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Biomedical subjects

Q Zheng

Publications and source records attributed to Q Zheng.

At least 19 recordsLinked to original sources
PubMed2011

Overexpression of ribosomal RNA in prostate cancer is common but not linked to rDNA promoter hypomethylation.

Alterations in nucleoli, including increased numbers, increased size, altered architecture and increased function are hallmarks of prostate cancer cells. The mechanisms that result in increased nucleolar size, number and function in prostate cancer have not been fully elucidated. The nucleolus is formed around repeats of a transcriptional unit encoding a 45S ribosomal RNA (rRNA) precursor that is then processed to yield the mature 18S, 5.8S and 28S RNA species. Although it has been generally accepted that tumor cells overexpress rRNA species, this has not been examined in clinical prostate cancer. We find that indeed levels of the 45S rRNA, 28S, 18S and 5.8S are overexpressed in the majority of human primary prostate cancer specimens as compared with matched benign tissues. One mechanism that can alter nucleolar function and structure in cancer cells is hypomethylation of CpG dinucleotides of the upstream rDNA promoter region. However, this mechanism has not been examined in prostate cancer. To determine whether rRNA overexpression could be explained by hypomethylation of these CpG sites, we also evaluated the DNA methylation status of the rDNA promoter in prostate cancer cell lines and the clinical specimens. Bisulfite sequencing of genomic DNA revealed two roughly equal populations of loci in cell lines consisting of those that contained densely methylated deoxycytidine residues within CpGs and those that were largely unmethylated. All clinical specimens also contained two populations with no marked changes in methylation of this region in cancer as compared with normal. We recently reported that MYC can regulate rRNA levels in human prostate cancer; here we show that MYC mRNA levels are correlated with 45S, 18S and 5.8S rRNA levels. Further, as a surrogate for nucleolar size and number, we examined the expression of fibrillarin, which did not correlate with rRNA levels. We conclude that rRNA levels are increased in human prostate cancer, but that hypomethylation of the rDNA promoter does not explain this increase, nor does hypomethylation explain alterations in nucleolar number and structure in prostate cancer cells. Rather, rRNA levels and nucleolar size and number relate more closely to MYC overexpression.

Adult↗
PubMed1997

Determination of CAG repeat length in the androgen-receptor gene using frozen serum.

OBJECTIVES: To determine CAG repeat length in exon one of the androgen-receptor gene, using frozen serum as a source of deoxyribonucleic acid (DNA). METHODS: Samples from previously frozen serum samples were prepared for polymerase chain reaction (PCR) by heating thawed serum to 100 degrees C and subsequent centrifugation at 16,000 g. Three microliters of supernatant were added to the PCR in combination with primers flanking the CAG repeat in exon one of the human androgen-receptor gene. After 35 cycles, the PCR amplicons were electrophoresed on an agarose gel, excised, purified, and sequenced. CAG repeat length was directly determined from DNA sequencing gels. RESULTS: Amplified DNA fragments were obtained after PCR from 140 of the 200 specimens examined to date. The DNA amplicon was successfully sequenced in 111 samples derived from 104 individuals. Within this group, the androgen receptor CAG repeat length varied from 11 to 27. The median CAG repeat length was 21; the lower and upper quartiles were 18 or less and 23 or more, respectively. Results were consistent in each case that CAG repeat length was repetitively determined. CONCLUSIONS: The establishment of a methodology to determine androgen-receptor gene CAG repeat length from frozen serum samples opens multiple new opportunities to explore the potential clinical significance of this genetic polymorphism.

Adenine↗
PubMed1996

Allelic variants of human TCR BV17S1 defined by restriction fragment length polymorphism, single strand conformation polymorphism, and amplification refractory mutation system analyses.

Several human TCR BV gene subfamilies, including BV3, BV14, and BV17S1, are single member genes but are overutilized among activated CD4+ synovial T cells in the rheumatoid arthritis (RA). To define the role of these TCR BV genes in the pathogenesis of disease, it is critical to characterize the genomic organization and the allelic variations of these genes. In this study we describe allelic variations of BV17S1 defined by restriction fragment length polymorphism (RFLP), single strand conformation polymorphism (SSCP), and amplification refractory mutation system (ARMS) analyses. A single nucleotide replacement (C/T) results in an amino acid substitution (F/L) in the leader and distinguishes BV17S1*1 from BV17S1*2. This nucleotide substitution was found to create a BsmAI restriction enzyme recognition site in BV17S1*2. Therefore genotypic analyses can be performed either by the SSCP or RFLP method. The analyses of 75 unrelated individuals show that the frequency for allele BV17S1*1 is 52.7% and for allele BV17S1*2 is 47.3%. Both alleles are functionally expressed and are distributed within CD4+/CD8+ T cell subsets. Another point mutation in the CDR2 region of BV17S1, which results in the amino acid replacement of Gln by His, originally identified form a cDNA clone, has now been confirmed as an allele by ARMS analysis using genomic DNA preparations and designated to as BV17S1*3. Screening of this CDR2 related variant among normal populations indicates that this is a rare allele (1 of 75). Although this variant may be of functional significance, the genotypic analysis and functional studies are difficult due to the low frequency of BV17S1*3. In an attempt to define a correlation between BV17S1 allelic usage and susceptibility to RA, the germline distribution of BV17S1 alleles *1 and *2 has been examined in a small number of RA patients and no skewed usage has been identified.

Alleles↗
PubMed1996

Role of postreplicative DNA mismatch repair in the cytotoxic action of thioguanine.

It is proposed here that the delayed cytotoxicity of thioguanine involves the postreplicative DNA mismatch repair system. After incorporation into DNA, the thioguanine is chemically methylated by S-adenosylmethionine to form S6-methylthioguanine. During DNA replication, the S6-methylthioguanine directs incorporation of either thymine or cytosine into the growing DNA strand, and the resultant S6-methylthioguanine-thymine pairs are recognized by the postreplicative mismatch repair system. Azathioprine, an immunosuppressant used in organ transplantation, is partly converted to thioguanine. Because the carcinogenicity of N-nitrosamines depends on formation of O6-alkylguanine in DNA, the formation of the analog S6-methylthioguanine during azathioprine treatment may partly explain the high incidence of cancer after transplantation.

Animals↗
PubMed1996

Accuracy and reliability of the scaling-relaxation method for loop closure: an evaluation based on extensive and multiple copy conformational samplings.

The accuracy and reliability of the recently proposed scaling-relaxation method for loop closure were examined by using extensive conformational sampling. For each of the eight heptapeptides chosen to represent a variety of protein conformations, 1,000-2,000 conformations were sampled. Each segment contained 14 rotatable backbone dihedral angles. The average root mean square deviations (RMSDs) between the predicted and the native conformations were 0.7 angstrom for the backbone and 1.2 angstroms for the side chain atoms. These predictions were substantially more accurate than the previous predictions (1.1 angstroms for the backbone and 2.2 angstroms for the side chain atoms) of the same eight protein segments based on limited conformational sampling (100 conformations for each segment). Large prediction errors mostly occurred at polar and surface side chains that are unlikely to have any meaningful conformation. Moreover, the reliability of seven of the eight predictions was demonstrated with their energy-RMSD and stability-RMSD correlations of the low-energy conformations, where the conformational stability was estimated by using the multiple copy simultaneous sampling method.

Amino Acid Sequence↗
PubMed1996

Fluorescent indicators give biased estimates of intracellular free calcium change in aggregating platelets: implication for studies with human von Willebrand factor.

The ratiometric fluorescent indicators Fura-2 and Indo-1 are considered optimal probes for monitoring intracellular free calcium concentration ([Ca2+]i). Unique problems arise, however, in studying [Ca2+]i changes induced in platelets by von Willebrand factor (vWF). Binding of native multimeric vWF causes extensive platelet aggregation, and is reported to evoke a gradual [Ca2+]i increase. the present investigation examined the reliability of platelet [Ca2+]i measurements in these circumstances. Ristocetin-mediated binding of vWF to human platelets promoted a slow rise in Fura-2 fluorescence ratio. Fura-2 extrusion contributed substantially to this rise, unless blocked by probenecid. Despite this precaution, the platelets were invariably contaminated slightly with extracellular indicator. As aggregation progressively reduced the number of platelets in the spectrofluorometer beam, through settling of the larger aggregates, such extracellular Fura-2 contributed proportionately more to the observed fluorescence. This extraneous signal accounted completely for the fluorescence ratio increase, and apparent [Ca2+]i rise, in response to native multimeric vWF. The same problem arose with Indo-1, whereas the single wavelength indicator Fluo-3 showed the opposite pattern of apparent [Ca2+]i changes. Thus, none of these indicators provides reliable data on [Ca2+]i signals in aggregating platelets. Use of a dimeric form of vWF eliminated the problem of platelet aggregates settling out of suspension, but also virtually abolished the [Ca2+]i increase. These observations may explain some of the inconsistencies among previous investigations of vWF-induced calcium signaling. Moreover, similar problems may arise in studies with other adhesive proteins.

Alkylation↗
PubMed1996

Prevention and management of related complication due to laparoscopic operation: pneumothorax, pneumomediastinum and subcutaneous emphysema.

Essential prerequisite of laparoscopic operation is establishing and maintaining pneumoperitoneum with a certain pressure. But under certain circumstances CO2-gas insufflating could induce pneumothorax, pneumomediastinum and subcutaneous emphysema during the operation. to probe the mechanism of the above complications. 2 typical cases were reported with attempt to probe the mechanism of the development of such applications. We believe that high intra-abdominal pressure during operation is the primary cause of the complications. The essentials of prevention and management of such complications were proposed.

Adult↗
PubMed1996

Computational screening of combinatorial libraries.

We first review existing computational methods with an intrinsic combinatorial feature, then describe a new computational method for screening combinatorial libraries using a recently developed multicopy sampling technique. The new method differs from the existing ones in that it can be used to screen simultaneously an entire library of molecules, instead of the individual molecules in a library. As an example, we have applied the method to study site-directed amino acid substitutions in a protein. After two rounds of library screening, we identified the energetically most stable substitutions along with their optimal conformations from all natural amino acids. In principle, the method is generally applicable to study ligand-host systems.

Amino Acids↗
PubMed1996

Risk assessment of nongenotoxic carcinogens based upon cell proliferation/death rates in rodents.

Increased cell proliferation increases the opportunity for transformations of normal cells to malignant cells via intermediate cells. Nongenotoxic cytotoxic carcinogens that increase cell proliferation rates to replace necrotic cells are likely to have a threshold dose for cytotoxicity below which necrosis and hence, carcinogenesis do not occur. Thus, low dose cancer risk estimates based upon nonthreshold, linear extrapolation are inappropriate for this situation. However, a threshold dose is questionable if a nongenotoxic carcinogen acts via a cell receptor. Also, a nongenotoxic carcinogen that increases the cell proliferation rate, via the cell division rate and/or cell removal rate by apoptosis, by augmenting an existing endogenous mechanism is not likely to have a threshold dose. Whether or not a threshold dose exists for nongenotoxic carcinogens, it is of interest to study the relationship between lifetime tumor incidence and the cell proliferation rate. The Moolgavkar-Venzon-Knudson biologically based stochastic two-stage clonal expansion model is used to describe a carcinogenic process. Because the variability in cell proliferation rates among animals often makes it impossible to detect changes of less than 20% in the rate, it is shown that small changes in the cell proliferation rate, that may be obscured by the background noise in rates, can produce large changes in the lifetime tumor incidence as calculated from the Moolgavkar-Venzon-Knudson model. That is, dose response curves for cell proliferation and tumor incidence do not necessarily mimic each other. This makes the use of no observed effect levels (NOELs) for cell proliferation rates often inadmissible for establishing acceptable daily intakes (ADIs) of nongenotoxic carcinogens. In those cases where low dose linearity is not likely, a potential alternative to a NOEL is a benchmark dose corresponding to a small increase in the cell proliferation rate, e.g., 1%, to which appropriate safety (uncertainty) factors can be applied to arrive at an ADI.

Animals↗
PubMed1995

Induction of tissue factor on monocytes by adhesion to endothelial cells.

Activated monocytes express tissue factor (TF), a protein that is important in the pathogenesis of thrombotic disorders. We sought to characterize an adhesion-dependent pathway for monocyte activation. In this study, we showed that adhesion of monocytes to cytokine-activated endothelial cells (EC) increased (approximately 5- to 10-fold) monocyte procoagulant activity (PCA). The PCA was attributed to TF because it was dependent on the coagulation factors VII and X, but not VIII, and was completely blocked by an anti-TF mAb. Direct cell-cell contact between monocytes and EC was required. The induction of TF was rapid, peaked at 30 min, and persisted for 4 h. Northern analysis revealed a rapid (approximately 30 min) increase in TF mRNA following adhesion, distinct from that induced by LPS (approximately 2-4 h). Four-hour TNF-treated EC supported TF expression, but 0.5- and 24-h TNF-treated EC had no effect. An anti-E-selectin mAb (H18/7) exerted partial inhibition, whereas anti-VCAM-1, ICAM-1, and CD11/CD18 mAbs had no inhibition. Synthetic Lewis X (Le(x)) oligosaccharide partially blocked TF induction, whereas sialyl-Le(x) (sLex) oligosaccharide had no effect. Cross-linking Le(x) on monocytes, but not sLex, significantly increased (approximately 10-fold) the TF expression. Le(x) cross-linking induced TF in 30 min and lasted for 4 h. All seventeen anti-Le(x) mAbs induced significant amount of TF generation, and epitope mapping revealed a single binding epitope on Le(x). These findings indicate that adhesion of monocytes to activated EC induces TF generation, and also suggest that Le(x) may represent an important signaling molecule on monocytes.

Blood Coagulation↗
PubMed1995

Describing the spread of biological populations using stochastic compartmental models with births.

This paper derives new models for describing the spread of biological populations in space and time from classical birth-death-migration processes. The spatial aspect is incorporated using compartmental analysis and is developed for two spatial areas (or compartments). The exact bivariate distributions for such processes are intractable; hence approximating distributions are constructed by matching cumulants. A basic Markovian model with exponential waiting times between births is investigated first. The individual effects of swarming, multiple births, and Erlang distributed waiting times, all of which enhance the biological realism, are investigated. A full model which includes all of these effects is then studied. The models are illustrated with observed data on the spread of the Africanized honey bee in French Guiana. A full model with swarming, with an average of 2.64 colonies per swarming episode, and with waiting times following an Erlang distribution with shape parameter 5 is found to provide the best description of the observed data. The methodology is very general and should have broad application for other biological population models involving dispersal and growth.

Africa↗
PubMed1995

Glucose regulation of glucose transporters in cultured adult and fetal hepatocytes.

GLUT2 is the major glucose transporter of adult hepatocytes. In vivo, membrane GLUT1 is localized to a ring of perivenous cells and increases slightly after fasting or insulin deprivation. GLUT1 also increases in vitro after prolonged culture of isolated adult hepatocytes. We have previously shown that GLUT1 mRNA, protein, and activity are present in the rat fetal hepatocyte, and that both GLUT1 and GLUT2 are important for the pattern of glucose transport in the fetal hepatocyte. We tested the hypothesis that the hypothesis that the postnatal increase in circulating glucose is one of the regulators of the changed pattern of GLUT1 and GLUT2 in the hepatocyte after the fetal to neonatal transition. Fetal and adult rat hepatocytes were cultured for 45 hours in supplemented Dulbecco's modified Eagle's medium at glucose concentrations of 1, 8.3, or 30 mmol/L. Culture at 8.3 and 30 mmol/L glucose diminished GLUT1 mRNA levels were lower in adult versus fetal hepatocyte cultures at 8.3 and 30 mmol/L (P < .05). Similarly, GLUT1 protein levels were significantly diminished in hepatocytes cultured at higher medium glucose (P < .05 for fetal cells at 30 v 1 mmol/L; P < .05 for adult cells at 8.3 and 30 v 1 mmol/L). GLUT2 mRNA abundance was enhanced by medium glucose in adult hepatocytes (P < .05 at 8.3 and 30 v 1 mmol/L) and was unchanged by medium glucose in fetal hepatocytes. In contrast, GLUT2 protein level was unchanged by medium glucose in adult hepatocytes, and was diminished at 30 mmol/L as compared with mmol/L glucose in fetal hepatocytes (P < .05). In confirmation of these findings, uptake of 2-deoxyglucose (2-DOG) by fetal hepatocytes was significantly diminished after culture in 8.3 or 30 mmol/L glucose versus 1 mmol/L glucose (P < .05 and < .01, respectively). These studies confirm that the fetal hepatocyte glucose transporter pattern could be maintained in part by low fetal portal glucose levels. However, the resistance of the fetal hepatocyte glucose transporter pattern as compared with that of the adult hepatocyte to the effects of hyperglycemia suggests additional undefined control mechanisms.

Animals↗
PubMed1995

Flexible docking of peptides to class I major-histocompatibility-complex receptors.

We present a new method for docking flexible peptides to class I Major-Histocompatibility-Complex (MHC) receptors. Docking is performed in two steps: (a) The charged terminal peptide residues are located by randomly distributing multiple copies of each in volumes of approximately 150 A at either end of the binding groove, and then minimizing the system energy using a modified multiple-copy search algorithm. This is followed by (b) construction of the intervening chain using the multiple-copy bond-scaling-relaxation loop closure algorithm. In both steps, the copies tend to cluster and the size of the resulting clusters is proportional to the basin of attraction of the corresponding energy well. We show that native MHC-bound peptides have broad minima and, consequently, that misfolded, low-energy peptide conformations can be eliminated by restricting consideration to groups of peptides which cluster into broad minima. The accuracy of the method is assessed by comparing the predictions with crystallographic data for three different MHC peptide systems, at various degrees of stringency: (a) the extent to which we can determine side chain function (anchor vs. T-cell epitopes); (b) the extent to which we can determine the peptide-receptor orientation; and (c) the accuracy with which we can predict atomic coordinates. We find the method correct on (a) for 19 of the 22 non-Gly positions; the failures appearing to be a consequence of omitting solvation. Predictions related to (b) are also very encouraging, with the overall orientation of the predicted peptides being very similar to the crystal conformation, when measured by the hydrogen bonding pattern between the two. The degree of success in predicting atomic coordinates varied considerably, however, from 1.4 A for the HLA-A2 peptide to 2.7 A for the Kb peptide. The inaccuracy of the latter appears to reflect an incomplete target function, most likely the ommission of solvation. The calculations thus define the current limits of accuracy in docking flexible peptides to Class I receptors and identify the methodological improvements that must be made for the next advance in accuracy.

Algorithms↗
PubMed1995

On the MVK stochastic carcinogenesis model with Erlang distributed cell life lengths.

This paper proposes extending the MVK carcinogenesis model by adopting the Erlang distribution for the life length of the intermediate cells. The investigation concentrates on the survival function and the mean value functions. The approach is basically numerical, making use of the Mathematica software system. The paper also provides a closed form expression for the survival function for a variation of the original MVK model, where all the model parameters are piecewise constants.

Algorithms↗
PubMed1995

Quantitative reverse transcription polymerase chain reaction shows that ethanol enhances interleukin-6 mRNA expression in cultured mesangial cells.

IgA nephropathy, a form of mesangial glomerulonephritis, is associated with chronic ethanol ingestion in humans and in a rat model. We investigated the hypothesis that ethanol has a direct effect on a mesangial cell cytokine, interleukin-6 (IL-6). We measured IL-6 mRNA in cultured mesangial cells using a novel method, quantitative reverse transcription-polymerase chain reaction (Q-RT-PCR). Primers were used to amplify a 346-bp segment. To quantify the results, we generated an internal standard using site-directed mutagenesis which resulted in a restriction site for EcoRI, absent in target IL-6 cDNA. In the presence of the same primers, the mutated internal standard (exogenous template) amplifies with equal efficiency as the target IL-6 cDNA. Q-RT-PCR, using 250 ng of total RNA, showed that after ethanol incubation, IL-6 mRNA was 65 (+/-30) attomol, a 1.5-fold increase from 44 (+/-28) attomol in control cells. This study shows that in vitro, ethanol enhances IL-6 mRNA expression in rat mesangial cells.

Adjuvants, Immunologic↗
PubMed1995

[Constituents of lignanoids in Siphonostegia chinensis Benth].

A trace monomeric compound was isolated from the aerial part of Siphonostegia chinensis, and determined by X-ray diffraction as a lignanoid compound named syringaresinol. It is obtained from this plant as well as from Scrophulariaceae for the first time.

Drugs, Chinese Herbal↗