Biomedical subjects

Peng Zhang

Publications and source records attributed to Peng Zhang.

At least 163 records · Page 9Linked to original sources

PubMed2004

Different age distribution patterns of human, nematode, and Arabidopsis duplicate genes.

We studied the age distribution of duplicate genes in each of four eukaryotic genomes: human, Arabidopsis thaliana, Caenorhabditis elegans, and Drosophila melanogaster. The four distributions differ greatly from each other, contrary to the previous proposal of a universal L-shaped distribution in all eukaryotic genomes studied. Indeed, only the distribution in humans is L-shaped. The distribution in Arabidopsis is consistent with the hypothesis of an ancient genome duplication with no recent burst of duplication events, while the distribution in C. elegans is nearly uniform. We also applied a nonparametric method to the human distribution to show that the rate of loss of duplicate genes decreases over time, contrary to the proposal of an exponential decay. One possible explanation of the decreasing rate of loss of duplicate genes over time could be rapid functional divergence between duplicate genes, providing an advantage for the retention of both duplicates.

Algorithms↗

PubMed2004

Ion-molecule rate constants and branching ratios for the reaction of N(3) (+)+O(2) from 120 to 1400 K.

The kinetics of the reaction of N(3) (+) with O(2) has been studied from 120 to 1400 K using both a selected ion flow tube and high-temperature flowing afterglow. The rate constant decreases from 120 K to approximately 1200 K and then increases slightly up to the maximum temperature studied, 1400 K. The rate constant compares well to most of the previous measurements in the overlapping temperature range. Comparing the results to drift tube data shows that there is not a large difference between increasing the translational energy available for reaction and increasing the internal energy of the reactants over much of the range, i.e., all types of energies drive the reactivity equally. The reaction produces both NO(+) and NO(2) (+), the latter of which is shown to be the higher energy NOO(+) linear isomer. The ratio of NOO(+) to NO(+) decreases from a value of over 2 at 120 K to less than 0.01 at 1400 K because of dissociation of NOO(+) at the higher temperatures. This ratio decreases exponentially with increasing temperature. High-level theoretical calculations have also been performed to compliment the data. Calculations using multi-reference configuration interaction theory at the MRCISD(Q)/cc-pVTZ level of theory show that singlet NOO(+) is linear and is 4.5 eV higher in energy than ONO(+). A barrier of 0.9 eV prevents dissociation into NO(+) and O((1)D); however, a crossing to a triplet surface connects to NO(+) and O((3)P) products. A singlet and a triplet potential energy surface leading to products have been determined using coupled cluster theory at the CCSD(T)/aug-cc-pVQZ level on structures optimized at the Becke3-Lee, Yang, and Parr (B3LYP)/aug-cc-pVTZ level of theory. The experimental results and reaction mechanism are evaluated using these surfaces.

Journal Article↗

PubMed2004

Cyclic-N3. I. An accurate potential energy surface for the ground doublet electronic state up to the energy of the 2A2/2B1 conical intersection.

A sophisticated adiabatic ground electronic state potential energy surface for a pure nitrogen ring (cyclic-N3) molecule is constructed based on extensive high-level ab initio calculations and accurate three-dimensional spline representation. Most of the important features of the potential energy surface are presented using various reduced dimensionality slices in internal hyperspherical coordinates as well as full dimensional isoenergy surfaces. Very significant geometric phase effects are predicted in the spectra of rotational-vibrational states of cyclic-N3.

Journal Article↗

PubMed2004

Is mRNA and protein level of CD46 altered in measles virus vaccine strain S191-infected cells?

Previous research showed that the expression of measles virus receptor CD46 was downregulated after expression of measles virus hemagglutinin protein on the surface of the virus infected cell or triggered by infected cell-to-cell contact. We reported here that the mRNA level of CD46 in MV infected cells was not changed which was tested by real-time quantitative PCR. To further analyse the surface expression alteration of CD46 after MV infection, flow cytometric analysis and indirect immunofluorescence were used to detect the protein level of CD46. Altogether, our results provided a demonstration that the expression of CD46 was not downregulated by the infection of MV strain S191 both on mRNA level and cellular surface protein level. Previous results reported that the "downregulation" of CD46 expression on the cell surface may take place because H protein masks the antibody recognition site on CD46 which results in "downregulation" of the expression of CD46.

Animals↗

PubMed2004

A family of variably expressed outer-membrane proteins (Vomp) mediates adhesion and autoaggregation in Bartonella quintana.

Bartonella species are fastidious, Gram-negative human pathogens that can persist in the host bloodstream for years and bind to and invade several types of host cells. For many pathogens, adhesion to host cells and extracellular matrix (ECM) components is a critical virulence determinant. Bacteria often vary expression of surface adhesins by phase or antigenic variation to subvert the host immune response and permit adaptive interaction with different host structures. We developed a macaque animal model for Bartonella quintana infection to detect changes in bacterial outer-membrane proteins (OMP) during prolonged bloodstream infection. We identified a gene family encoding four highly conserved, 100-kDa, variably expressed OMP (Vomp), two of which function as adhesins. The variable expression of Vomp family members appears to be mediated by deletion of one or more vomp genes during chronic bloodstream infection. vomp deletion was observed also in isolates from humans with chronic B. quintana infection. The Vomp are closely related to the afimbrial adhesin, YadA, a virulence factor of Yersinia enterocolitica. The surface-expressed Vomp contain conserved structural features of YadA, including collagen-binding motifs. We demonstrate that the B. quintana Vomp are multifunctional OMP involved in binding to collagen and autoaggregation: VompC confers the ability to bind collagen IV, and VompA is necessary and sufficient for autoaggregation. The B. quintana Vomp are members of the newly recognized family of YadA-like trimeric autotransporters; the Vomp constitute a multigene family, they are variably expressed, and different virulence properties are attributable to individual Vomp family members.

Adhesins, Bacterial↗

PubMed2004

Characterization of Bcl10 as a potential transcriptional activator that interacts with general transcription factor TFIIB.

The importance of aberrant Bcl10 nuclear expression implicated in lymphomagenesis is becoming increasingly apparent. Our previous works indicate that Bcl10 can transactivate gene expression in yeast, nevertheless, little is known about the activities of nuclear Bcl10 in the mammalian cells and the mechanisms by which it modulates transcription. To understand it better, we mapped the location of the activation domain of Bcl10. This was done in the context of its interaction with TFIIB, as well as its ability to activate transcription as a fusion protein linked to the DNA-binding domain of Gal4 in the mammalian cells. Both approaches demonstrated that Bcl10 contains an activation domain in its N-terminal 13 amino acids. Together, these findings suggest that Bcl10 nuclear expression may modulate gene expression and Bcl10 is a potential transcriptional activator apart from its traditional roles that have been found.

Adaptor Proteins, Signal Transducing↗

PubMed2004

Reductive deposition of Rh nanostructures on n-type porous silicon: X-ray absorption and X-ray excited optical luminescence studies.

22Porous silicon (PS) prepared from an n-type Si(100) wafer was utilized as a reducing agent and a nanosubstrate for the reduction of rhodium complex ions [RhCl6]3- from aqueous solution to metallic Rh nanostructures on the surface of the n-type PS. The morphology and the electronic properties of the PS layers as well as the rhodium nanostructures were studied by field emission scanning electron microscopy, X-ray absorption fine structures spectroscopy, and X-ray excited optical luminescence (XEOL). The average particle size of Rh nanostructures on PS was estimated to be approximately 7 nm by the X-ray diffraction pattern. The specificity ofXEOL allowed for the investigation of the effect of Rh nanostructures on the optical properties of PS.

Journal Article↗

PubMed2004

Characterization of a region involved in binding of measles virus H protein and its receptor SLAM (CD150).

Signaling lymphocyte activation molecule (SLAM; also known as CD150) is a newly identified cellular receptor for measles virus (MV). MV Hemagglutinin protein (H) mediates MV entry into host cells by specifically binding to SLAM. Amino acid 27-135 of SLAM was previously shown to be the functional domain to interact with H and used to screen a 10-mer phage display peptide library in this study. After four rounds of screening and sequence analysis, the deduced amino acid sequence of screened peptides SGFDPLITHA and SDWDPLFTHK showed to be highly homologous with amino acid 429-438 of MV H (SGFGPLITHG). Peptides SGFDPLITHA and SDWDPLFTHK specifically inhibited binding of H to SLAM and further inhibition of MV infection suggests that these peptides can be developed to MV blocking reagents and amino acid 429-438 in H protein is functionally involved in receptor binding and may constitute part of the receptor-binding determinants on H protein.

Animals↗

PubMed2004

Synthesis and controlling the morphology of CdS nanocrystals via hydrothermal microemulsions.

Wurtzite CdS nanocrystals were synthesized via a hydrothermal microemulsion method. With the preaddition of increasing amounts of dodecanethiol, the resulting crystals changed from nanorods to pyramidal particles with decreasing sizes. The control effect of dodecanethiol was attributed to the competition process during the crystal growth and the relevant change in the film flexibility of inverse micelles. The effects of water content, ion concentration, and hydrothermal temperature on the crystal morphologies and size distributions were also investigated.

Journal Article↗

PubMed2004

BAC-FISH in wheat identifies chromosome landmarks consisting of different types of transposable elements.

Fluorescence in situ hybridization (FISH) has been widely used in the physical mapping of genes and chromosome landmarks in plants and animals. Bacterial artificial chromosomes (BACs) contain large inserts making them amenable for FISH mapping. We used BAC-FISH to study genome organization and evolution in hexaploid wheat and its relatives. We selected 56 restriction fragment length polymorphism (RFLP) locus-specific BAC clones from libraries of Aegilops tauschii (the D-genome donor of hexaploid wheat) and A-genome diploid Triticum monococcum. Different types of repetitive sequences were identified using BAC-FISH. Two BAC clones gave FISH patterns similar to the repetitive DNA family pSc119; one BAC clone gave a FISH pattern similar to the repetitive DNA family pAs1. In addition, we identified several novel classes of repetitive sequences: one BAC clone hybridized to the centromeric regions of wheat and other cereal species, except rice; one BAC clone hybridized to all subtelomeric chromosome regions in wheat, rye, barley and oat; one BAC clone contained a localized tandem repeat and hybridized to five D-genome chromosome pairs in wheat; and four BAC clones hybridized only to a proximal region in the long arm of chromosome 4A of hexaploid wheat. These repeats are valuable markers for defined chromosome regions and can also be used for chromosome identification. Sequencing results revealed that all these repeats are transposable elements (TEs), indicating the important role of TEs, especially retrotransposons, in genome evolution of wheat.

Biological Evolution↗

PubMed2004

[Gene expression profiles and effects of transforming growth factor-beta1 intervention in Peyronie's disease].

OBJECTIVE: To demonstrate molecular insight into the pathology of Peyronie's disease (PD). A preliminary profile of differential gene expression between the PD plaque and control tunica albuginea was obtained with DNA microarrays. Also, to investigate the effect of intervention in PD cells, transforming growth factor-beta1 (TGF-beta1) was recruited to treat PD cell lines. METHODS: Three PD plaques and control tunica albugineas were constructed and studied. cDNA probes were prepared from RNA isolated from those cells and hybridized with the Clontech Atlas 3.6 Array. Relative changes of greater than 2.0 defined up-regulation and down-regulation, respectively. The expression of selected individual gene MCP-1 and the effect of TGF-beta1 on MCP-1 were analyzed by reverse transcriptase-polymerase chain reaction. RESULTS: Some up-regulated genes in the PD plaque detected by the Clontech assay were screened, one of them was monocyte chemotactic protein. One involved the pathogenesis of PD as a downstream gene and responded to the TGF-beta1 treatment but not CTGF. The results were also confirmed by TR-PCR in all the types of cell. CONCLUSIONS: The cell lines from plaque tissue and normal tunica from men with PD were successfully established. The findings indicate a potential role for MCP-1 over expression in the pathogenesis of PD as a downstream gene regulated by some genes and could be a new therapeutic target in PD. The information may allow a better understanding of the basic mechanisms involved in the etiology and pathogenesis of PD. Furthermore, it may permit some strategies of therapeutic interventions combine routine methods with Chinese herbal medicine.

Cell Line↗

PubMed2004

A new quantitative method for circulating DNA level in human serum by capillary zone electrophoresis with laser-induced fluorescence detection.

We present a method for the quantification of circulating DNA in serum by capillary zone electrophoresis (CZE) with laser-induced fluorescence detection (LIF). The serum was digested by proteinase to release free DNA. SYBR Gold was utilized as DNA intercalating dye, fluorescein as internal standard (ISTD). CZE-LIF was applied for the separation and quantification of total circulating DNA. Good linearity (R = 0.9992) in the low range of DNA concentrations (0.5-40 ng/mL) and a detection limit of 0.5 ng/mL for DNA (S/N = 3) were obtained. Our data demonstrated that CZE-LIF system has a good linearity with excellent sensitivity and satisfactory reproducibility in the quantification of circulating DNA in serum. This method was successfully used for the quantification of circulating DNA levels in serum. We observed that the circulating DNA levels in certain cancer patients were significantly higher than that in healthy individuals. Compared to current methods, our protocol does not need the extraction of DNA from serum. Our preliminary results have illustrated that CZE-LIF system is simple, rapid, and sensitive, and it is well suitable for large-scale quantification of circulating DNA levels in clinical diagnosis.

Adult↗

PubMed2004

A new cycloartane glycoside from Camptosorus sibiricus Rupr.

A new cycloartane glycoside was isolated from the dried whole herbs of Camptosorus sibiricus Rupr By means of chemical (hydrolysis) and spectroscopic methods (IR, 1D, and 2D NMR, ESI-MS), the structure was established as 3beta, 7beta, 24beta, 25, 30-pentahydroxycycloartane-3-omicron-beta-D-glucopyranoside-24-omicron-beta-D-glucopyranoside (1).

Glycosides↗

PubMed2004

Development and application of transgenic technologies in cassava.

The capacity to integrate transgenes into the tropical root crop cassava (Manihot esculenta Crantz) is now established and being utilized to generate plants expressing traits of agronomic interest. The tissue culture and gene transfer systems currently employed to produce these transgenic cassava have improved significantly over the past 5 years and are assessed and compared in this review. Programs are underway to develop cassava with enhanced resistance to viral diseases and insects pests, improved nutritional content, modified and increased starch metabolism and reduced cyanogenic content of processed roots. Each of these is described individually for the underlying biology the molecular strategies being employed and progress achieved towards the desired product. Important advances have occurred, with transgenic plants from several laboratories being prepared for field trails.

Animals↗

PubMed2004

Sequence composition, organization, and evolution of the core Triticeae genome.

We investigated the composition and the basis of genome expansion in the core Triticeae genome using Aegilops tauschii, the D-genome donor of bread wheat. We sequenced an unfiltered genomic shotgun (trs) and a methylation-filtration (tmf) library of A. tauschii, and analyzed wheat expressed sequence tags (ESTs) to estimate the expression of genes and transposable elements (TEs). The sampled D-genome sequences consisted of 91.6% repetitive elements, 2.5% known genes, and 5.9% low-copy sequences of unknown function. TEs constituted 68.2% of the D-genome compared with 50% in maize and 14% in rice. The DNA transposons constituted 13% of the D-genome compared with 2% in maize. TEs were methylated unevenly within and among elements and families, and most were transcribed which contributed to genome expansion in the core Triticeae genome. The copy number of a majority of repeat families increased gradually following polyploidization. Certain TE families occupied discrete chromosome territories. Nested insertions and illegitimate recombination occurred extensively between the TE families, and a majority of the TEs contained internal deletions. The GC content varied significantly among the three sequence sets examined ranging from 42% in tmf to 46% in trs and 52% in the EST. Based on enrichment of genic sequences, methylation-filtration offers one option, although not as efficient as in maize, for isolating gene-rich regions from the large genome of wheat.

Edible Grain↗

PubMed2004

Simultaneous painting of three genomes in hexaploid wheat by BAC-FISH.

Fluorescence in situ hybridization (FISH) is widely used in the physical mapping of genes and chromosome landmarks in plants and animals. Bacterial artificial chromosomes (BACs) contain large inserts, making them amenable for FISH mapping. In our BAC-FISH experiments, we selected 56 restriction fragment length polymorphism (RFLP)-locus-specific BAC clones from the libraries of Triticum monococcum and Aegilops tauschii, which are the A- and D-genome donors of wheat (Triticum aestivum, 2n = 6x = 42), respectively. The BAC clone 676D4 from the T. monococcum library contains a dispersed repeat that preferentially hybridizes to A-genome chromosomes, and two BAC clones, 9I10 and 9M13, from the Ae. tauschii library contain a dispersed repeat that preferentially hybridizes to the D-genome chromosomes. These repeats are useful in simultaneously discriminating the three different genomes in hexaploid wheat, and in identifying intergenomic translocations in wheat or between wheat and alien chromosomes. Sequencing results show that both of these repeats are transposable elements, indicating the importance of transposable elements, especially retrotransposons, in the genome evolution of wheat.

Chromosomes, Artificial, Bacterial↗

PubMed2004

Assembly of silica nanoparticles for two-dimensional nanomaterials.

To realize the great potential of nanoparticles as new materials for biomedical applications, the nanoparticles will have to be assembled in such a way that the newly created assembly will have unique properties that conventional materials do not possess. This will enable nanomaterials to be used for many novel applications. We have attempted to assemble silica nanoparticles to create a two-dimensional nanomaterial, which might be useful for biosensor and biochip production. The silica nanoparticles are synthesized and assembled in a monolayer fashion through the use of halogenated silanes. Photolithography techniques are used to pattern the glass surface prior to nanoparticle attachment. The concentration of the silica nanoparticles in the solution controls the surface coverage of nanoparticles on the glass surface. Different patterned silica arrays can be made with controlled surface coverage. The nanoparticle-covered surface is successfully tested for surface-enhanced enzymatic reactivity for the detection of a neurotransmitter, glutamate. This report demonstrates the feasibility of assembling nanoparticles for biosensor development.

Biosensing Techniques↗

PubMed2004

Measurement of DNA damage and apoptosis in Molt-4 cells after in vitro exposure to radiofrequency radiation.

To determine whether exposure to radiofrequency (RF) radiation can induce DNA damage or apoptosis, Molt-4 T lymphoblastoid cells were exposed with RF fields at frequencies and modulations of the type used by wireless communication devices. Four types of frequency/modulation forms were studied: 847.74 MHz code-division multiple-access (CDMA), 835.62 MHz frequency-division multiple-access (FDMA), 813.56 MHz iDEN(R) (iDEN), and 836.55 MHz time-division multiple-access (TDMA). Exponentially growing cells were exposed to RF radiation for periods up to 24 h using a radial transmission line (RTL) exposure system. The specific absorption rates used were 3.2 W/kg for CDMA and FDMA, 2.4 or 24 mW/kg for iDEN, and 2.6 or 26 mW/kg for TDMA. The temperature in the RTLs was maintained at 37 degrees C +/- 0.3 degrees C. DNA damage was measured using the single-cell gel electrophoresis assay. The annexin V affinity assay was used to detect apoptosis. No statistically significant difference in the level of DNA damage or apoptosis was observed between sham-treated cells and cells exposed to RF radiation for any frequency, modulation or exposure time. Our results show that exposure of Molt-4 cells to CDMA, FDMA, iDEN or TDMA modulated RF radiation does not induce alterations in level of DNA damage or induce apoptosis.

Apoptosis↗