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Biomedical subjects

Q Deng

Publications and source records attributed to Q Deng.

17 recordsLinked to original sources
PubMed1999

Evolution of shape complementarity and catalytic efficiency from a primordial antibody template.

The crystal structure of an efficient Diels-Alder antibody catalyst at 1.9 angstrom resolution reveals almost perfect shape complementarity with its transition state analog. Comparison with highly related progesterone and Diels-Alderase antibodies that arose from the same primordial germ line template shows the relatively subtle mutational steps that were able to evolve both structural complementarity and catalytic efficiency.

Antibodies, Catalytic↗
PubMed1998

An antibody exo Diels-Alderase inhibitor complex at 1.95 angstrom resolution.

A highly specific Diels-Alder protein catalyst was made by manipulating the antibody repertoire of the immune system. The catalytic antibody 13G5 catalyzes a disfavored exo Diels-Alder transformation in a reaction for which there is no natural enzyme counterpart and that yields a single regioisomer in high enantiomeric excess. The crystal structure of the antibody Fab in complex with a ferrocenyl inhibitor containing the essential haptenic core that elicited 13G5 was determined at 1.95 angstrom resolution. Three key antibody residues appear to be responsible for the observed catalysis and product control. Tyrosine-L36 acts as a Lewis acid activating the dienophile for nucleophilic attack, and asparagine-L91 and aspartic acid-H50 form hydrogen bonds to the carboxylate side chain that substitutes for the carbamate diene substrate. This hydrogen-bonding scheme leads to rate acceleration and also pronounced stereoselectivity. Docking experiments with the four possible ortho transition states of the reaction explain the specific exo effect and suggest that the (3R,4R)-exo stereoisomer is the preferred product.

Antibodies, Catalytic↗
PubMed1998

Self-gelatinizable copolymer immobilized glucose biosensor based on prussian blue modified graphite electrode.

A novel poly(vinyl alcohol) grafting 4-vinylpyridine self-gelatinizable copolymer was adapted to immobilize glucose oxidase. The reduction of hydrogen peroxide (H2O2) was detected at a Prussian Blue (PB) modified graphite electrode. A stable and sensitive glucose amperometric biosensor is described. The copolymer is a good biocompatible polymer in which the glucose oxidase retains high activity. Moreover, the copolymer can adhere firmly to the inorganic PB membrane. The sensor showed an apparent Michaelis-Menten constant of 18 +/- 0.2 mM and a maximum current density of 1.14 microA cm-2 mM-1. The linear range is from 5 microM to 4.5 mM glucose and the detection limit is 0.5 microM glucose. The catalytic efficiency of PB for the reduction of H2O2 is higher than that for the oxidation of H2O2. Glucose concentrations in serum samples from healthy persons and diabetic patients were determined using the sensor. The results compared well with those provided by the hospital using a spectroscopy method.

Biosensing Techniques↗
PubMed1996

Increasing the information content of STS-based genome maps: identifying polymorphisms in mapped STSs.

Physical maps of the human genome are being constructed by many groups using a mapping strategy that relies on the development of sequence-tagged sites (STSs). Thousands of physically mapped STSs, representing hundreds of kilobases (kb) of unique human DNA sequence, have been generated by these efforts. Since sequence variations are found every 1-2 kb in the genome, it is possible to extract additional information from mapped STSs by scanning them for variations. By screening 154 of the STSs published by the Whitehead Institute/MIT Genome Center, we have identified 47 new DNA sequence polymorphisms among the 37.2 kb of unique DNA sequence contained in these STSs. Using a sequence-based approach to estimate allele frequencies for these variations, 29 of the substitution polymorphisms (1 in 1.3 kb) were found to have heterozygosities exceeding 32%. Our study shows that the information content of STS-based genome maps can be increased with minimal additional effort by scanning for DNA polymorphisms, and that ambiguities and errors in the initial STS sequence can be resolved and corrected in the process.

Alleles↗
PubMed1996

AmpliTaq DNA polymerase, FS dye-terminator sequencing: analysis of peak height patterns.

Taq DNA polymerases in which the phenylalanine is substituted by a tyrosine at position 667 (Taq F667Y) are members of a new class of DNA polymerases that incorporate chain-terminating dideoxyribonucleoside triphosphates (ddNTPs) much more efficiently than the wild-type Taq DNA polymerase. Improved incorporation of ddNTPs into DNA during cycle sequencing using AmpliTaq DNA polymerase, FS (Taq-FS, a member of the Taq F667Y family), and dye-labeled primers results in nearly uniform peak heights in the sequencing trace. This is not the case when dye-labeled ddNTPs are used in Taq-FS cycle sequencing reactions. While the rate of dye-terminator incorporation is more efficient with Taq-FS, the peak pattern is still highly variable and different from that produced by the wild-type enzyme. We have systematically examined pairs of sequence-tagged sites that vary at only a single nucleotide to determine how base changes influence the peak heights of neighboring bases in sequencing traces generated by the Taq-FS dye-terminator chemistry. In 31 of 64 possible 3-base windows (48%), we find that the peak height of a particular base can be predicted by knowing just one or two bases 5' to the base in question. We have also compared and contrasted the peak patterns produced by the Taq-FS enzyme with those previously identified for the wild-type enzyme. Establishing the patterns in peak heights within local sequence contexts can improve the accuracy of base-calling and the identification of polymorphisms/mutations when using the Taq-FS dye-terminator cycle-sequencing chemistry.

DNA-Directed DNA Polymerase↗
PubMed1996

Testing the feasibility of DNA typing for human identification by PCR and an oligonucleotide ligation assay.

The use of DNA typing in human genome analysis is increasing and finding widespread application in the area of forensic and paternity testing. In this report, we explore the feasibility of typing single nucleotide polymorphisms (SNPs) by using a semiautomated method for analyzing human DNA samples. In this approach, PCR is used to amplify segments of human DNA containing a common SNP. Allelic nucleotides in the amplified product are then typed by a colorimetric implementation of the oligonucleotide ligation assay (OLA). The results of the combined assay, PCR/OLA, are read directly by a spectrophotometer; the absorbances are compiled; and the genotypes are automatically determined. A panel of 20 markers has been developed for DNA typing and has been tested using a sample panel from the CEPH pedigrees (CEPH parents). The results of this typing, as well as the potential to apply this method to larger populations, are discussed.

Alleles↗
PubMed1995

Coronary flow reserve after ischemia and reperfusion of the isolated heart. Divergent results with crystalloid versus blood perfusion.

Mechanical function and coronary hemodynamics were assessed in 73 isolated rabbit hearts randomly subjected to 0, 10, 20, 30, or 45 minutes of 37 degrees C global ischemia and 45 minutes of reperfusion in either a modified Krebs buffer or homologous blood-perfused Langendorff mode (n = 7 to 9 hearts per group). Isovolumic developed pressure, resting coronary flow, and response to endothelium-dependent (bradykinin) and -independent (nitroglycerin) agonists were quantitated at defined preload and heart rate. Perfusate did not influence systolic performance, which was impaired after 30 minutes of ischemia and fell to 64% to 72% of preischemic values after 45 minutes of ischemia (p < 0.05). However, basal coronary flow was at least sixfold greater in crystalloid-perfused hearts. Moreover, coronary hyperemia (p < 0.05) persisted for Krebs-perfused hearts subjected to all but the longest ischemic interval. After equilibration, all postischemic blood-perfused hearts had basal flow unchanged from before ischemia. Bradykinin and nitroglycerin induced similar increases in coronary flow for each group before and after each ischemia interval. However, the magnitude of this increase was greater in blood-perfused hearts (p < 0.01) and was not attenuated by the ischemic times encompassed in this protocol. In contrast, endothelium-dependent and -independent coronary flow reserve was abolished after 20 minutes of ischemia or longer in Krebs-perfused hearts. These data suggest that the unphysiologic resting flow patterns of crystalloid-perfused isolated hearts obfuscate interpretation of the interaction between coronary flow reserve and ischemic injury.

Animals↗
PubMed1995

Endothelial function following ischemia.

The consequences of ischemia and reperfusion on endothelial dependent and independent coronary flow patterns following a variety of ischemic insults in isolated perfused rabbit hearts were studied. A blood perfused ex vivo model was developed that provided reliable and stable systolic performance comparable to crystalloid perfused hearts, but with a four to sevenfold decrease in resting coronary flow and a three to six fold increase in coronary flow reserve compared to Krebs' perfusion. Following incremental graded 37 degrees C ischemia of 10 to 45 minutes, blood perfused hearts had compromised systolic performance, but unaffected response to exogenous endothelial dependent and independent agonists whereas in crystalloid perfused hearts, the response to these same agonists was blunted prior to noting a decrement in systolic function. Further studies assessed the consequences of 30 and 45 minutes of ischemia on the regulatory role of basal nitric oxide released by the coronary endothelium. In both blood and crystalloid perfused hearts, basal nitric oxide secretion had a significant and persistent regulatory role on coronary vascular tonus over a tenfold range of coronary flow despite ischemic injury that severely depressed systolic performance. Finally, hearts were preserved in University of Wisconsin (UW) or St. Thomas' (ST) solutions for 4 hours at 4 degrees C. With crystalloid perfusion, ST results in impaired postischemic response to both endothelial dependent and independent agonists. After UW preservation and with all blood perfused hearts, postischemic flow patterns were unchanged. Using physiological blood perfusion protocols, the endothelium and arterial smooth muscle were found more resistant to ischemia-reperfusion injury than the myocyte.

Animals↗
PubMed1995

Peak height variations in automated sequencing of PCR products using Taq dye-terminator chemistry.

Direct sequencing of PCR products using Taq DNA polymerase with dye-labeled dideoxy chain terminators results in traces with uneven peaks. The peak height variations reflect the disproportionate rate of incorporation of deoxynucleotides vs. their analogs, a phenomenon that is highly dependent on the neighboring DNA sequence. Such peak height variations make it difficult to call bases correctly or to interpret whether or not a polymorphism is present. We have systematically examined pairs of sequence-tagged sites that vary at only one nucleotide to determine how a single base change will affect the peak heights of neighboring bases. We have found that the peak height of a particular base can often be predicted from the knowledge of just one or two nucleotides 5'- to the base in question. We have also observed several artifacts that occur consistently in the sequencing traces. These artifacts can be misinterpreted as polymorphisms or can obscure the real peak at that site. The empirically derived trends presented in this report can be utilized profitably when one is editing sequence data or examining them for polymorphisms and mutations.

Coloring Agents↗
PubMed1994

Recency, duration, and progestin content of oral contraceptives in relation to the incidence of endometrial cancer (Washington, USA).

Women who have used combined oral contraceptives (COC) have a reduced risk of endometrial cancer relative to that of women who have never used oral contraceptives, but it is unclear whether the size of the reduction is influenced by the progestin content of the preparation. We analyzed data from two population-based case-control studies of endometrial cancer to investigate this question. Among women aged 40 to 59 years who were residents of King or Pierce Counties, Washington (United States), incident cases who were diagnosed during 1975-77 or 1985-87 were identified. Personal interviews were conducted with 316 such women and their responses compared with those of 501 controls who were selected by household surveys or random-digit dialing. A reduced risk of endometrial cancer associated with COC use was present only among users of five or more years' duration, and even then only in women who were not long-term users of unopposed postmenopausal estrogens. Among these women, the relative risk (RR) of endometrial cancer did not differ according to the progestin potency of the COC used: it was equally low for women who had used a COC with low progestin content (RR = 0.2, 95 percent confidence interval [CI] = 0.1-0.8) as for women who had used a COC with high progestin content (RR = 0.3, CI = 0.1-0.9). Our results argue that, if the reduced risk of endometrial cancer in long-term users of COCs is due to the progestins contained in these preparations, that amount of progestin in most COCs exceeds the threshold amount needed to produce this beneficial effect.

Adult↗