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Biomedical subjects

Y Ding

Publications and source records attributed to Y Ding.

At least 19 recordsLinked to original sources
PubMed1999

Structure and function of HNK-1 sulfotransferase. Identification of donor and acceptor binding sites by site-directed mutagenesis.

HNK-1 glycan, sulfo-->3GlcAbeta1-->3Galbeta1-->4GlcNAc-->R, is uniquely enriched in neural cells and natural killer cells and is thought to play important roles in cell-cell interaction. HNK-1 glycan synthesis is dependent on HNK-1 sulfotransferase (HNK-1ST), and cDNAs encoding human and rat HNK-1ST have been recently cloned. HNK-1ST belongs to the sulfotransferase gene family, which shares two homologous sequences in their catalytic domains. In the present study, we have individually mutated amino acid residues in these conserved sequences and determined how such mutations affect the binding to the donor substrate, adenosine 3'-phosphate 5'-phosphosulfate, and an acceptor. Mutations of Lys(128), Arg(189), Asp(190), Pro(191), and Ser(197) to Ala all abolished the enzymatic activity. When Lys(128) and Asp(190) were conservatively mutated to Arg and Glu, respectively, however, the mutated enzymes still maintained residual activity, and both mutant enzymes still bound to adenosine 3',5'-diphosphate-agarose. K128R and D190E mutant enzymes, on the other hand, exhibited reduced affinity to the acceptor as demonstrated by kinetic studies. These findings, together with those on the crystal structure of estrogen sulfotransferase and heparan sulfate N-deacetylase/sulfotransferase, suggest that Lys(128) may be close to the 3-hydroxyl group of beta-glucuronic acid in a HNK-1 acceptor. In contrast, the effect by mutation at Asp(190) may be due to conformational change because this amino acid and Pro(191) reside in a transition of the secondary structure of the enzyme. These results indicate that conserved amino acid residues in HNK-1ST play roles in maintaining a functional conformation and are directly involved in binding to donor and acceptor substrates.

Amino Acid Sequence↗
PubMed1999

A bayesian statistical algorithm for RNA secondary structure prediction.

A Bayesian approach for predicting RNA secondary structure that addresses the following three open issues is described: (1) the need for a representation of the full ensemble of probable structures; (2) the need to specify a fixed set of energy parameters; (3) the desire to make statistical inferences on all variables in the problem. It has recently been shown that Bayesian inference can be employed to relax or eliminate the need to specify the parameters of bioinformatics recursive algorithms and to give a statistical representation of the full ensemble of probable solutions with the incorporation of uncertainty in parameter values. In this paper, we make an initial exploration of these potential advantages of the Bayesian approach. We present a Bayesian algorithm that is based on stacking energy rules but relaxes the need to specify the parameters. The algorithm returns the exact posterior distribution of the number of destabilizing loops, stacking energy matrices, and secondary structures. The algorithm generates statistically representative structures from the full ensemble of probable secondary structures in exact proportion to the posterior probabilities. Once the forward recursions for the algorithm are completed, the backward recursive sampling executes in O(n) time, providing a very efficient approach for generating representative structures. We demonstrate the utility of the Bayesian approach with several tRNA sequences. The potential of the approach for predicting RNA secondary structures and presenting alternative structures is illustrated with applications to the Escherichia coli tRNA(Ala) sequence and the Xenopus laevis oocyte 5S rRNA sequence.

Algorithms↗
PubMed1999

Assessing heterogeneity and correlation of paired failure times with the bivariate frailty model.

We consider bivariate survival times for heterogeneous populations, where heterogeneity induces deviations in an individual's risk of an event as well as associations between survival times. The heterogeneity is characterized by a bivariate frailty model. We measure the heterogeneity effects through deviations associated with hazard functions and an association function defined through the conditional hazard functions: the cross-ratio function proposed by Oakes. We show how the deviation and association measures are determined by the frailty distribution. A Gibbs sampling method is developed for Bayesian inferences on regression coefficients, frailty parameters and the heterogeneity measures. The method is applied to a mental health care data set.

Algorithms↗
PubMed1999

Contig assembly of bacterial artificial chromosome clones through multiplexed fluorescence-labeled fingerprinting.

A rapid multiplexed fingerprinting method has been developed for bacterial artificial chromosome (BAC) contig assembly. Defined subsets of BAC DNA fragments that result from digestion by three paired restriction endonucleases are labeled with unique fluorescent F-ddATP for each subset. Lists of the labeled fragment size are generated by an ABI 377 DNA sequencer and the GeneScan analysis software and then processed by an assembly program, FPC (Fingerprinted Contigs), to produce contig maps. Data obtained from the multiplexed labeling permit detection of smaller overlaps than is observed when data from a single double-digest are analyzed. The method has been tested on 98 BACs from chromosome 22 regions where large-scale sequencing is under way and also through simulation, using randomly generated BAC clones derived from existing DNA sequence data. In each case, contig assembly results demonstrated the advantages of multiplexed fingerprinting.

Chromosomes, Bacterial↗
PubMed1999

Study on the isolation, purification and physicochemical properties of polysaccharides from Indocalamus tesselatus.

Polysaccharides prepared from Chinese traditional medicine "Ruoye" (Indocalamus tesselatus), a kind of bamboo leaves, were studied. Eight crude polysaccharides were isolated from the dried leaves by successive extraction with 85% ethanol (FE), 0.9% sodium chloride (FS), hot water (FI), 1% ammonium oxalate (FII), 5% NaOH (FIII-a, FIII-b) and 20% NaOH (FIV-a, FIV-b). They were decolorized by hydrogen peroxide treatment and the protein was removed with Savag's method. The polysaccharides were precipitated by three volumes of absolute ethanol. After further purification by gel filtration chromatography on a Sephadex G-200 column, these polysaccharides were lyophilized. Their physicochemical properties and structural feature were elucidated by modern analytical technique such as UV, elemental analysis and high performance gel permeation chromatography. From the results of partial hydrolysis, FE and FIII-b have a main chain comprised solely of glucuronic acid and xylose residues, respectively.

Chromatography, Gel↗
PubMed1999

Study of enantioselective interactions between chiral drugs and serum albumin by capillary electrophoresis.

The separation of the enantiomers of three basic drugs, i.e., ofloxacin, propranolol and verapamil, was achieved by affinity capillary electrophoresis (ACE), with human serum albumin (HSA) and bovine serum albumin (BSA) as chiral selectors in phosphate buffer at pH 7.4. Ofloxacin was only separated in the presence of BSA, and verapamil only with HSA, while propranolol was separated with either HSA or BSA. The effects of protein concentration and column wall adsorption on the degree of separation were investigated. Two displacers, ketoprofen and warfarin, respectively, when added to the protein containing buffer, both showed significant effects on the separation behavior. From these data it was argued that verapamil may bind to HSA at both locations known, the warfarin binding site (I) and the ketoprofen binding site (II). While with BSA, binding of ofloxacin may also occur at site I, the preferential binding site for propanolol remains controversial. A drug-drug interaction between propranolol and ketoprofen due to opposite charges was concluded from the increase in migration time in BSA solution. The unbound concentration of verapamil enantiomers in solution in the presence of HSA, as estimated from CD-modified capillary zone electrophoresis, was triggered not only by the HSA concentration but also by the coadditive concentration.

Adsorption↗
PubMed1999

Study of interaction between drug enantiomers and serum albumin by capillary electrophoresis.

The interaction between drugs and human serum albumin (HSA) was investigated by capillary electrophoresis (CE). It involves stereoselectivity, drug displacement and synergism effects. Under protein-drug binding equilibrium, the unbound concentrations of drug enantiomers were measured by frontal analysis (FA). The stereoselectivity of verapamil (VER) binding to HSA was proved by the different free fractions of two enantiomers. In physiological pH (7.4, ionic strength 0.17 phosphate buffer) when 300 microM (+/-) VER were equilibrated with 500 microM HSA, the concentration of unbound S-VER was about 1.7 times its antipode. The binding constants of two enantiomers, K(R-VER) and K(S-VER), were 2670 and 850 M(-1), respectively. However, no obvious stereoselective binding of propranolol (PRO) to HSA was observed. Trimethyl-beta-cyclodextrin (45 mM) was used as a chiral selector in pH 2.5 phosphate buffer. Several drug systems were studied by the method. When ibuprofen (IBU) was added into VER-HSA solution. R-VER was partially displaced while S-VER was not displaced at all. A binding synergism effect between bupivacaine (BUP) and verapamil was observed and further study suggested that verapamil and bupivacaine occupy different binding site of HSA (site II and site III, respectively).

Binding, Competitive↗
PubMed1999

Tetrodotoxin suppresses morphological enhancement of the metastatic MAT-LyLu rat prostate cancer cell line.

Voltage-gated Na+ channels are expressed by highly metastatic MAT-LyLu cells, but not by poorly metastatic AT-2 cells, derived from the rodent Dunning model of prostatic cancer. We have investigated the possible involvement of these channels in the morphological development of the cells. Incubation of both the MAT-LyLu and the AT-2 cell line for 24 h with the Na+ channel blocker tetrodotoxin (TTX) at 6 microM altered the morphology only of the MAT-LyLu cell line. TTX produced significant decreases in: (a) cell process length and (b) field diameter, and increases in (c) cell body diameter and (d) process thickness. Importantly, 6 microM TTX had no significant effects on proliferation rates or cellular toxicity. The results suggest that Na+ channel activity plays a significant role in determining the morphological development of MAT-LyLu cells in such a way as to enhance their metastatic potential.

Animals↗
PubMed1999

Direct binding of purified HLA class I antigens by soluble NKG2/CD94 C-type lectins from natural killer cells.

Human natural killer (NK) cell cytotoxicity is inhibited following human leucocyte antigen (HLA) class I binding by killer cell inhibitory receptors belonging to the immunoglobulin or C-type lectin protein families. Of the latter family, CD94 and NKG2A or -B associate to inhibit NK cell cytotoxicity. We have constructed C-Myc epitope-tagged soluble NKG2A, -B, -C, -D and human NKR-P1 lectin domains, and studied their ability to associate with Flu-tagged soluble CD94 lectin domains. Furthermore, their ability to bind solubilized immunoaffinity-purified HLA class I antigens, either alone or following association with CD94 lectin domains, was evaluated using flow cytometry and Western blot analyses. We show that soluble NKG2A, -B and -C lectin domains interact with CD94 lectin domains to form complexes, whereas NKG2D and human NKR-P1 lectin domains do not. Soluble NKG2C, -D and CD94 lectin domains bind solubilized affinity purified HLA class I antigens on their own, whereas NKG2A and -B require association with CD94 lectin domains for binding. Soluble human NKR-P1 lectin domains do not bind solubilized HLA class I antigens in our system.

Animals↗
PubMed1999

Growth inhibition of A549 human lung adenocarcinoma cells by L-canavanine is associated with p21/WAF1 induction.

L-Canavanine (CAV) is a higher plant nonprotein amino acid and a potent L-arginine antimetabolite. CAV can inhibit the proliferation of tumor cells in vitro and in vivo, but little is known regarding the molecular mechanisms mediating these effects. We demonstrated that the treatment of human lung adenocarcinoma A549 cells with CAV caused growth inhibition; G1 phase arrest is accompanied by accumulation of an incompletely phosphorylated form of the retinoblastoma protein, whose phosphorylation is necessary for cell cycle progression from G1 to S phase. In addition, CAV induces the expression of p53 and subsequent expression of a cyclin-dependent kinase inhibitor, p21/WAF1. The p53-dependent induction of p21/WAF1 and the following dephosphorylation of the retinoblastoma protein by CAV could account for the observed CAV-mediated G1 phase arrest.

Adenocarcinoma↗
PubMed1999

A 12-Mb complete coverage BAC contig map in human chromosome 16p13.1-p11.2.

We have constructed a complete coverage BAC contig map that spans a 12-Mb genomic segment in the human chromosome 16p13.1-p11.2 region. The map consists of 68 previously mapped STSs and 289 BAC clones, 51 of which-corresponding to a total of 7.721 Mb of genomic DNA-have been sequenced, and provides a high resolution physical map of the region. Contigs were initially built based mainly on the analysis of STS contents and restriction fingerprint patterns of the clones. To close the gaps, probes derived from BAC clone ends were used to screen deeper BAC libraries. Clone end sequence data obtained from chromosome 16-specific BACs, as well as from public databases, were used for the identification of BACs that overlap with fully sequenced BACs by means of sequence match. This approach allowed precise alignment of clone overlaps in addition to restriction fingerprint comparison. A freehand contig drawing software tool was developed and used to manage the map data graphically and generate a real scale physical map. The map we present here is approximately 3.5 x deep and provides a minimal tiling path that covers the region in an array of contigous, overlapping BACs.

Base Sequence↗
PubMed1998

Nitric oxide does not initiate but potentiates glucose-induced insulin secretion in pancreatic beta-cells.

The role of nitric oxide (NO) in glucose-induced insulin secretion was studied in pancreatic beta-cells, HIT-T15. A role for NO is suggested since glucose stimulated NO production in a concentration-dependent manner. NG-monomethyl-L-arginine, a potent inhibitor of nitric oxide synthase, significantly inhibited glucose-induced nitric oxide production as well as insulin release in HIT-T15. Furthermore, this inhibitory effect can be reversed by sodium nitroprusside (SNP), a well known NO donor. While SNP alone did not stimulate insulin release, it potentiated the secretory response of HIT-T15 cells to glucose by approximately two-fold. Potentiation by SNP appears to be mediated by NO, since (i) the potentiation was completely abolished by 10 microM hemoglobin, a scavenger of NO; and (ii) was not affected by rhodanese plus sodium thiosulphate. Neither hemoglobin alone nor the combination of rhodanese and sodium thiosulphate had any effect on glucose induced insulin release. These results are consistent with the hypothesis that glucose-induced formation of NO may potentiate the effect of glucose by a positive feedback mechanism.

Drug Interactions↗
PubMed1998

Promoter activation and following induction of the p21/WAF1 gene by flavone is involved in G1 phase arrest in A549 lung adenocarcinoma cells.

Flavonoids are present in many plants including edible fruits and vegetables. Recently, many of the biological activities of flavonoids have been elucidated. Flavone is a well known flavonoid, and many of its derivatives have been shown to have anti-proliferative effects on several cancer cells. We report here that flavone can effectively inhibit the cell growth of human lung adenocarcinoma A549 cells in a dose-dependent manner, and 100 microM flavone causes cell cycle arrest at the G1 phase. As a mechanism underlying the cell cycle arrest, flavone markedly increases the mRNA and protein levels of a universal inhibitor of cyclin-dependent kinase, p21/WAF1, and inhibits phosphorylation of retinoblastoma (RB) protein. Although A549 cells possess wild-type p53, flavone does not induce the p53 protein, suggesting that p21/WAF1 induction is p53-independent. In addition, 100 microM flavone significantly increases the promoter activity of the p21/WAF1 gene by 5-fold. These results suggest that the G1 phase arrest by flavone is due to p53-independent transcriptional induction of the p21/WAF1 gene and the subsequent dephosphorylation of RB protein.

Adenocarcinoma↗
PubMed1998

Efficient synthesis of 3'-glycosylated LacNAc-based oligosaccharides.

LacNAc-based oligosaccharides, including sialyl-(2-->3)-LacNAc, dimeric sialyl-(2-->3)-LacNAc, trimeric sialyl-(2-->3)-LacNAc, beta-glucuronyl-(1-->3)-LacNAc, and 3-sulfo-beta-glucuronyl-(1-->3)-LacNAc, were synthesized efficiently from a single protected LacNAc derivative having both OH-3' and 4' unprotected.

Amino Sugars↗
PubMed1998

A reduction-pyrolysis-catalysis synthesis of diamond

Diamond powder was synthesized through a metallic reduction-pyrolysis-catalysis route with the reaction of carbon tetrachloride and sodium at 700 degreesC, in which the sodium was used as reductant and flux. This temperature is much lower than that of traditional methods. The x-ray powder diffraction patterns showed three strong peaks of diamond. The Raman spectrum showed a sharp peak at 1332 inverse centimeters, which is characteristic of diamond. Although the yield was only 2 percent, this method is a simple means of forming diamond.

Journal Article↗
PubMed1998

Efficient transfer of genes into murine cardiac grafts by Starburst polyamidoamine dendrimers.

Starburst dendrimer, a structurally defined, spherical macromolecule composed of repeating polyamidoamino subunits, was investigated to augment plasmid-mediated gene transfer efficiency in a murine cardiac transplantation model. The grafts were directly injected with naked pCH110, a plasmid encoding beta-galactosidase (beta-Gal), or pCH110-dendrimer complex, and reporter gene expression determined by X-Gal staining. The grafts injected with pCH110-dendrimer demonstrated widespread and extended beta-Gal expression in both myocytes and the graft infiltrating cells from 7 to 28 days, compared to the grafts injected with naked pCH110 that expressed beta-Gal only in myocytes for less than 14 days. p alphaMHC-vIL-10, as plasmid encoding viral interleukin-10 (vIL-10) under the control of alpha-myosin heavy chain promoter, was able to prolong allograft survival from 13.9 +/- 0.9 days to 21.4 +/- 2.3 days (p < 0.005). When dendrimer G5EDA was used with p alphaMHC-vIL-10, 60-fold less DNA resulted in significant prolongation of graft survival to 38.6 +/- 4.7 days (p < 0.0005). The dose of DNA, the charge ratio of DNA to dendrimer, and the size generation of the dendrimers were all determined to be critical variables for prolongation of allograft survival in this model system. Thus, the use of the Starburst dendrimer dramatically increased the efficiency of plasmid-mediated gene transfer and expression. Production of immunosuppressive cytokines at higher amounts for longer periods of time in a greater expanse of tissue enhanced the immunosuppressive effect and prolonged graft survival further.

Animals↗