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Q Zhang

Publications and source records attributed to Q Zhang.

At least 145 records · Page 8Linked to original sources
PubMed2001

The sequence of the human genome.

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

Algorithms↗
PubMed2001

Transport of methyl tert-butyl ether through alfalfa plants.

Concentrations measured in alfalfa plant stem segments indicated that plants grown in methyl tert-butyl ether (MTBE)-contaminated soil took up the chemical through their roots. Assuming a cylindrical shape for the plant stem, a mathematical model was developed to describe the transport of MTBE through the stems. Simulation results from uniform and nonuniform initial concentration distributions across the stem radius were compared with steady-state experimental data. With known values of plant stem radius, water usage, water content, and the distance over which the concentration decreased by 50%, the diffusion coefficient of MTBE radial transport across the plant stem was estimated with 95% confidence to be in the range of 8.43-16.2 x 10(-8) cm2/s with a mean of 1.23 x 10(-7) cm2/s. When the diffusion coefficient was calculated based on transient experimental data, the values with 95% confidence interval ranged from 4.14 x 10(-7) to 8.00 x 10(-7) cm2/s with a mean value of 6.07 x 10(-7) cm2/s. The difference between these two results can be reduced by more accurate estimation of the water flow velocity through plant stems. The model is applicable to other species including sunflowers and poplars upon substitution of appropriate parameters.

Carcinogens↗
PubMed2001

STAT3-mediated constitutive expression of SOCS-3 in cutaneous T-cell lymphoma.

A characteristic feature of neoplastic transformation is the loss of external control by cytokines and extracellular matrix of cellular differentiation, migration, and mitogenesis. Because suppressors of cytokine signaling (SOCS) proteins are negative regulators of cytokine-induced signaling, it has been hypothesized that an aberrant SOCS expression plays a role in neoplastic transformation. This study reports on a constitutive SOCS-3 expression in cutaneous T-cell lymphoma (CTCL) cell lines. SOCS-3 protein is constitutively expressed in tumor cell lines (but not in nonmalignant T cells) obtained from affected skin from a patient with mycosis fungoides (MF) and from peripheral blood from a patient with Sezary syndrome (SS). In contrast, constitutive SOCS-3 expression is not found in the leukemic Jurkat T-cell line, the MOLT-4 acute lymphoblastic leukemia cell line, and the monocytic leukemic cell line U937. Expression of SOCS-3 coincides with a constitutive activation of STAT3 in CTCL tumor cells, and stable transfection of CTCL tumor cells with a dominant negative STAT3 strongly inhibits SOCS-3 expression, whereas transfection with wild-type STAT3 does not. Moreover, the reduced SOCS-3 expression in cells transfected with the dominant negative STAT3 is associated with an increased sensitivity to interferon-alpha (IFN-alpha). In conclusion, evidence is provided for a constitutive SOCS-3 expression in cancer cells obtained from patients with CTCL. Moreover, the findings indicate that the aberrant expression of SOCS-3 is mediated by a constitutive activation of STAT3 in CTCL cells and affects the IFN-alpha sensitivity of these cells. (Blood. 2001;97:1056-1062)

Cell Transformation, Neoplastic↗
PubMed2001

Structural basis of diverse sequence-dependent target recognition by the 8 kDa dynein light chain.

Dyneins are multi-subunit molecular motors that translocate molecular cargoes along microtubules. Other than acting as an essential component of the dynein motor complex, the 89-residue subunit of dynein light chain (DLC8) also regulates a number of other biological events by binding to various proteins and enzymes. Currently known DLC8 targets include neuronal nitric oxide synthase; the proapoptotic Bcl-2 family member protein designated Bim; a Drosophila RNA localization protein Swallow, myosin V, neuronal scaffolding protein GKAP, and IkappaBalpha, an inhibitor of the NFkappaB transcription factor. The DLC8-binding domains of the various targets are confined within a short, continuous stretch of amino acid residues. However, these domains do not share any obvious sequence homology with each other. Here, the three-dimensional structures of DLC8 complexed with two peptides corresponding to the DLC8-binding domains of neuronal nitric oxide synthase and Bim, respectively, were determined by NMR spectroscopy. Although the two DLC8-binding peptides have entirely different amino acid sequences, both peptides bind to the protein with a remarkable similar conformation by engaging the symmetric DLC8 dimer through antiparallel beta-sheet augmentation via the beta2 strand of the protein. Structural comparison indicates that the two target peptides use different regions within the conformational flexible peptide-binding channels to achieve binding specificity. We have also re-determined the apo-form solution structure of DLC8 in this work. The structures of the DLC8/target peptide complexes, together with the dynamic properties of the protein, provide a molecular basis of DLC8's diverse amino acid sequence-dependent target recognition.

Amino Acid Sequence↗
PubMed2001

Chemical synthesis of UDP-beta-L-arabinofuranose and its turnover to UDP-beta-L-arabinopyranose by UDP-galactopyranose mutase.

Uridine-5'-diphospho-beta-L-arabinofuranose, a possible donor of L-arabinofuranose residues in plants, was synthesized. This compound, in the presence of UDP-galactopyranose mutase, underwent interconversion with UDP-beta-L-arabinopyranose that is a likely precursor of L-arabinofuranose in vivo. This result provided a working model for the biogenesis of arabinofuranose in plants.

Chromatography, High Pressure Liquid↗
PubMed2001

p300 does not require its acetylase activity to stimulate p73 function.

We previously reported that p73, like p53, utilizes p300 or cAMP-response element-binding protein-binding protein as its coactivator. Here, we extended this work by further examining whether the intrinsic acetylase activity of p300 is necessary for stimulating p73 function. Although p300 acetylated the C-terminal fragment of p73 (amino acids 311-636) in vitro, it was unable to efficiently acetylate the full-length p73. Consistently, p300 did not acetylate p73 in vivo when both the proteins were overexpressed in cells. Also, an acetylase-defective mutant p300 named p300AT2 was able to elevate p73-dependent transcription in cells. p300 associated with p73 when forming DNA-protein complexes and stabilized p73 proteins. These results demonstrate that p300 does not need its acetylase activity to be a coactivator of p73.

Acetylation↗
PubMed2001

How does alteration of hepatic blood flow affect liver perfusion and radiofrequency-induced thermal lesion size in rabbit liver?

The purpose of this study was to test the hypothesis that decreasing liver perfusion in rabbits results in an increase in thermal lesion size and that these effects can be accurately monitored using magnetic resonance imaging (MRI). We additionally tested the hypothesis that the increase in thermal lesion size would depend on the particular vessel or vessels occluded (hepatic artery, portal vein, or both). Using an Institutional Animal Care and Use Committee approved protocol, 20 New Zealand white rabbits were randomly assigned to four treatment groups (five in each group): control and ligation of portal vein (PV), hepatic artery (HA), or both PV and HA (HAPV). Surgical ligation of the appropriate vessel was performed under general anesthesia. Immediately after ligation, the rabbits were placed in a 0.2-T open MR system, and an 18-G copper radiofrequency (RF) electrode with a 2-cm exposed tip was inserted into the liver. RF was applied for 10 minutes with the tip temperature maintained at 90 degrees +/- 2 degrees C. Before and after ablation, perfusion data were obtained for 90 seconds using 30 3-second sequential single oblique-slice fast imaging with steady-state progression (FISP) acquisitions after injection of gadolinium-diethylene triamine pentaacetic acid (Gd-DTPA) via the inferior vena cava. Postablation scanning included axial and oblique turbo spin-echo (TSE) T2-weighted (T2w), STIR, and Gd-enhanced T1w sequences. Lesion size was determined perpendicular to the RF electrode using software calipers on the imager. The rabbits were sacrificed after completion of the post-therapy scans, and their livers were harvested for histologic analysis. The liver showed a mean increase in signal amplitude (SA) of 76% 24 seconds after Gd contrast injection in the control group. After contrast injection, the SA increased to a mean of only 66% in the group with ligated hepatic arteries, with no difference in the time to peak compared with the control group. No significant SA increase over baseline could be found in the groups with ligated PV or ligated PV and HA. T2-weighted images demonstrated the highest lesion-to-liver contrast-to-noise ratios (CNRs; mean -5.5) on postprocedure images, followed by STIR images (mean -2.2) in the control group. The lesions were poorly delineated on the Gd-enhanced images. Average maximum lesion sizes (mean +/- 95% confidence interval) were 22 +/- 4.3 mm after ligation of PV, 22 +/- 2.6 mm after ligation of both PV and HA, 14 +/- 2.0 mm after ligation of HA, and 13 +/- 1.9 mm in the control group. We accept the hypothesis that the diameter of the region of coagulation necrosis achieved by standardized RF ablation in the liver increases with reduced organ perfusion and that this effect can be accurately monitored using MRI. The major factor influencing the size of the coagulation area is the portal venous flow. Occlusion of the hepatic artery alone does not significantly increase lesion size. T2w sequences are best suited for postprocedure imaging due to the high lesion-to-liver CNR in rabbits with normal hepatic perfusion. J. Magn. Reson. Imaging 2001;13:57-63.

Animals↗
PubMed2001

Effects of dexamethasone on tooth eruption in rats: differences in incisor and molar eruption.

A requirement for tooth eruption is the resorption of alveolar bone. Because bone resorption is stimulated by dexamethasone both in vivo and in vitro, dexamethasone 21-phosphate, a soluble form of dexamethasone, was injected into rats to determine its effect on tooth eruption. Such dexamethasone injections accelerate the time of intra-osseous eruption in rat incisors but do not accelerate the eruption time of rat molars when injected into rats. The injections of dexamethasone 21-phosphate also accelerate the time of eyelid opening in the postnatal rats, as well as retarding growth, as measured by body weight. These effects of dexamethasone 21-phosphate parallel the effects of epidermal growth factor injections, including the absence of an effect on molar eruption. This suggests that the molecular signals for the initiation of tooth eruption (i.e., onset of bone resorption) differ between rat incisors and molars. Given that rat incisors are teeth of continuous eruption whereas rat molars are teeth of limited eruption, as are human teeth, care must be taken in extrapolating results derived from rat incisors to human dentition. In vitro, dexamethasone has no effect on the gene expression of either osteoprotegerin or epidermal growth factor in dental follicle cells derived from molars. Because osteoprotegerin expression during normal tooth eruption is transitorily inhibited early postnatally in the molar dental follicle to allow osteoclast formation, the absence of inhibition of its expression by dexamethasone could explain why dexamethasone does not accelerate eruption in molars.

Animals↗
PubMed2001

Hair-forming activity of human lymphocyte specific protein 1 requires cooperation between its caldesmon-like domains and the villin headpiece-like domains.

LSP1 is an F-actin binding with multiple F-actin binding domains. Overexpression of LSP1 in NAD 47/89 patient's neutrophils created hair-like projections on the patient's neutrophil cell surfaces and inhibited neutrophil cell motility and transfection of LSP1 in serial cell lines recreate the NAD 47/89 phenotype and produce branching hair-like surface projections. Although LSP1 contains hair-forming ability and LSP1 F-actin binding domains have been defined, the LSP1 domains responsible for its hair-forming activity, the relationship to the F-actin binding domains, and the required domain interactions, if any, for hair formation are not well understood. To define the hair-forming domains of LSP1, the relationship to the known F-actin binding domains, and binding domain interactions, LSP1 truncates, which include or exclude the different F-actin binding domains, were created by PCR. LSP1 mutants were created by site-directed mutagenesis to define the amino acids important for hair formation. Sf9 cells were infected with recombinant baculovirus expressing the cDNA of LSP1 truncates and mutants, and the morphology of infected Sf9 cells was documented by DIC optics. Results show that (1) the hair-forming activity of LSP1 is localized to the basic C-terminal half of the molecule, which contains all of the F-actin binding domains; (2) both the caldesmon-like domains and the villin headpiece-like domains are required for the hair-forming activity of LSP1; (3) basic amino acids in the villin headpiece regions are crucial for the hair-forming activity of LSP1 molecule. The results suggest cooperation between the caldesmon-like domains and the villin headpiece-like domains are required for the hair-forming activity of human LSP1 in cells.

Amino Acid Motifs↗
PubMed2001

A multielement RF coil for MRI guidance of interventional devices.

Accurate localization of minimally invasive devices is critical to the success of interventional procedures. Device orientation and tip position are two of the most important pieces of information needed to define device location for magnetic resonance imaging (MRI)-guided interventional procedures. While a single one-element micro coil incorporated into an interventional device has proven to be effective in some applications, it can only supply tip position information. However, multiple positions on the device are necessary to also determine its orientation. For this purpose, a novel single micro coil design with three separate winding elements that provides both the device orientation and tip position is described in this study. Definition of MR scan planes, by using the device orientation and the target tissue location, permits automatic tracking of the insertion of the device. Furthermore, devices that include this coil design are permitted to bend to a limited extent. This makes the micro coil design appropriate for many flexible interventional devices. Reliable near-real-time tracking of three points on an interventional device is demonstrated on a 0.2T MRI system with modest gradient performance. Phantom and in vivo animal experiments are used to demonstrate the utility of this new coil design.

Animals↗
PubMed2001

The gene mutated in cocoa mice, carrying a defect of organelle biogenesis, is a homologue of the human Hermansky-Pudlak syndrome-3 gene.

Hermansky-Pudlak syndrome (HPS) is a group of human disorders of organelle biogenesis characterized by defective synthesis of melanosomes, lysosomes, and platelet dense granules. In the mouse, at least 15 loci are associated with mutant phenotypes similar to human HPS. We have identified the gene mutated in cocoa (coa) mice, which is associated with an HPS-like mutant phenotype and thus represents a strong candidate for human HPS. Analysis of coa-mutant mice and cultured coa-mutant mouse melanocytes indicates that the normal coa gene product is involved in early stages of melanosome biogenesis and maturation.

Alleles↗
PubMed2001

Molecular characterization of a cryptic plasmid from Campylobacter jejuni.

Campylobacter jejuni is a leading bacterial cause of human enterocolitis. Molecular genetic characterization of this pathogen has been hampered by the lack of genetic tools that are functional in this organism. Cloning vectors commonly used in other organisms usually do not replicate within C. jejuni. To develop a system for functional analysis of C. jejuni genes, a small plasmid (pCJ01) identified in a poultry isolate of C. jejuni was sequenced and characterized in this study. By using inverse PCR, the full sequence of pCJ01 was amplified and subsequently determined. Results indicate that pCJ01 is a circular molecule of 3212 bp, with a G + C content of 33.5%. A typical plasmid replication origin with iteron sequences is identified upstream of the DNA sequences encoding replication initiation proteins. Four open reading frames (ORFs) are present in pCJ01. ORF1 and ORF2 share high homology with the putative RepA and RepB proteins, respectively, of known C. coli plasmids. ORF3 and ORF4, of unknown function, do not exhibit homology with any sequences deposited in the GenBank database. Hydropathy analysis predicts that ORF3 and ORF4 contain multiple stretches of hydrophobic amino acids, suggesting that they may encode transmembrane proteins. Since pCJ01 is a small plasmid and can be readily prepared from C. jejuni, it may be modified for use in molecular characterization of C. jejuni virulence genes.

Base Sequence↗
PubMed2001

The effect of interleukin-6 on the proliferation of prostate cancer cells in vitro and the modulation of this procedure.

The role of interleukin-6 (IL-6) in the growth of an androgen-independent prostate cancer cell line (PC-3 m) was defined and the effect of dexamethasone, which was previously shown to modulate IL-6/IL-6 receptor (IL-6R) on this procedure was investigated. By using a pretty sensitive and specific enzyme immunoassay (ELISA), it was found that PC-3 m produced certain IL-6, but there was no difference in IL-6 secretion between the group with or without dexamethasone treatment. It was also found that PC-3 m cells could not be stimulated to grow by exogenous IL-6 (P > 0.05), while it could be inhibited to grow by anti-IL-6 monoclonal antibody and dexamethasone with a dose-dependent fashion. Our observation indicated that IL-6 acted as an autocrine growth factor for PC-3 m, and dexamethasone could inhibit cell proliferation by a mechanism independent of its effect on IL-6 mRNA expression.

Androgens↗
PubMed2001

A preliminary clinical study of three-dimensional ultrasonography in prenatal diagnosis.

To evaluate the clinical value of three-dimensional ultrasonography (3DUS) in prenatal diagnosis, 134 pregnant women with high-risk factors in second and third trimester were examined by 3DUS. The results showed that 3DUS could provide more diagnostic information, exclude the abnormalities and enhance the confidence level of physician in 102 normal pregnant women. 3DUS was helpful in the diagnosis in 17 (60.7%) of 28 cases of fetal anomalies. However, 3DUS was not useful in evaluating intrauterine growth retardation in 4 cases. It is concluded that 3DUS is helpful in prenatal diagnosis.

Adult↗
PubMed2001

Three-dimensional ultrasonography in obstetrics: the clinical value.

To investigate the clinical value of three-dimensional ultrasonography (3DUS) in obstetrics, various 3DUS rendering methods including surface mode, transparent mode and multiplanar mode were employed to scan 30 fetuses in second and third trimester by using the transabdominal volume transducer. The results showed that surface mode could vividly demonstrate the surface morphologic features of the fetuses, as well as the stereo-shape and the spatial relationship among the surface structures. The face, limbs, umbilical cord and outer genitalia of the fetus could be well displayed by surface mode. Transparent mode could reveal the bony structures under the surface, such as ribs, vertebrae, crania, etc. The result was not affected by the sophisticated curvature of these bony structures and the success rate was up to 100%. When rendered by multiplanar mode, the region of interest (ROI) could be viewed from different directions. It should be concluded that 3DUS could serve as a supplement to two-dimensional ultrasonography (2DUS). 3DUS might play an important role in prenatal diagnosis and enhance the diagnostic confidence level of the physicians.

Female↗
PubMed2001

Preconcentration by coprecipitation of arsenic and tin in natural waters with a Ni-pyrrolidine dithiocarbamate complex and their direct determination by solid-sampling atomic-absorption spectrometry.

A method for the determination of trace amounts of arsenic and tin in natural waters is described. Trace amounts of arsenic and tin were preconcentrated by coprecipitation with a Ni-ammonium pyrrolidine dithiocarbamate (APDC) complex. The coprecipitates obtained were directly analyzed by graphite-furnace atomic-absorption spectrometry (GFAAS) using the Ni-APDC complex solid-sampling technique. The coprecipitation conditions used for the trace amounts of arsenic and tin in natural water were investigated in detail. It was found that arsenic and tin at sub-ng mL(-1) levels were both coprecipitated quantitatively by Ni(PDC)2 in the pH range 2-3. The concentration factors by coprecipitation reached approximately 40,000 when 2 mg nickel was added as a carrier element to 500 mL of the water sample. The proposed method has been applied to the determination of trace amounts of arsenic and tin in river water and seawater reference materials, and the detection limits for arsenic and tin, which were calculated from three times of the standard deviation of the procedural blanks, are 0.02 ng mL(-1) and 0.04 ng mL(-1), respectively, for 500-mL volumes of water sample.

Arsenic↗
PubMed2001

Direct determination of silicon in powdered aluminium oxide by use of slurry sampling with in situ fusion graphite-furnace atomic-absorption spectrometry.

A direct method for determination of silicon in powdered high-purity aluminium oxide samples, by slurry sampling with in situ fusion graphite-furnace atomic-absorption spectrometry (GF-AAS), has been established. A slurry sample was prepared by 10-min ultrasonication of a powdered sample in an aqueous solution containing both sodium carbonate and boric acid as a mixed flux. An appropriate portion of the slurry was introduced into a pyrolytic graphite furnace equipped with a platform. Silicon compounds to be determined and aluminium oxide were fused by the in situ fusion process with the flux in the furnace under optimized heating conditions, and the silicon absorbance was then measured directly. The calibration curve was prepared by use of a silicon standard solution containing the same concentration of the flux as the slurry sample. The accuracy of the proposed method was confirmed by analysis of certified reference materials. The proposed method gave statistically accurate values at the 95% confidence level. The detection limit was 3.3 microg g(-1) in solid samples, when 300 mg/20 mL slurry was prepared and a 10 microL portion of the slurry was measured. The precision of the determination (RSD for more than four separate determinations) was 14% and 2%, respectively, for levels of 10 and 100 microg g(-1) silicon in aluminium oxide.

Aluminum Oxide↗