 38 ku, respectively. Moreover, the respiratory parameters of hypocotyl, true leaf and cotyledon of mung bean seedlings show that true leaf has the highest total respiration (Vt), alternative pathway (AP) capacity (Valt) and the activity of AP (ρValt) among the three organs. Vt andρV alt of cotyledon ranked the second. Hypocotyl has the lowest Vt andρV alt, but its Valt is higher than that of cotyledon. These results are consistent with the analysis of Western blotting of expression of AOX. The highest Vt andρV alt in true leaf are accompanied two hybridizable polypeptides of AOX protein, 35 ku and 38 ku respectively. The next is cotyledon Vt andρV alt with only one 38 ku hybridizable polypeptide of AOX protein. HypocotylV t andρV alt is the lowest and its immunoblotting band is similar to that of cotyledon, but the expressive amount of 38 ku protein is less than that of cotyledon. The results suggest that the 35 ku AOX may contribute mainly to true leafρV alt.
Imaging Studies of Characteristics for a Slab of a Lossy Left-handed Material
Linfang Shen,Sailing He
Physics , 2003, DOI: 10.1016/S0375-9601(03)00168-3
Abstract: The characteristics of an imaging system formed by a slab of a lossy left-handed material (LHM) are studied. The transfer function of the LHM imaging system is written in an appropriate product form with each term having a clear physical interpretation. A tiny loss of the LHM may suppress the transmission of evanescent waves through the LHM slab and this is explained physically. An analytical expression for the resolution of the imaging system is derived. It is shown that it is impossible to make a subwavelength imaging by using a realistic LHM imaging system unless the LHM slab is much thinner than the wavelength.
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