Biomedical subjects

W Wang

Publications and source records attributed to W Wang.

At least 163 records · Page 9Linked to original sources

PubMed2001

Nonsense-mediated mRNA decay in Saccharomyces cerevisiae.

Cell survival depends on the precise and correct production of polypeptides. Eukaryotic cells have evolved conserved proofreading mechanisms to get rid of incomplete and potentially deleterious proteins. The nonsense-mediated mRNA decay (NMD) pathway is an example of a surveillance mechanism that monitors premature translation termination and promotes degradation of aberrant transcripts that code for nonfunctional or even harmful proteins. In this review we will describe our current knowledge of the NMD pathway, analyzing primarily the results obtained from the yeast Saccharomyces cerevisiae, but establishing functional comparisons with those obtained in higher eukaryotes. Based on these observations, we present two related working models to explain how this surveillance pathway recognizes and selectively degrades aberrant mRNAs.

Codon, Nonsense↗

PubMed2001

Ternary complexes and cooperative interplay between NCoA-62/Ski-interacting protein and steroid receptor coactivators in vitamin D receptor-mediated transcription.

The vitamin D receptor (VDR) is a ligand-dependent transcriptional factor that binds to vitamin D-responsive elements as a heterodimer with retinoid X receptor (RXR) to regulate target gene transcription. The steroid receptor coactivator (SRC) proteins are coactivators that interact with the AF-2 domain of VDR to augment 1,25-dihydroxyvitamin D3-dependent transcription. In contrast, NCoA-62/Ski-interacting protein (SKIP) is a distinct, activation function-2-independent coactivator for VDR. The current study examined whether these two distinct classes of coactivators impact functionally on VDR-mediated transcription. Using a ternary complex binding assay, we observed a marked preference for the direct interaction of NCoA-62/SKIP with the VDR-RXR heterodimer as compared with the VDR-VDR homodimer or VDR monomer. The liganded VDR also formed a ternary complex with NCoA-62/SKIP and SRC proteins in vitro. Competition experiments using LXXLL peptides showed that NCoA-62/SKIP and SRC coactivators contact different domains of the VDR-RXR heterodimer. Synergistic interplays were observed between NCoA-62/SKIP and SRC coactivators in VDR-mediated transcriptional assays, and protein interference assays indicated a requirement for both NCoA-62/SKIP and SRCs in VDR- mediated transcription. These studies suggest that the ligand-dependent and simultaneous interaction of NCoA-62/SKIP and SRC coactivators with distinct interaction domains within the VDR-RXR heterodimer results in cooperative interplays between coactivators in VDR-mediated transcription.

Amino Acid Sequence↗

PubMed2001

SCID in Jack Russell terriers: a new animal model of DNA-PKcs deficiency.

We recently described the incidence of a SCID disease in a litter of Jack Russell terriers. In this study, we show that the molecular defect in these animals is faulty V(D)J recombination. Furthermore, we document a complete deficit in DNA-dependent protein kinase activity that can be explained by a marked diminution in the expression of the catalytic subunit DNA-dependent protein kinase catalytic subunit (DNA-PKcs). We conclude that as is the case in C.B-17 SCID mice and in Arabian SCID foals, the defective factor in these SCID puppies is DNA-PKcs. In mice, it has been clearly established that DNA-PKcs deficiency produces an incomplete block in V(D)J recombination, resulting in "leaky" coding joint formation and only a modest defect in signal end ligation. In contrast, DNA-PKcs deficiency in horses profoundly blocks both coding and signal end joining. Here, we show that although DNA-PKcs deficiency in canine lymphocytes results in a block in both coding and signal end joining, the deficit in both is intermediate between that seen in SCID mice and SCID foals. These data demonstrate significant species variation in the absolute necessity for DNA-PKcs during V(D)J recombination. Furthermore, the severity of the V(D)J recombination deficits in these three examples of genetic DNA-PKcs deficiency inversely correlates with the relative DNA-PK enzymatic activity expressed in normal fibroblasts derived from these three species.

Alleles↗

PubMed2001

Quaternary ammonium palmitoyl glycol chitosan--a new polysoap for drug delivery.

A new polysoap, quaternary ammonium palmitoyl glycol chitosan (GCPQ, M(w)=178,000 g mole(-1)) with drug solubilising potential has been synthesised and characterised. In solution hydrophobic domains of GCPQ polymeric micelles were identified by the hypsochromic shift in the lambda(max) of methyl orange and by the increase in the ratio of the fluorescence emission intensity of the third and first pyrene vibronic peaks (I(3)/I(1)). At high aqueous concentrations (>10 mg ml(-1)) GCPQ presents as a gel which solubilises pyrene (2.5 mM, normal solubility in water approximately 2 microM) on probe sonication. Dilution of the gel to a liquid solution of polymeric micelles (< or =3.75 mg ml(-1) of GCPQ), results in the observation of fluorescent pyrene excimers (excited dimers) and a high excimer to monomer fluorescence ratio (I(E)/I(M)). However, attempts to solubilise pyrene at a concentration of 2.5 mM in a liquid solution of GCPQ (3.75 mg ml(-1)) results in a reduced I(E)/I(M) value and pyrene precipitation. Viscometry measurements show a more compact conformation for the polymer solubilising pyrene than the polymer alone. The polymer is non-haemolytic when present as the liquid solution and relatively non cytotoxic. In conclusion, a new biocompatible polysoap (potential drug solubiliser) is described which forms hydrophobic domains in solution and shows hysteresis in its solubilisation of pyrene.

Azo Compounds↗

PubMed2001

Paternal population history of East Asia: sources, patterns, and microevolutionary processes.

Asia has served as a focal point for human migration during much of the Late Pleistocene and Holocene. Clarification of East Asia's role as a source and/or transit point for human dispersals requires that this region's own settlement history be understood. To this end, we examined variation at 52 polymorphic sites on the nonrecombining portion of the Y chromosome (NRY) in 1,383 unrelated males, representing 25 populations from southern East Asia (SEAS), northern East Asia (NEAS), and central Asia (CAS). The polymorphisms defined 45 global haplogroups, 28 of which were present in these three regions. Although heterozygosity levels were similar in all three regions, the average pairwise difference among haplogroups was noticeably smaller in SEAS. Multidimensional scaling analysis indicated a general separation of SEAS versus NEAS and CAS populations, and analysis of molecular variance produced very different values of Phi(ST) in NEAS and SEAS populations. In spatial autocorrelation analyses, the overall correlogram exhibited a clinal pattern; however, the NEAS populations showed evidence of both isolation by distance and ancient clines, whereas there was no evidence of structure in SEAS populations. Nested cladistic analysis demonstrated that population history events and ongoing demographic processes both contributed to the contrasting patterns of NRY variation in NEAS and SEAS. We conclude that the peopling of East Asia was more complex than earlier models had proposed-that is, a multilayered, multidirectional, and multidisciplinary framework is necessary. For instance, in addition to the previously recognized genetic and dental dispersal signals from SEAS to NEAS populations, CAS has made a significant contribution to the contemporary gene pool of NEAS, and the Sino-Tibetan expansion has left traces of a genetic trail from northern to southern China.

Animals↗

PubMed2001

Expression cloning of two genes that together mediate organic solute and steroid transport in the liver of a marine vertebrate.

Uptake of organic solutes and xenobiotics by mammalian cells is mediated by ATP-independent transporters, and four families of transporters have now been identified. To search for novel organic solute transporters, a liver cDNA library from an evolutionarily primitive marine vertebrate, the little skate Raja erinacea, was screened for taurocholate transport activity by using Xenopus laevis oocytes. In contrast to the organic anion transporters identified to date, a transport activity was identified in this library that required the coexpression of two distinct gene products, termed organic solute transporter alpha and beta (Ostalpha, Ostbeta). Ostalpha cDNA encodes for a protein of 352 aa and seven putative transmembrane (TM) domains. Ostbeta contains 182 aa and has at least one and perhaps two TM domains. There is no significant sequence identity between Ostalpha and Ostbeta, and only low identity with sequences in the databases; however, Ostalpha bears a resemblance to some G protein-coupled receptors, and Ostbeta exhibits 22% amino acid identity with the C-terminal TM and intracellular domains of protocadherin-gamma, a cell surface glycoprotein. Xenopus oocytes injected with the cRNA for both Ostalpha and Ostbeta, but not each separately, were able to take up taurocholate, estrone sulfate, digoxin, and prostaglandin E(2), but not p-aminohippurate or S-dinitrophenyl glutathione. Transport was sodium-independent, saturable, and inhibited by organic anions and steroids, including the major skate bile salt, scymnol sulfate. These results identify an organic anion transporter composed of a putative seven-helix TM protein and an ancillary membrane polypeptide.

Amino Acid Sequence↗

PubMed2001

Changes of the expression of 5-HT receptor subtype mRNAs in rat dorsal root ganglion by complete Freund's adjuvant-induced inflammation.

By using the reverse transcriptase polymerase chain reaction technique, the expression of 5-hydroxytryptamine (5-HT) receptor subtype mRNAs in the rat lumbar dorsal root ganglion (DRG) was investigated following unilateral injection of complete Freund's adjuvant (CFA) into the rat hind paw. The results showed that 5-HT(1A), 5-HT(1B), 5-HT(1D), 5-HT(1F), 5-HT(2A), 5-HT(3), 5-HT(4), 5-HT(5A) and 5-HT(7) receptor subtypes were present in the rat lumbar DRG. CFA injection resulted in a significant increase in mRNA level of 5-HT(1A), 5-HT(1B), 5-HT(1F), 5-HT(2A), 5-HT(3), 5-HT(4) and 5-HT(7) receptor subtypes and a marked induction of 5-HT(2C) subtype mRNA in the DRG. The present results suggest the important roles for these 5-HT receptor subtypes in generating peripheral nociceptive signaling and provide evidence to elucidate the mechanism of 5-HT in nociception.

Actins↗

PubMed2001

The forensic DNA implications of genetic differentiation between endogamous communities.

In many indigenous minority populations, and among migrants from Asian and African populations now resident in western Europe, North America and Australia, there is a strong tradition of endogamy and a preference for consanguineous unions. These marriage practices can result in F(ST) values greatly in excess of the maximum value (0.01) currently recommended for forensic DNA purposes under guidelines established by the National Research Council (NRC) of the USA. To examine the possible extent of deviation from this accepted norm, three co-resident Pakistani communities were studied using 10 autosomal dinucleotide markers and six tetranucleotide markers on the Y-chromosome. The mean population subdivision coefficient (FST) value was 0.13 for the autosomal loci, and Y-chromosome loci exhibited even stronger differentiation with unique alleles identified in all three communities. The data indicate that even when sub-populations are virtually indistinguishable in terms of anthropology, geography, ethnicity or culture, they may still exhibit major genetic differentiation. Where significant population stratification is known to exist, more detailed genetic databases should be developed for forensic DNA purposes, based on reference data from each of the appropriate sub-populations and not on random or combined samples.

Consanguinity↗

PubMed2001

Pharmacogenomic dissection of resistance to thymidylate synthase inhibitors.

Chemoresistance is a major obstacle for successful cancer treatment. Gene amplification and altered expression are the main genetic mechanisms of tumor chemoresistance. Previously, only a limited number of genes were analyzed in each individual study using traditional molecular methods such as Northern and Southern blotting. In this study, the global gene expression patterns of 1176 genes in a panel of five thymidylate synthase (TS) inhibitor [raltitrexed (TDX) and 5-fluorouracil (5-FU)] resistant and sensitive parent cell lines were investigated using cDNA array technology. Only 28 of 1176 genes were altered >1.5-fold among resistant cells, with 2 genes (TS and YES1) consistently higher in the panel. TS mRNA and protein were consistently overexpressed in all drug-resistant tumor cell lines compared with the sensitive parent cell lines. Southern blot and FISH analysis demonstrated that the TS gene was amplified in 5-FU- and TDX-resistant cell lines. YES1 mRNA and protein were overexpressed in four drug-resistant tumor cell lines but were not overexpressed in the lymphoblast cell line W1L2(TDX), although the YES1 gene was highly amplified in these cells. The fact that W1L2 has high level (>10-fold) resistance to TS inhibitor in the absence of high YES1 expression leads to a conclusion that YES1 has no direct role in this drug resistance process. By narrowing the search from 1176 to 2 genes, the analysis of in vitro TDX and 5-FU resistance becomes more straightforward for confirmatory studies. These data provide encouragement that comprehensive transcript analysis will aid the quest for more enlightened therapeutics.

Blotting, Northern↗

PubMed2001

BeF(3)(-) acts as a phosphate analog in proteins phosphorylated on aspartate: structure of a BeF(3)(-) complex with phosphoserine phosphatase.

Protein phosphoaspartate bonds play a variety of roles. In response regulator proteins of two-component signal transduction systems, phosphorylation of an aspartate residue is coupled to a change from an inactive to an active conformation. In phosphatases and mutases of the haloacid dehalogenase (HAD) superfamily, phosphoaspartate serves as an intermediate in phosphotransfer reactions, and in P-type ATPases, also members of the HAD family, it serves in the conversion of chemical energy to ion gradients. In each case, lability of the phosphoaspartate linkage has hampered a detailed study of the phosphorylated form. For response regulators, this difficulty was recently overcome with a phosphate analog, BeF(3)(-), which yields persistent complexes with the active site aspartate of their receiver domains. We now extend the application of this analog to a HAD superfamily member by solving at 1.5-A resolution the x-ray crystal structure of the complex of BeF(3)(-) with phosphoserine phosphatase (PSP) from Methanococcus jannaschii. The structure is comparable to that of a phosphoenzyme intermediate: BeF(3)(-) is bound to Asp-11 with the tetrahedral geometry of a phosphoryl group, is coordinated to Mg(2+), and is bound to residues surrounding the active site that are conserved in the HAD superfamily. Comparison of the active sites of BeF(3)(-) x PSP and BeF(3)(-) x CeY, a receiver domain/response regulator, reveals striking similarities that provide insights into the function not only of PSP but also of P-type ATPases. Our results indicate that use of BeF(3)(-) for structural studies of proteins that form phosphoaspartate linkages will extend well beyond response regulators.

Aspartic Acid↗

PubMed2001

Elevated plasma tissue plasminogen activator and anti-THP-1 antibodies are independently associated with decreased graft survival in cardiac transplant recipients.

Hemostatic and immunologic factors have been implicated in future cardiac events in patients with coronary artery disease. The role of these factors and their interaction is less established in cardiac transplant recipients. We sought to characterize the role of these factors in these patients. Cardiac transplant patients who presented for surveillance coronary angiography and/or endomyocardial biopsy were eligible for enrollment. Ninety-nine consecutive patients were enrolled. Plasma levels of tissue-type plasminogen activator (t-PA), plasminogen activator inhibitor-1, von Willebrand factor, fibrin D-dimer, and anti-t-PA antibody were determined by enzyme-linked immunosorbent assays. Anti-THP-1 cell antibodies directed against a monocytic leukemia cell line were detected by incubating patient plasma with THP-1 cells. Bound antibody was detected using goat peroxidase-labeled immunoglobulin G directed against human immunoglobulins. Lipids were measured by enzymatic methods. Multivariate analysis identified the presence of anti-THP-1 cell antibodies (risk ratio 4.41, p = 0.002), t-PA antigen (risk ratio 1.10, p = 0.033), donor age 20 to 26 years (risk ratio 8.83, p = 0.042), and donor age >36 years (risk ratio 15.53, p = 0.009) as predictors of allograft failure. Altered hemostatic function, as demonstrated by elevated plasma t-PA antigen levels, is predictive of subsequent allograft failure in cardiac transplant recipients. In addition, the presence of anti-THP-1 cell antibodies in these patients is predictive of allograft failure.

Chi-Square Distribution↗

PubMed2001

Cytokine and cyclooxygenase-2 protein in brain areas of tumor-bearing mice with prostanoid-related anorexia.

Evidence suggests that cytokines in the central nervous system are mediators behind anorexia in tumor-bearing hosts. We have therefore evaluated, by immunohistochemical image analyses, time course changes of interleukin (IL)-1beta, IL-6, tumor necrosis factor (TNF) alpha, IL-6 receptor (gp130), IL-1 receptor I, and cyclooxygenase (Cox)-2 protein in brain cortex, hippocampus and the ventromedial hypothalamic nucleus (VMH) in tumor-bearing mice with prostanoid-related anorexia. Pair-fed non-tumor-bearing mice were used as controls. Prostaglandin E(2) was provided systemically to freely fed, non-tumor-bearing mice to confirm a role for prostanoids in modulation of brain cytokines and food intake. Time course changes of IL-1beta were significantly different between tumor-bearing mice and pair-fed controls in the hippocampus but not in the VMH. TNF-alpha in the hippocampus and VMH did not show any significant difference between tumor-bearing mice and pair-fed controls, whereas TNF-alpha showed a small increase over time in brain VMH. IL-6 content did not show any significant alterations among tumor-bearing and pair-fed mice but increased significantly over time in both the study and control group. Cox-2 in brain hippocampus and VMH showed a statistically significant rise in both tumor-bearing and pair-fed controls, with no difference between animal groups. Systemic provision of exogenous PGE(2) to non-tumor-bearing mice altered brain cytokines significantly in the hippocampus and VMH with associated changes in food intake. Our results demonstrate that some differences (IL-1beta) occurred in brain cytokines comparing tumor-bearing and pair-fed, non-tumor-bearing mice but within unexpected decreased levels in brain tissue from tumor-bearing mice. Surprisingly, many time course changes in brain cytokines were similarly altered in tumor-bearing and pair-fed mice. Our observations do not support that up-regulation of brain cytokines explains or promotes anorexia in cancer disease. Rather, cytokine and Cox-dependent alterations in brain tissue seemed to be secondary to a decline in food intake and related to subsequent stress hormone activities.

Animals↗

PubMed2001

Nocistatin, a peptide reversing acute and chronic morphine tolerance.

It has been reported that intracerebroventricular (i.c.v.) injection of nociception/orphanin FQ (OFQ) can antagonize morphine analgesia, whereas i.c.v. OFQ antibody can reverse morphine tolerance. Nocistatin (NST) is a recently characterized neuropeptide possessing an antagonizing effect on OFQ. Here we examine whether i.c.v. NST would result in a reversal of morphine tolerance. The results showed that: (1) i.c.v. NST at doses of 0.005, 0.05, 0.5, 5 or 50 ng per rat produced a bell-shaped dose-dependent reversal of chronic morphine tolerance, with maximum response at 0.5 ng. (2) Acute morphine tolerance could also be reversed, albeit partially, by i.c.v. NST at 0.5 ng. (3) The reversal of acute and chronic morphine tolerance by NST was completely abolished when NST (0.5 ng) was co-injected with (8 microg) OFQ. Since OFQ and NST are derived from the same preprohormone, the profile of its splicing in the CNS may play an important role in determining the effectiveness of morphine analgesia.

Analgesics, Opioid↗

PubMed2001

Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA.

In this work, a new ansatz is presented that combines molecular dynamics simulations with MM-PBSA (Molecular Mechanics Poisson-Boltzmann/surface area) to rank the binding affinities of 12 TIBO-like HIV-1 RT inhibitors. Encouraging results have been obtained not only for the relative binding free energies, but also for the absolute ones, which have a root-mean-square deviation of 1.0 kcal/mol (the maximum error is 1.89 kcal/mol). Since the root-mean-square error is rather small, this approach can be reliably applied in ranking the ligands from the databases for this important target. Encouraged by the results, we decided to apply MM-PBSA combined with molecular docking to determine the binding mode of efavirenz SUSTIVA(TM) another promising HIV-1 RT inhibitor for which no ligand-protein crystal structure had been published at the time of this work. To proceed, we define the following ansatz: Five hundred picosecond molecular dynamics simulations were first performed for the five binding modes suggested by DOCK 4.0, and then MM-PBSA was carried out for the collected snapshots. MM-PBSA successfully identified the correct binding mode, which has a binding free energy about 7 kcal/mol more favorable than the second best mode. Moreover, the calculated binding free energy (-13.2 kcal/mol) is in reasonable agreement with experiment (-11.6 kcal/mol). In addition, this procedure was also quite successful in modeling the complex and the structure of the last snapshot was quite close to that of the measured 2,3 A resolution crystal (structure the root-mean-square deviation of the 54 C(alpha) around the binding site and the inhibitor is 1.1 A). We want to point out that this result was achieved without prior knowledge of the structure of the efavirenz/RT complex. Therefore, molecular docking combined with MD simulations followed by MM-PBSA analysis is an attractive approach for modeling protein complexes a priori.

Alkynes↗

PubMed2001

Degradation of dye solution by an activated carbon fiber electrode electrolysis system.

Degradation of 29 dyes by means of an activated carbon fiber (ACF) electrode electrolysis system was performed successfully. Almost all dye solutions tested were decolorized effectively in this ACF electrolysis process. Internal relationships between treatment mechanisms and chemical composition of the dye have been discussed in this paper. Generally, it is shown that higher solubility leads to greater degradation in the process. Dyes with many -SO3-, COO-, -SO2NH2, -OH, hydrophilic groups, and azo linkages are susceptible to reduction. However, dyes with many -C=O, -NH-and aromatic groups, and hydrophobic groups, tend to be adsorbed. For dyes with -SO3-, COOH and -OH groups, if their molecules linearly spread in solution and have a significant tendency to form colloids by hydrogenous bonding, they also tend to be adsorbed and flocculated. Typical dynamic electrolysis of dye Acid Red B, Vat Blue BO and Disperse Red E-4B shows how the two major mechanisms, degradation and adsorption, act differently during treatment. Reduction occurs evenly during treatment. During the dominant adsorption process, after certain amount of iron is generated, colloid precipitation occurs and TOC and color are rapidly removed.

Adsorption↗

PubMed2001

Development of a new reaction system for the synthesis of highly optically active alpha,gamma-substituted gamma-butyrolactones.

A highly useful method for the synthesis of optically active alpha,gamma-substituted gamma-butyrolactones has been developed. The SmI(2)-induced reductive coupling of chiral 2-alkyl acrylates derived from isosorbide with ketones in the presence of (1S)-(-)-2,10-camphorsultam as a proton source give the chiral alpha,gamma-substituted gamma-butyrolactones in good yields and high enantiomeric purities (up to >99% ee for trans and 75% ee for cis). The reaction system has been investigated with various ketones, and it is demonstrated that this system is very effective for trans-alpha,gamma-substituted gamma-butyrolactones. Both the chiral auxiliary and the hindered proton source in this system are necessary for the observed excellent ee values of the products. The absolute configuration of the trans products is assigned on the basis of the X-ray crystal structure.

4-Butyrolactone↗

PubMed2001

Cloning and expression pattern of the human NDRG3 gene.

We report the cloning and expression pattern of a novel N-myc downstream-regulated gene 3 (NDRG3), located on human chromosome 20q11.21-11.23. The NDRG3 cDNA is 2588 base pair in length, encoding a 363 amino acid polypeptide highly related to mouse Ndr3 protein. Northern blot reveals that NDRG3 is highly expressed in testis, prostate and ovary. By in situ hybridization, the NDRG3 mRNA was localized to the outer layers of seminiferous epithelium, indicating that it may play a role in spermatogenesis.

Amino Acid Sequence↗

PubMed2001

Clustering of arrays of chaotic chemical oscillators by feedback and forcing.

Feedback and external forcing are applied to an array of chaotic electrochemical oscillators through variations in the applied potential. We see transitions from intermittent clusters to stable chaotic clusters to stable periodic clusters to synchronized states as the feedback gain and forcing amplitude, respectively, are varied. With forcing up to four clusters are observed in stable states. The transition to synchronization with feedback occurs by the increase in the size of one cluster at the expense of the others.

Journal Article↗