Search PubMed⌕ Search

Biomedical subjects

Ting Chen

Publications and source records attributed to Ting Chen.

At least 73 records · Page 4Linked to original sources
PubMed2004

[Expression of aquaporin in rats' endolymphatic sac and kidney and the effect of anti-diuretic hormone on the expression of aquaporin].

OBJECTIVE: To confirm the expression of aquaporin2,3,4 (AQP2,3,4, water channel protein) in rats' endolymphatic sac (ES) and kidney, and to investigate and compare the effects of antidiuretic hormone (AVP) and DDAVP [(deamino-Cys1,D-Arg8)-Vasopressin, V2-receptor agonist] on the expression of AQP2 in rats' ES and kidney. METHODS: Thirty healthy Swards white rats were divided into the negative control, AVP group and dDAVP group, respectively, and were cardiaca perfused. The temporal bones and kidneys were taken out, then processed and sectioned by paraffin-embedded technique. The sections of ES were labeled with fluorescent antibody by immunohistochemical method, and kidney's with avidin-biotin-peroxidase complex method (ABC). The expression of AQP-2,3,4 were confirmed in the ES of rats, and the different effects of the AVP and DDAVP onto the ES and kidney were observed. The slides used were analyzed by image-analyzer and the subsequent data were dealt with statistically. RESULTS: In the cytomembrane and cytoplasm of ES' epithelia, the constant and clear fluorescent reaction could be observed in normal control group with the first antibody of AQP2,3,4. Significant feeble fluorescent reaction of the first antibody of AQP-2 was revealed in AVP group and DDAVP group and showed much lower of gray (P < 0.01), less intensive of fluorescent (P < 0.01) under the fluorescence microscope. In the principal cell of renal collecting duct, it was on the contrary. Compared with the control group, significant stain was revealed in AVP group and DDAVP group and showed lower of gray (P < 0.05), greater density (P < 0.05), higher IOD (P < 0.05) and more stained area (P < 0.05). There is no different between the AVP group and DDAVP group in expression of AQP-2 in two sites. CONCLUSIONS: AQP-2,3,4 were expressed both in rats' epithelia of endolymphatic sac (ES) and principal cell of renal collecting duct. AVP promotes the expression of AQP2 in kidney but inhibits in ES. AVP maybe play important role to control the expression of AQP-2 in ES and kidney probably by the role of AVP-V2R-cAMP-AQP2.

Animals↗
PubMed2004

[Study on constituents in rhizome of Astilbe chinensis].

OBJECTIVE: To study the chemical constituents in rhizome of Astilbe chinensis. METHOD: The constituents were isolated with column chromatographies and the structures were identified by physicochemical properties and spectral analysis (UV, IR, MS, 1H-NMR, 13C-NMR and 2D-NMR). RESULT: The structures were identified as bergenin (1), 11-O-galloylbergenin (2), 4-O-galloylbergenin (3), catechin (4), respectively. CONCLUSION: Compound 3 was isolated from Astilbe for the first time.

Benzopyrans↗
PubMed2003

A nitric oxide biosensor based on the multi-assembly of hemoglobin/montmorillonite/polyvinyl alcohol at a pyrolytic graphite electrode.

Direct electron transfer of hemoglobin (Hb) can be achieved in a Hb/montmorillonite (MMT)/polyvinyl alcohol multi-assembly at a pyrolytic graphite (PG) electrode. Accordingly, a novel nitric oxide (NO) biosensor is proposed. The reduction of NO is observed at a potential of approximately -783 mV (vs. SCE) at pH 5.5. At optimum pH, this biosensor shows a wide linear range of 1.0x10(-6)-2.5x10(-4) mol/l with a detection limit of 5.0x10(-7) mol/l. The sensor-to-sensor reproducibility is good consideringmacr; a relative standard deviation of 3.5% in five independent determinations at 5.0x10(-5) mol/l NO. The modified electrode is conveniently constructed and durable in long-term operations.

Bentonite↗
PubMed2003

Haplotype block partition with limited resources and applications to human chromosome 21 haplotype data.

Recent studies have shown that the human genome has a haplotype block structure such that it can be decomposed into large blocks with high linkage disequilibrium (LD) and relatively limited haplotype diversity, separated by short regions of low LD. One of the practical implications of this observation is that only a small fraction of all the single-nucleotide polymorphisms (SNPs) (referred as "tag SNPs") can be chosen for mapping genes responsible for human complex diseases, which can significantly reduce genotyping effort, without much loss of power. Algorithms have been developed to partition haplotypes into blocks with the minimum number of tag SNPs for an entire chromosome. In practice, investigators may have limited resources, and only a certain number of SNPs can be genotyped. In the present article, we first formulate this problem as finding a block partition with a fixed number of tag SNPs that can cover the maximal percentage of the whole genome, and we then develop two dynamic programming algorithms to solve this problem. The algorithms are sufficiently flexible to permit knowledge of functional polymorphisms to be considered. We apply the algorithms to a data set of SNPs on human chromosome 21, combining the information of coding and noncoding regions. We study the density of SNPs in intergenic regions, introns, and exons, and we find that the SNP density in intergenic regions is similar to that in introns and is higher than that in exons, results that are consistent with previous studies. We also calculate the distribution of block break points in intergenic regions, genes, exons, and coding regions and do not find any significant differences.

Chromosomes, Human, Pair 21↗
PubMed2003

Prediction of protein function using protein-protein interaction data.

Assigning functions to novel proteins is one of the most important problems in the postgenomic era. Several approaches have been applied to this problem, including the analysis of gene expression patterns, phylogenetic profiles, protein fusions, and protein-protein interactions. In this paper, we develop a novel approach that employs the theory of Markov random fields to infer a protein's functions using protein-protein interaction data and the functional annotations of protein's interaction partners. For each function of interest and protein, we predict the probability that the protein has such function using Bayesian approaches. Unlike other available approaches for protein annotation in which a protein has or does not have a function of interest, we give a probability for having the function. This probability indicates how confident we are about the prediction. We employ our method to predict protein functions based on "biochemical function," "subcellular location," and "cellular role" for yeast proteins defined in the Yeast Proteome Database (YPD, www.incyte.com), using the protein-protein interaction data from the Munich Information Center for Protein Sequences (MIPS, mips.gsf.de). We show that our approach outperforms other available methods for function prediction based on protein interaction data. The supplementary data is available at www-hto.usc.edu/~msms/ProteinFunction.

Bayes Theorem↗
PubMed2003

A suboptimal algorithm for de novo peptide sequencing via tandem mass spectrometry.

Tandem mass spectrometry has emerged to be one of the most powerful high-throughput techniques for protein identification. Tandem mass spectrometry selects and fragments peptides of interest into N-terminal ions and C-terminal ions, and it measures the mass/charge ratios of these ions. The de novo peptide sequencing problem is to derive the peptide sequences from given tandem mass spectral data of k ion peaks without searching against protein databases. By transforming the spectral data into a matrix spectrum graph G = (V, E), where |V| = O(k(2)) and |E| = O(k(3)), we give the first polynomial time suboptimal algorithm that finds all the suboptimal solutions (peptides) in O(p|E|) time, where p is the number of solutions. The algorithm has been implemented and tested on experimental data. The program is available at http://hto-c.usc.edu:8000/msms/menu/denovo.htm.

Algorithms↗
PubMed2003

A suffix tree approach to the interpretation of tandem mass spectra: applications to peptides of non-specific digestion and post-translational modifications.

MOTIVATION: Tandem mass spectrometry combined with sequence database searching is one of the most powerful tools for protein identification. As thousands of spectra are generated by a mass spectrometer in one hour, the speed of database searching is critical, especially when searching against a large sequence database, or when the peptide is generated by some unknown or non-specific enzyme, even or when the target peptides have post-translational modifications (PTM). In practice, about 70-90% of the spectra have no match in the database. Many believe that a significant portion of them are due to peptides of non-specific digestions by unknown enzymes or amino acid modifications. In another case, scientists may choose to use some non-specific enzymes such as pepsin or thermolysin for proteolysis in proteomic study, in that not all proteins are amenable to be digested by some site-specific enzymes, and furthermore many digested peptides may not fall within the rang of molecular weight suitable for mass spectrometry analysis. Interpreting mass spectra of these kinds will cost a lot of computational time of database search engines. OVERVIEW: The present study was designed to speed up the database searching process for both cases. More specifically speaking, we employed an approach combining suffix tree data structure and spectrum graph. The suffix tree is used to preprocess the protein sequence database, while the spectrum graph is used to preprocess the tandem mass spectrum. We then search the suffix tree against the spectrum graph for candidate peptides. We design an efficient algorithm to compute a matching threshold with some statistical significance level, e.g. p = 0.01, for each spectrum, and use it to select candidate peptides. Then we rank these peptides using a SEQUEST-like scoring function. The algorithms were implemented and tested on experimental data. For post-translational modifications, we allow arbitrary number of any modification to a protein. AVAILABILITY: The executable program and other supplementary materials are available online at: http://hto-c.usc.edu:8000/msms/suffix/.

Algorithms↗
PubMed2003

Astilbin suppresses delayed-type hypersensitivity by inhibiting lymphocyte migration.

This study examined the effects of astilbin, a flavanone, on delayed-type hypersensitivity reactions and its mechanisms of action on cell migration. Astilbin significantly inhibited the sheep-red-blood-cell-induced footpad reaction and picryl-chloride-induced ear dermatitis without affecting the organ weights, when administered during the effector phase but not the induction phase. The flavanone also significantly inhibited the migration to gelatin of spleen cells isolated from mice with ear dermatitis in a transwell system. Furthermore, the isolated spleen cells from normal mice were incubated with astilbin in the presence of concanavalin A, or those from mice with ear dermatitis were cultured with astilbin. In the supernatants collected, the activity of matrix metalloproteinases (MMPs) MMP-2 and MMP-9 was remarkably inhibited by astilbin. These results suggest that astilbin may inhibit delayed-type hypersensitivity reactions through selectively suppressing the lymphocyte functions, including cell migration, via down-regulating MMP activity.

Animals↗
PubMed2003

Si-Ni-San, a traditional Chinese prescription, and its drug-pairs suppress contact sensitivity in mice via inhibition of the activity of metalloproteinases and adhesion of T lymphocytes.

In this paper, the effect of Si-Ni-San, a famous traditional Chinese prescription, on ear contact sensitivity was examined. Si-Ni-San significantly inhibited the ear swelling when administered during the induction phase of picryl-chloride-induced ear contact sensitivity in mice. The adhesion to type I collagen of isolated spleen cells was significantly decreased in the Si-Ni-San group, especially in the presence of protein kinase C activator, phorbol 12,13-dibutyrate. The inhibition of adhesion was seen in purified T cells from the spleen, as well as in Jurkat cells. Furthermore, the adhesion to collagen involves the production of matrix metalloproteinase-2 and -9 in spleen cells, and the oral administration of Si-Ni-San remarkably reduced the matrix metalloproteinase production. Three drug-pairs composed in Si-Ni-San were used for comparison. The combination of Chaihu and Shaoyao showed a similar effect to Si-Ni-San, while Chaihu and Zhishi, and Shaoyao and Gancao only showed a tendency in most situations. These results suggest that Si-Ni-San may contribute to the treatment of immunologically related diseases by down-regulating the activation and function of T lymphocytes, especially the cell adhesion and matrix metalloproteinase production. Its effect is mainly displayed by the combination of Chaihu and Shaoyao.

Animals↗
PubMed2003

Assessment of the reliability of protein-protein interactions and protein function prediction.

As more and more high-throughput protein-protein interaction data are collected, the task of estimating the reliability of different data sets becomes increasingly important. In this paper, we present our study of two groups of protein-protein interaction data, the physical interaction data and the protein complex data, and estimate the reliability of these data sets using three different measurements: (1) the distribution of gene expression correlation coefficients, (2) the reliability based on gene expression correlation coefficients, and (3) the accuracy of protein function predictions. We develop a maximum likelihood method to estimate the reliability of protein interaction data sets according to the distribution of correlation coefficients of gene expression profiles of putative interacting protein pairs. The results of the three measurements are consistent with each other. The MIPS protein complex data have the highest mean gene expression correlation coefficients (0.256) and the highest accuracy in predicting protein functions (70% sensitivity and specificity), while Ito's Yeast two-hybrid data have the lowest mean (0.041) and the lowest accuracy (15% sensitivity and specificity). Uetz's data are more reliable than Ito's data in all three measurements, and the TAP protein complex data are more reliable than the HMS-PCI data in all three measurements as well. The complex data sets generally perform better in function predictions than do the physical interaction data sets. Proteins in complexes are shown to be more highly correlated in gene expression. The results confirm that the components of a protein complex can be assigned to functions that the complex carries out within a cell. There are three interaction data sets different from the above two groups: the genetic interaction data, the in-silico data and the syn-express data. Their capability of predicting protein functions generally falls between that of the Y2H data and that of the MIPS protein complex data. The supplementary information is available at the following Web site: http://www-hto.usc.edu/-msms/AssessInteraction/.

Computational Biology↗
PubMed2003

[Cloning and prokaryotic expression of yeast GCN5 and RPD3].

The yeast histone acetyltransferase (HAT) gene gcn5 and histone deacetylase (HDAC) gene rpd3 were cloned from yeast genomic DNA by PCR amplification. The two genes,both with additional 6xHis tag,were subcloned into pBV220 vector to construct expression plasmids pBVgcn5 and pBVrpd3,respectively. Both pBVgcn5 and pBVrpd3 were over-expressed in Escherichia coli upon temperature induction,as revealed by SDS-PAGE. The recombinant GCN5 and RPD3 were purified by using a 6xHis affinity column. The purified GCN5 was tested to possess the HAT activity by using a (14)C-labeling assay. This work has laid down the basis for further in vitro studies into roles of histone acetylation/deacetylation in modulating chromatin conformation and transcription activity.

English Abstract↗
PubMed2002

Histone acetylation is involved in hsp70 gene transcription regulation in Drosophila melanogaster.

The acetylation/deacetylation modifications of N-terminal tails of core histones play critical roles in activation/repression of many eukaryotic genes. However, the role of acetylation in transcription regulation of heat shock protein genes (hsp) is still a disputed issue. In this study, we investigated the influences of histone acetylation modification on changes in structure of polytene chromosomes and in expression of hsp70 gene in Drosophila melanogaster, by using histone deacetylase (HDAC) inhibitors Trichostatin A (TSA) and sodium butyrate (BuA), and the heat shock treatment of larvae of the flies. The results presented in this paper demonstrate that both TSA and BuA were able to affect the chromatin structure at the site where hsp70 gene is located along the polytene chromosome. Furthermore, the HDAC inhibitors significantly promoted the hsp70 gene transcription, at an extent similar to that induced by heat shock. The immunofluorescence in situ localization study further confirmed that the hsp70 gene locus was hyperacetylated after the heat induction. We therefore conclude that histone acetylation can significantly enhance both the basal and the inducible expression of hsp70 gene in D. melanogaster and hence plays important roles in hsp gene regulation. This study has provided a basis and a framework for further investigations aimed at the establishment of the correlation between acetylation modification and hsp gene regulation.

Acetylation↗
PubMed2002

A dynamic programming algorithm for haplotype block partitioning.

We develop a dynamic programming algorithm for haplotype block partitioning to minimize the number of representative single nucleotide polymorphisms (SNPs) required to account for most of the common haplotypes in each block. Any measure of haplotype quality can be used in the algorithm and of course the measure should depend on the specific application. The dynamic programming algorithm is applied to analyze the chromosome 21 haplotype data of Patil et al. [Patil, N., Berno, A. J., Hinds, D. A., Barrett, W. A., Doshi, J. M., Hacker, C. R., Kautzer, C. R., Lee, D. H., Marjoribanks, C., McDonough, D. P., et al. (2001) Science 294, 1719-1723], who searched for blocks of limited haplotype diversity. Using the same criteria as in Patil et al., we identify a total of 3,582 representative SNPs and 2,575 blocks that are 21.5% and 37.7% smaller, respectively, than those identified using a greedy algorithm of Patil et al. We also apply the dynamic programming algorithm to the same data set based on haplotype diversity. A total of 3,982 representative SNPs and 1,884 blocks are identified to account for 95% of the haplotype diversity in each block.

Algorithms↗
PubMed2002

Inferring domain-domain interactions from protein-protein interactions.

The interaction between proteins is one of the most important features of protein functions. Behind protein-protein interactions there are protein domains interacting physically with one another to perform the necessary functions. Therefore, understanding protein interactions at the domain level gives a global view of the protein interaction network, and possibly of protein functions. Two research groups used yeast two-hybrid assays to generate 5719 interactions between proteins of the yeast Saccharomyces cerevisiae. This allows us to study the large-scale conserved patterns of interactions between protein domains. Using evolutionarily conserved domains defined in a protein-domain database called PFAM (http://PFAM.wustl.edu), we apply a Maximum Likelihood Estimation method to infer interacting domains that are consistent with the observed protein-protein interactions. We estimate the probabilities of interactions between every pair of domains and measure the accuracies of our predictions at the protein level. Using the inferred domain-domain interactions, we predict interactions between proteins. Our predicted protein-protein interactions have a significant overlap with the protein-protein interactions (MIPS: http://mips.gfs.de) obtained by methods other than the two-hybrid assays. The mean correlation coefficient of the gene expression profiles for our predicted interaction pairs is significantly higher than that for random pairs. Our method has shown robustness in analyzing incomplete data sets and dealing with various experimental errors. We found several novel protein-protein interactions such as RPS0A interacting with APG17 and TAF40 interacting with SPT3, which are consistent with the functions of the proteins.

Computational Biology↗
PubMed2002

Ruscogenin glycoside (Lm-3) isolated from Liriope muscari inhibits lymphocyte adhesion to extracellular matrix.

We examined the effects of ruscogenin glycoside (Lm-3), isolated from Liriope muscari, on lymphocyte adhesion to extracellular matrix. Adhesion of Jurkat cells activated by anti-CD3 to type I collagen was inhibited by Lm-3 in a concentration- and time-dependent manner. Lm-3 also inhibited the cell attachment to fibronectin and laminin. However, the saponin did not influence anti-CD3-induced cell proliferation and Mn2+-induced adhesion. Protein kinase C activator, phorbol 12,13-dibutyrate, significantly enhanced, while its inhibitor, chlorpromazine, almost completely blocked, the adhesion of anti-CD3-activated Jurkat cells to collagen. Against phorbol 12,13-dibutyrate-activated Jurkat cells, Lm-3 treatment, either before or after activation, significantly inhibited the cell adhesion to collagen. Lm-3 also inhibited the adhesion activated by both anti-CD3 and phorbol 12,13-dibutyrate. Similar inhibition by Lm-3 of the phorbol 12,13-dibutyrate-induced adhesion to collagen was also observed in lymphocytes freshly isolated from mice with contact dermatitis. Furthermore, Lm-3 significantly decreased the leucocyte accumulation in an animal model of experimental pleurisy. These results suggest that the blockade of lymphocyte adhesion to extracellular matrix through interference with the protein kinase C pathway may be one of the mechanisms by which Lm-3 exerts anti-inflammatory activity.

Animals↗
PubMed2002

Defining the period of recovery of the glucose concentration after its local perturbation by the implantation of a miniature sensor.

At the wound caused by implanting a subcutaneous glucose sensor, the concentration of glucose differs transiently from that in the subcutaneous fluid near non-wounded skin. The period of recovery differs for different wounds and is difficult to predict. A diabetic patient implanting a subcutaneous sensor needs to know whether the transient difference subsided sufficiently for the sensor readings and the sensor's in vivo calibration to be valid. The miniature amperometric glucose sensor has a compound membrane including a layer of glucose oxidase the reaction centers of which are electrically connected to the electrode through a redox polymer; layers excluding interferents and poisons of the electrocatalytic oxidation of glucose; and a layer reducing fouling by components of the biological fluids. We show that the sensor maintains its in vitro sensitivity after its implantation for four hours in the jugular vein and in the peritoneal fluid of the rat. For a diabetic patient who implants the sensor the four-hour period is long enough for the insertion-trauma-caused local perturbation of the glucose concentration to subside and to safely rely on the readings of the implanted sensor.

Animals↗
PubMed2002

Prediction of protein function using protein-protein interaction data.

Assigning functions to novel proteins is one of the most important problems in the post-genomic era. Several approaches have been applied to this problem, including analyzing gene expression patterns, phylogenetic profiles, protein fusions and protein-protein interactions. We develop a novel approach that applies the theory of Markov random fields to infer a protein's functions using protein-protein interaction data and the functional annotations of its interaction protein partners. For each function of interest and a protein, we predict the probability that the protein has that function using Bayesian approaches. Unlike in other available approaches for protein annotation where a protein has or does not have a function of interest, we give a probability for having the function. This probability indicates how confident we are about the prediction. We apply our method to predict cellular functions (43 categories including a category "others") for yeast proteins defined in the Yeast Proteome Database (YPD), using the protein-protein interaction data from the Munich Information Center for Protein Sequences (MIPS, http://mips.gsf.de). We show that our approach outperforms other available methods for function prediction based on protein interaction data.

Amino Acid Sequence↗