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Tao Jiang

Publications and source records attributed to Tao Jiang.

At least 163 records · Page 9Linked to original sources
PubMed2002

Crystallization and preliminary crystallographic studies of pyridoxal kinase from sheep brain.

Pyridoxal kinase (ATP:pyridoxal 5'-phosphotransferase; EC 2.7.1.35) is a key enzyme in the transformation of vitamin B(6) to pyridoxal-5'-phosphate. Pyridoxal-5'-phosphate is the crucial cofactor required by numerous enzymes involved in the metabolism of amino acids and the synthesis of many neurotransmitters. Pyridoxal kinase from sheep brain was crystallized in an orthorhombic form using the hanging-drop vapour-diffusion method with sodium citrate as the precipitant. The crystals belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 59.8, b = 94.4, c = 128.2 A, and diffract to a resolution of 2.1 A. Crystals were transferred into a soaking liquid without citrate and two heavy-atom derivatives were prepared.

Animals↗
PubMed2002

Crystal structure of earthworm fibrinolytic enzyme component a: revealing the structural determinants of its dual fibrinolytic activity.

Earthworm fibrinolytic enzyme component A (EFEa) from Eisenia fetida is a strong fibrinolytic enzyme that not only directly degrades fibrin, but also activates plasminogen. Proteolytic assays further revealed that it cleaved behind various P1 residue types. The crystal structure of EFEa was determined using the MIR method and refined to 2.3A resolution. The enzyme, showing the overall polypeptide fold of chymotrypsin-like serine proteases, possesses essential S1 specificity determinants characteristic of elastase. However, the beta strand at the west rim of the S1 specificity pocket is significantly elongated by a unique four-residue insertion (Ser-Ser-Gly-Leu) after Val217, which not only provides additional substrate hydrogen binding sites for distal P residues, but also causes extension of the S1 pocket at the south rim. The S2 subsite of the enzyme was partially occluded by the bulky side-chain of residue Tyr99. Structure-based inhibitor modeling demonstrated that EFEa's S1 specificity pocket was preferable for elastase-specific small hydrophobic P1 residues, while its accommodation of long and/or bulky P1 residues was also feasible if enhanced binding of the substrate and induced fit of the S1 pocket were achieved. EFEa is thereby endowed with relatively broad substrate specificity, including the dual fibrinolysis. The presence of Tyr99 at the S2 subsite indicates a preference for P2-Gly, while an induced fit of Tyr99 was also suggested for accommodation of bigger P2 residues. This structure is the first reported for an earthworm fibrinolytic enzyme component and serine protease originating from annelid worms.

Amino Acid Sequence↗
PubMed2002

Three-dimensional structure of manganese superoxide dismutase from Bacillus halodenitrificans, a component of the so-called "green protein".

A so-called "green protein" has been purified from a moderate halophilic eubacterium, Bacillus halodenitrificans (ATCC 49067), under anaerobic conditions. The protein, which might play an important role in denitrification, dissociates mainly into two components after exposure to air: a manganese superoxide dismutase (GP-MnSOD) and a nucleoside diphosphate kinase. As a first step in elucidating the overall structure of the green protein and the role of each component, the 2.8-A resolution crystal structure of GP-MnSOD was determined. Compared with other manganese dismutases, GP-MnSOD shows two significant characteristics. The first is that the entrance to its substrate channel has an additional basic residue-Lys38. The second is that its surface is decorated with an excess of acidic over basic residues. All these structural features may be related to GP-MnSOD's high catalytic activity and its endurance against the special cytoplasm of B. halodenitrificans. The structure of GP-MnSOD provides the basis for recognizing its possible role and assembly state in the green protein.

Amino Acid Sequence↗
PubMed2002

Quantitative analysis of (styrene/acrylonitrile/methyl methacrylate) co-polymer systems by infrared resonance spectroscopy.

A detailed careful analysis of the infrared resonance (IR) spectra of polystyrene (PSt), polymethyl methacrylate (PMMA), polyacrylonitrile (PAN) and their co-mixtures were performed. Through this study the absorption peak area to weight ratios as well as working curves were obtained to test for their reliability as well as their suitability. Satisfactory results were achieved and these working curves were then used to measure the polymerized components of binary and ternary co-polymers. By investigating the acquired data we conclude that the monomer preferential polymeric sequence is St > MMA > AN. A quantitative method to measure P (St/AN/MMA) concentrations by IR spectroscopy is proposed in this work.

Acrylonitrile↗
PubMed2002

Dynamic mechanical analysis of the SAN co-polymer and the SBR latex co-mixture.

Useful experimental data based on the dynamic effects of the SAN/SBR mixture at higher temperatures were acquired. This data can allow us to gather information about the molecular motion and any interesting behavior of this mixture at elevated temperatures and increases in the SAN to SBR weight proportion. The importance of dynamic mechanical experiments of multi-phase polymer systems is presented. A series of (SAN/SBR) co-mixed samples were prepared with varying weight proportions over a temperature interval. TBA equipment (a type of torsional braid set of equipment) was used to make the dynamic mechanical analysis of the SAN/SBR co-mixture.

Acrylonitrile↗
PubMed2002

A general edit distance between RNA structures.

Arc-annotated sequences are useful in representing the structural information of RNA sequences. In general, RNA secondary and tertiary structures can be represented as a set of nested arcs and a set of crossing arcs, respectively. Since RNA functions are largely determined by molecular confirmation and therefore secondary and tertiary structures, the comparison between RNA secondary and tertiary structures has received much attention recently. In this paper, we propose the notion of edit distance to measure the similarity between two RNA secondary and tertiary structures, by incorporating various edit operations performed on both bases and arcs (i.e., base-pairs). Several algorithms are presented to compute the edit distance between two RNA sequences with various arc structures and under various score schemes, either exactly or approximately, with provably good performance. Preliminary experimental tests confirm that our definition of edit distance and the computation model are among the most reasonable ones ever studied in the literature.

Algorithms↗
PubMed2002

Identifying transcription factor binding sites through Markov chain optimization.

Even though every cell in an organism contains the same genetic material, each cell does not express the same cohort of genes. Therefore, one of the major problems facing genomic research today is to determine not only which genes are differentially expressed and under what conditions, but also how the expression of those genes is regulated. The first step in determining differential gene expression is the binding of sequence-specific DNA binding proteins (i.e. transcription factors) to regulatory regions of the genes (i.e. promoters and enhancers). An important aspect to understanding how a given transcription factor functions is to know the entire gamut of binding sites and subsequently potential target genes that the factor may bind/regulate. In this study, we have developed a computer algorithm to scan genomic databases for transcription factor binding sites, based on a novel Markov chain optimization method, and used it to scan the human genome for sites that bind to hepatocyte nuclear factor 4 alpha (HNF4alpha). A list of 71 known HNF4alpha binding sites from the literature were used to train our Markov chain model. By looking at the window of 600 nucleotides around the transcription start site of each confirmed gene on the human genome, we identified 849 sites with varying binding potential and experimentally tested 109 of those sites for binding to HNF4alpha. Our results show that the program was very successful in identifying 77 new HNF4alpha binding sites with varying binding affinities (i.e. a 71% success rate). Therefore, this computational method for searching genomic databases for potential transcription factor binding sites is a powerful tool for investigating mechanisms of differential gene regulation.

Algorithms↗
PubMed2002

Oligonucleotide fingerprinting of rRNA genes for analysis of fungal community composition.

Thorough assessments of fungal diversity are currently hindered by technological limitations. Here we describe a new method for identifying fungi, oligonucleotide fingerprinting of rRNA genes (OFRG). ORFG sorts arrayed rRNA gene (ribosomal DNA [rDNA]) clones into taxonomic clusters through a series of hybridization experiments, each using a single oligonucleotide probe. A simulated annealing algorithm was used to design an OFRG probe set for fungal rDNA. Analysis of 1,536 fungal rDNA clones derived from soil generated 455 clusters. A pairwise sequence analysis showed that clones with average sequence identities of 99.2% were grouped into the same cluster. To examine the accuracy of the taxonomic identities produced by this OFRG experiment, we determined the nucleotide sequences for 117 clones distributed throughout the tree. For all but two of these clones, the taxonomic identities generated by this OFRG experiment were consistent with those generated by a nucleotide sequence analysis. Eighty-eight percent of the clones were affiliated with Ascomycota, while 12% belonged to BASIDIOMYCOTA: A large fraction of the clones were affiliated with the genera Fusarium (404 clones) and Raciborskiomyces (176 clones). Smaller assemblages of clones had high sequence identities to the Alternaria, Ascobolus, Chaetomium, Cryptococcus, and Rhizoctonia clades.

DNA Fingerprinting↗
PubMed2002

Analysis of bacterial community composition by oligonucleotide fingerprinting of rRNA genes.

One of the first steps in characterizing an ecosystem is to describe the organisms inhabiting it. For microbial studies, experimental limitations have hindered the ability to depict diverse communities. Here we describe oligonucleotide fingerprinting of rRNA genes (OFRG), a method that permits identification of arrayed rRNA genes (rDNA) through a series of hybridization experiments using small DNA probes. To demonstrate this strategy, we examined the bacteria inhabiting two different soils. Analysis of 1,536 rDNA clones revealed 766 clusters grouped into five major taxa: Bacillus, Actinobacteria, Proteobacteria, and two undefined assemblages. Soil-specific taxa were identified and then independently confirmed through cluster-specific PCR of the original soil DNA. Near-species-level resolution was obtained by this analysis as clones with average sequence identities of 97% were grouped in the same cluster. A comparison of these OFRG results with the results obtained in a denaturing gradient gel electrophoresis analysis of the same two soils demonstrated the significance of this methodological advance. OFRG provides a cost-effective means to extensively analyze microbial communities and should have applications in medicine, biotechnology, and ecosystem studies.

Bacteria↗
PubMed2002

Restriction enzyme recognition sequence search program.

A critical and difficult part of characterizing restriction enzymes and methylases is the identification of recognition sequences. To simplify this process, we have developed a plasmid transformation method along with a computer program named RM search that determines the exact recognition sequences for given restriction and modification systems.

Algorithms↗
PubMed2002

[Study on epidemic trend and control policy of tuberculosis in Sichuan province].

OBJECTIVE: To evaluate efficacy of tuberculosis control policy and provide scientific evidence for drawing up tuberculosis control program. METHODS: Data of the epidemiological survey for tuberculosis in Sichuan in 2000 were analyzed and part of the results were compared with that before. RESULTS: The prevalence of active pulmonary tuberculosis, the bacteriological positive prevalence and smear positive prevalence of pulmonary tuberculosis in 2000 were 544/100 000, 250/100 000 and 144/100 000, respectively, decreased by 41.8%, 30.0% and 35.0% respectively in comparison with 1990, and the annual reduction rates were 5.3%, 3.5% and 4.2% respectively during the past 10 years. The mortality of tuberculosis and pulmonary tuberculosis was 24/100 000 and 22/100 000, respectively, decreased by 20.0% and 12.0% respectively in comparison with 1990. The prevalence of tuberculosis in minority area and mountainous area were higher than that in city, countryside and hills. 71% of infectious patients were newly detected, 33.3% of which were re-treatment cases. The economic status was found the key factor affecting the implementation of tuberculosis control. CONCLUSIONS: The modern tuberculosis control strategy, which mainly targeted infectious patients and advocated DOTS policy, is the guarantee of sustainable development of tuberculosis control, though the prevalence of pulmonary tuberculosis decreased slowly in Sichuan during the past 10 years.

Adolescent↗
PubMed2002

[Levels and clinical significance of CD44 (intron 9) and CD44v6 in malignant cerebroma].

OBJECTIVE: To investigate the expression of CD44 (intron 9) and CD44v6 in brain neoplasm. METHODS: CD44 (intron 9) and CD44v6 were detected in malignant meningoma, encephalic glioma, and normal encephalic tissues around the brain noeplasm respectively by using RT-PCR. RESULTS: The positive expression rate of CD44v6 was 92.86% (26/28) in malignant meningoma and 88.0% (22/25) in encephalic glioma. They were significantly higher than 5.0% (1/20) in normal encephalic tissues (P < 0.01). Mass values of malignant meningoma and encephalic glioma were higher than that of normal encephalic tissues (P < 0.01). The expression of CD44 (intron 9) was higher in malignant meningoma and encephalic glioma than in normal encephalic tissues (P < 0.01). CONCLUSIONS: Detection of CD44 (intron 9) and CD44v6 might be helpful to the diagnosis of malignant cerebroma.

Adolescent↗
PubMed2002

[Serum levels of VEGF and nitric oxide in esophageal squamous carcinoma patients and the clinical significance].

BACKGROUND & OBJECTIVE: Angiogenesis is necessary for the growth and metastasis of malignant tumor and is closely related to vascular endothelial growth factor (VEGF) and nitric oxide (NO). This investigation was aimed to detect the serum levels of VEGF and NO in squamous carcinoma patients and analyze the clinical significance for prognosis evaluation. METHODS: Serum VEGF and NO levels were detected by enzyme-linked immunosorbant assay (ELISA) and spectrophotometry, respectively, and their clinical significance was analyzed. RESULTS: Serum levels of VEGF and NO in squamous carcinoma patients were significantly higher than that of in normal persons (P < 0.01). There was a positive correlation between serum VEGF, NO levels and tumor pathological phases, histological grades and lymph node metastasis (P < 0.01). There was also a positive correlation between serum VEGF level and serum NO level (P < 0.01). CONCLUSION: Serum levels of VEGF and NO in squamous carcinoma patients were significantly correlated to the growth, development and malignant behavior of tumor and thus may serve as the indexes for clinical prognosis evaluation.

Carcinoma, Squamous Cell↗
PubMed2002

[Preparation of calcium phosphate coatings on surfaces of commercially pure titanium induced by simulated body fluid].

All samples were divided into three groups and subjected to three different surface treatments, i.e. untreated group, group etched with mixed acid of 1:1 HCl and H2SO4 followed by immersion in 6N NaOH solution at 60 degrees C for 24 h and group etched with mixed acid of 1:1 HCl and H2SO4 followed by immersion in 6N NaOH solution at 60 degrees C for 24 h then heated at 600 degrees C for 1 h. After soaked in simulated body fluid for two weeks, a thin calcium phosphate coatings was precipitated on the surfaces of the two treated samples. Results of SEM and EDX showed that calcium phosphate coatings on the surfaces of the titanium samples etched and heated were more even than the titanium samples etched without heating. The analysis of XRD demonstrated the main component of calcium phosphate coating was hydroxyapatite.

Body Fluids↗
PubMed2002

Extended at-home bleaching of tetracycline-stained teeth with different concentrations of carbamide peroxide.

OBJECTIVE: The degree of color change and the dental sensitivity associated with the use of different concentrations (10%, 15%, and 20%) of carbamide peroxide every night for 6 months was evaluated in tetracycline-stained teeth. METHOD AND MATERIALS: Fifty-nine subjects were shown how to place two different concentrations of carbamide peroxide in the custom trays with reservoirs. For a period of 6 months, the patients were to insert the tray every evening before retiring. Patients returned in 1 and 2 weeks and at 1, 2, 3, 4, 5, 6, 7, 8, and 9 months for evaluation of the degree of color change by subjective shade matching and by photographic means. Sensitivity of hard or soft tissues was self-reported. RESULTS: Fifty-two subjects attended more than 90% of the recalls. A colorimeter was used to convert shade guide tabs to Commission Internationale de l'Eclairage color spaces (CIELAB). The most rapid whitening occurred in the first month. At 3 and 9 months, 91% and 85% of the subjects, respectively, were at least "a little pleased" with the results of the bleaching. In the professional evaluation, 90% of the teeth were deemed to have an excellent or satisfactory esthetic result. The higher the concentration of carbamide peroxide, the more rapidly the lightness value and color difference changed. There was no difference among the three concentrations in resulting gingival sensitivity. Patients experienced less tooth sensitivity with 10% gel than they did with 15% and 20% gels. CONCLUSION: Bleaching with 10%, 15%, and 20% carbamide peroxide is effective for removing tooth staining caused by tetracycline. The 10% concentration has the most advantages and the fewest disadvantages.

Adult↗
PubMed2002

[Research on the preparation of bacterial artificial chromosome (BAC) vector DNA].

Bacterial artificial chromosome (BAC) library plays a pivotal role in genomics studies. A crucial step in BAC library construction is preparation of BAC vector DNA. Preparation of highly purified vector DNA is affected by a series of factors including digestion of restriction enzyme and dephosphorylation of linearized vector DNA. In our study, the BAC vector pECBAC1 was digested by the restriction enzyme of BamHI and dephosphorylated by HK phosphatase respectively. In order to improve the ligation capability of vector DNA, gel purification of linearized vector DNA was also conducted in our study. At the same time, we did a series of experiments to get high quality of vector DNA for construction of BAC library. They included the optimal concentration of restriction enzyme, optimal digestion time, the type of phosphatase and gel purification of linearized vector DNA.

Bacteriophage T4↗
PubMed2002

An efficient branch-and-bound algorithm for the assignment of protein backbone NMR peaks.

NMR resonance assignment is one of the key steps in solving an NMR protein structure. The assignment process links resonance peaks to individual residues of the target protein sequence, providing the prerequisite for establishing intra- and inter-residue spatial relationships between atoms. The assignment process is tedious and time-consuming, which could take many weeks. Though there exist a number of computer programs to assist the assignment process, many NMR labs are still doing the assignments manually to ensure quality. This paper presents a new computational method based on our recent work towards automating the assignment process, particularly the process of backbone resonance peak assignment. We formulate the assignment problem as a constrained weighted bipartite matching problem. While the problem, in the most general situation, is NP-hard, we present an efficient solution based on a branch-and-bound algorithm with effective bounding techniques and a greedy filtering algorithm for reducing the search space. Our experimental results on 70 instances of (pseudo) real NMR data derived from 14 proteins demonstrate that the new solution runs much faster than a recently introduced (exhaustive) two-layer algorithm and recovers more correct peak assignments than the two-layer algorithm.

Algorithms↗