PubMed Health⌕ Search

Biomedical subjects

Z Zhang

Publications and source records attributed to Z Zhang.

At least 19 recordsLinked to original sources
PubMed2026

DNA methylome responses to biotic and abiotic stress in Arabidopsis thaliana: A multi-study analysis.

RATIONALE: Plants experience diverse biotic and abiotic stresses that can induce changes in DNA methylation. However, comparisons among existing studies are complicated by differences in analytical methods and experimental designs. We aimed to identify shared and stress-specific DNA methylation responses across studies. METHODS: We reanalysed 16 whole-genome bisulphite sequencing datasets from 13 Arabidopsis thaliana studies using a unified bioinformatics pipeline. Differentially methylated regions (DMRs) were assessed in the CG, CHG and CHH contexts and examined in relation to genes, transposable elements (TEs), Gene Ontology terms, gene-proximal TE superfamilies and epimutation-prone loci. RESULTS: Global methylation levels were generally stable, whereas the number and genomic distribution of DMRs varied according to stress type and methylation context. CG-DMRs occurred primarily in gene bodies, while CHG- and CHH-DMRs were enriched in TEs. Functional analysis identified shared stress-related processes across conditions. Gene-proximal LINE/L1, RathE1_cons and DNA/HAT elements were enriched for stress-responsive methylation changes. A subset of stress-associated CG-DMRs overlapped loci known to accumulate stable epimutations over generations. CONCLUSIONS: Standardized cross-study analysis revealed both shared and stress-specific methylation patterns. The association of stress-responsive DMRs with gene-proximal TEs and epimutation-prone loci suggests potential links among environmental responses, genome regulation and long-term epigenetic variation.

Arabidopsis thaliana↗
PubMed1995

High-level expression and purification of coffee bean alpha-galactosidase produced in the yeast Pichia pastoris.

alpha-Galactosidase isolated from coffee beans cleaves the terminal alpha-galactose residues from oligosaccharide chains on blood group B red cells, thus generating group O cells. Such enzymatically converted red cells not only maintain full erythrocyte integrity and viability in vitro, but also demonstrate immune tolerance and a normal life span in vivo. In order to produce large quantities of recombinant alpha-galactosidase for use in the study of blood-type conversion, we subcloned the cDNA coding for coffee bean alpha-galactosidase into the EcoRI site of the vector pPIC9 in order to express the enzyme in Pichia pastoris, a methylotrophic yeast strain. After P. pastoris transformation, colonies were screened for high-level expression of alpha-galactosidase, based on enzyme activity. In order to increase enzyme production, the growth conditions in the shake flask culture and fermentor culture were optimized. Under the conditions applied, biologically active alpha-galactosidase was produced and secreted into the culture medium at a level of approximately 0.4 g per liter of the fermentor culture. The protein was purified to apparent homogeneity by a simple chromatography procedure, as suggested by a single band of 41 kDa on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Its homogeneity was further confirmed by chromatofocusing and N-terminal sequencing. P. pastoris appears to be the choice as host for the large-scale production of recombinant alpha-galactosidase used for blood type conversion.

Amino Acid Sequence↗
PubMed1995

Iron-stimulated ring-opening of benzene in a mouse liver microsomal system. Mechanistic studies and formation of a new metabolite.

In the present study, we investigated the mechanism(s) of ring-opening of benzene in a mouse liver microsomal system in the presence of Fe2+.HPLC analysis based on coelution with authentic standards and on-line UV spectra obtained using a diode array detector indicated that benzene is metabolized to phenol, hydroquinone (HQ), trans,trans-muconaldehyde (muconaldehyde, MUC), 6-oxo-trans,trans-2,4-hexadienoic (COOH-M-CHO), 6-hydroxy-trans,trans-2,4-hexadienal (CHO-M-OH), and 6-hydroxy-trans,trans-2,4-hexadienoic acid (COOH-M-OH). CHO-M-OH was confirmed by mass spectrometry. Muconaldehyde was also metabolized to CHO-M-OH, COOH-M-CHO and COOH-M-OH, in the same microsomal system. The inhibition of muconaldehyde metabolism by microsomes in the presence of pyrazole indicates that there is cytosolic alcohol dehydrogenase (ADH) activity in the microsomes. Metabolism by contaminating ADH of muconaldehyde formed during microsomal incubation of benzene could be involved in the formation of CHO-M-OH and COOH-M-OH. The ring-opening of benzene was stimulated by added Fe2+. Hydrogen peroxide was produced in the microsomal system and consumed in the presence of added Fe2+. Addition of catalase inhibited the formation of ring-opened products, while superoxide dismutase increased their formation in the presence of azide. Singlet oxygen scavengers, i.e. histidine, deoxyguanosine, Tris and azide (at concentrations above 1.0 mM), dramatically decreased the ring-opening of benzene. Hydroxyl radical scavengers, DMSO, mannitol and formate, but not ethanol, also decreased the ring-opening of benzene. The data indicate that Fenton chemistry plays an important role in benzene ring-opening by microsomes. An unknown peak with UV absorption maxima at 275 and 345 nm was also detected. Based on pH sensitivity of the UV spectrum, the reactivity with thiobarbituric acid (giving a chromogen with absorption maximum at 532 nm) and the molecular weight (126), this compound was identified tentatively as alpha- or beta-hydroxymuconaldehyde.

Aldehydes↗
PubMed1995

The structural basis for pseudoreversion of the E165D lesion by the secondary S96P mutation in triosephosphate isomerase depends on the positions of active site water molecules.

The structural basis for the improvement in catalytic efficiency of the mutant E165D chicken triosephosphate isomerase by the secondary mutation, S96P, has been analyzed using a combination of X-ray crystallography and Fourier transform infrared spectroscopy. All X-ray structures were of the complex of phosphoglycolohydroxamate (PGH), an intermediate analog, with the isomerase, and each was solved to a resolution of 1.9 A. Comparison of the structure of the double mutant, E165D.S96P, with that of the single mutant, E165D, as well as with the wild-type isomerase shows only insignificant differences in the positions of the side chains in all of the mutants when compared with the wild-type isomerase, except that in both the E165D and E165D.S96P mutants, the aspartate side chain was approximately 0.7 A further away from the substrate analog than the glutamate side chain. Significant differences were observed in the crystal structure of the E165D.S96P double mutant in the positions of ordered water molecules bound at the active site. The loss of two water molecules located near the side chain at position 165 was observed in isomerases containing the S96P mutation. The resulting increase in hydrophobicity of the pocket probably causes an increase in the pKa of the catalytic base, D165, thereby improving its basicity. A new ordered water molecule was observed underneath the bound PGH in the E165D.S96P structure, which likely decreases the pKa's of the substrate protons, thereby increasing their acidity. An enzyme derived carbonyl stretch at 1746 cm-1 that is only observed in the IR spectrum of the E165D.S96P double mutant isomerase with bound substrates has been assigned to a stable ground state protonated D165-enediol(ate) intermediate complex. Thus, the gain in activity resulting from the S96P second site change probably results from a combination of improving the basicity of the enzyme, improving the acidity of the substrate protons, and stabilization of a reaction intermediate. All three of these effects seem to be caused by changes in bound water molecules.

Animals↗
PubMed1995

Characterization of the IL-6 responsive elements in the gamma fibrinogen gene promoter.

Fibrinogen, a hepatically derived class II acute phase protein, is the product of three separate genes, (A alpha, B beta, and gamma). The fibrinogen genes are expressed constitutively; however, their transcription can be significantly up-regulated by interleukin-6 (IL-6) and glucocorticoid. Inspection of the promoter region of the fibrinogen gamma gene revealed three hexanucleotide clusters of CTGGGA that are recognized as class II IL-6 responsive elements. Functional analyses of these regions (designated here as site I, site II, and site III according to their position in the promoter) were performed using luciferase reporter constructs and show a hierarchy of IL-6 response in which site II was the preferred functional site, site I was the next important site, and site III was the site least responsive to IL-6. Gel mobility shift assays using 25-base pair oligonucleotide probes derived from these three regions with the CTGGGA positioned in the middle and nuclear extracts from IL-6-treated primary hepatocytes reveal the presence of IL-6-induced high molecular weight complexes appearing 5 min after cytokine treatment. Supershift assays using anti-Stat3 antibody indicate that Stat3 is part of the IL-6-induced complex formed on the three gamma chain probes. The binding of Stat3 to the IL-6 responsive elements of the gamma probes is significantly weaker than to an alpha 2-macroglobulin probe. These findings show for the first time that Stat3 is involved in associating with the IL-6 responsive elements of fibrinogen gamma chain, a class II acute phase gene other than alpha 2-macroglobulin.

Acute-Phase Proteins↗
PubMed1995

Expression and physicochemical characterization of human proliferating cell nuclear antigen.

Human proliferating cell nuclear antigen (PCNA) was overexpressed in Escherichia coli as a soluble protein. Recombinant PCNA was purified to homogeneity by phosphocellulose, Q-Sepharose, Sephacryl S-200, and hydroxylapatite chromatography. Approximately 20 mg of PCNA was isolated from E. coli cells derived from 2 L of culture. Characterization of the recombinant protein showed that it was functionally active and that its properties were similar to those of purified human placental PCNA. Recombinant PCNA stimulated human DNA polymerase delta activity at least 25-fold with poly(dA)/oligo-(dT) as the template. Recombinant PCNA eluted with a M(r) = 102,000 and a Stokes radius of 37 Angstrum by high-performance gel-permeation chromatography. The sedimentation coefficient determined by glycerol gradient ultracentrifugation was 6.3 S. The molecular weight calculated from the Stokes radius and S value was 96,800. The behavior of PCNA was entirely consistent with its being a trimeric protein. Analytical ultracentrifugation and gel filtration revealed the existence of a dimeric species at low dilution. Cross-linking experiments revealed the presence of PCNA dimers which predominated, as well as a trimeric species. These studies provide biophysical evidence that PCNA is an oligomeric protein which behaves as a trimeric species at high protein concentrations but dissociates to a dimer at low protein concentrations.

Base Sequence↗
PubMed1995

The human medium chain Acyl-CoA dehydrogenase gene promoter consists of a complex arrangement of nuclear receptor response elements and Sp1 binding sites.

Expression of the gene encoding the mitochondrial fatty acid. beta-oxidation enzyme, medium-chain acyl-CoA dehydrogenase (MCAD), is regulated among tissues during development and in response to alterations in substrate availability. To identify and characterize cis-acting MCAD gene promoter regulatory elements and corresponding transcription factors, DNA-protein binding studies and mammalian cell transfection analyses were performed with hjman MCAD gene promoter fragments. DNA:protein binding studies with nuclear protein extracts prepared from hepatoma G2 cells, 3T3 fibroblasts, or Y-1 adrenal tumor cells identified three sequences (nuclear receptor response element 1 or NRRE-1, NRRE-2, and NRRE-3) that bind orphan members of the steroid/thyroid nuclear receptor superfamily including chicken ovalbumin upstream promoter transcription factor and steroidogenic factor 1. Sp1 binding sites (A-C) were identified in close proximity to each of the NRREs. NRRE-3 conferred cell line-specific transcriptional repression by interacting with chicken ovalbumin upstream promoter transcription factor or activation via steroidogenic factor 1. In contrast, the Sp1 binding site A behaved as a transcriptional activator in all cell lines examined. We propose that multiple nuclear receptor transcription factors interact with MCAD gene promoter elements to differentially regulate transcription among a variety of cell types.

3T3 Cells↗
PubMed1995

Mutational analysis of the peptide segment linking phosphorylation and Ca(2+)-binding domains in the sarcoplasmic reticulum Ca(2+)-ATPase.

The sarcoplasmic reticulum ATPase segment extending from the phosphorylation site (Asp-351) to the preceding transmembrane helix M4 (which is involved in Ca2+ binding in conjunction with transmembrane helices M5, M6, and M8) retains a marked sequence homology to the corresponding segments of other cation ATPases. We made 26 point mutations in this segment and found that nonconservative mutations of residues that are homologous in various cation ATPases result in strong inhibition of catalytic and transport function. Mutations of nonhomologous residues to match the corresponding residues of other cation ATPases are not inhibitory and, in some cases, produce higher activity. The inhibitory mutations affect the phosphorylated intermediate turnover, which is associated with the vectorial translocation of bound Ca2+. The same mutations do not affect the kinetics of ATPase activation by Ca2+ following enzyme preincubation with EGTA. This suggests that activation of the phosphoryl transfer reaction by Ca2+ binding and vectorial displacement of bound Ca2+ by enzyme phosphorylation do not occur simply as the forward and reverse directions of the same process, but are linked to distinct structural features of the enzyme. The peptide segment extending from the phosphorylation site in the enzyme extramembranous headpiece through the M4 helix in the membrane-bound region sustains a prominent role in transmission of the phosphorylation signal for displacement of bound Ca2+. A critical structural role of this segment is also demonstrated by the interference of specific mutations with membrane assembly of the expressed protein.

Animals↗
PubMed1995

High performance liquid chromatographic separation and pH-dependent electrochemical properties of pyrroloquinoline quinone and three closely related isomeric analogues.

Pyrroloquinoline quinone 1 (PQQ, methoxatin, 4,5-dihydro-4,5-dioxo-1H-pyrrolo[2,3-f]quinoline-2,7,9-tricarboxylic acid) is a novel coenzyme. Closely related isomeric analogues of PQQ may be formed in nature and may possess PQQ-like functions. Here, the electrochemical pH-dependent properties and the high performance liquid chromatographic (HPLC) separation protocols are reported for three major isomeric PQQ analogues likely to be formed in nature. The electrochemical data (cyclic voltammetry) provided the pKas of the five ionizable groups in each isomeric PQQ. The HPLC protocols provide the means of investigating the formation of PQQ and the PQQ isomers reported here during the normal turnover of eukaryotic amine oxidases containing integral topaquinone residues, as well as from direct enzyme-mediated reactions which remain to be characterized.

Chromatography, High Pressure Liquid↗
PubMed1995

The alpha 5 beta 1 integrin supports survival of cells on fibronectin and up-regulates Bcl-2 expression.

Anchorage-dependent cells that are prevented from attaching to an extracellular matrix substrate stop proliferating and may undergo apoptosis. Cell adhesion to a substrate is mediated by the integrin family of cell surface receptors, which are known to elicit intracellular signals upon cell adhesion. We show here that Chinese hamster ovary cells expressing the alpha 5 beta 1 integrin, which is a fibronectin receptor, do not undergo apoptosis upon serum withdrawal when the cells are plated on fibronectin. However, the alpha v beta 1 integrin, which is also a fibronectin receptor and binds fibronectin on the same RGD motif as alpha 5 beta 1, did not prevent apoptosis on fibronectin of the same cells. The cytoplasmic domain of the integrin alpha 5 subunit was required for the alpha 5 beta 1-mediated cell survival on fibronectin. The fibronectin-mediated survival effect appeared to be independent of the level of tyrosine phosphorylation of the focal adhesion kinase, which is induced by integrin-mediated cell attachment. The expression of the Bcl-2 protein, which counteracts apoptosis, was elevated in cells attaching to fibronectin through alpha 5 beta 1; cells attaching through alpha v beta 1 survived only if exogenous Bcl-2 was provided. Thus, alpha 5 beta 1, but not the closely related alpha v beta 1 integrin, appears to suppress apoptotic cell death through the Bcl-2 pathway.

Animals↗
PubMed1995

Evaluation of protective effects of sodium thiosulfate, cysteine, niacinamide and indomethacin on sulfur mustard-treated isolated perfused porcine skin.

Sulfur mustard (bis(2-chloroethyl)sulfide, HD), a bifunctional alkylating agent, causes severe cutaneous injury, including cell death, edema and vesication. However, the mechanisms underlying HD-induced cutaneous toxicity remain undefined. The isolated perfused porcine skin flap (IPPSF) has been utilized to investigate dermal toxic compounds and pharmacological intervention. In this study, 4 compounds with different pharmacological mechanisms were tested for their ability to prevent the dark basal cell formation, vesication and vascular response charcteristic of exposure to HD in the IPPSF. Reduction of HD-induced dark basal cells was observed in IPPSFs perfused with sodium thiosulfate and cysteine, which are HD scavengers; niacinamide, a possible NAD+ stabilizer and an inhibitor of poly (ADP-ribose) polymerase; or indomethacin, a cyclooxygenase inhibitor, respectively. Treatments with niacinamide and indomethacin, but not sodium thiosulfate or cysteine, resulted in an inhibition of the vascular response in IPPSF exposed to HD. Microvesicles caused by HD were only partially prevented in the indomethacin-perfused IPPSFs. These data suggest that none of these agents alone would be successful antivesicant agents and different mechanisms are involved in production of HD-induced dark basal cells, microvesicles and the vascular response; unfortunately, blocking of the cellular toxicity as evidenced by dark basal cell formation did not prevent vesication, suggesting that other mechanisms must be operative and that there is a multistep, biochemical process that leads to a final lesion.

Animals↗
PubMed1995

The proliferative response and anti-oncogene expression in old 2BS cells after growth factor stimulation.

The limited replicative lifespan of diploid human cells in vitro (cellular senescence) serves as a cellular model of aging. We examined the proliferative response of 2BS cells of different population doubling levels to fibroblast growth factor (FGF). DNA synthesis was measured by thymidine incorporation. As the cells aged, there was a significant decrease in the stimulation of DNA synthesis by FGF addition (P < 0.01). The effective concentration of FGF and the latent period prior to DNA synthesis did not change. Expression of Rb and p53 mRNA after growth factor stimulation was also examined. Young and old cells had similar Rb mRNA levels, whereas the p53 mRNA level was significantly reduced in old cells. After both cells were treated by FGF or epidermal growth factor (EGF), Rb expression increased 210-275% in young cells and 50-60% in old ones. However, no significant change was found in p53 gene transcriptions after FGF addition. The results further suggest that cell aging is associated with a progressive loss of the ability of cells to respond to growth factors.

Cell Division↗
PubMed1995

Expression, purification and characterization of 1-aminocyclopropane-1-carboxylate oxidase from tomato in Escherichia coli.

1-Aminocyclopropane-1-carboxylate (ACC) oxidase catalyses the final step in the biosynthesis of the plant hormone ethylene. The successful overexpression and characterization of active ACC oxidase from tomato has been achieved. PCR was used to insert the corrected cDNA coding for the tomato ACC oxidase into the pET-11a expression vector. Cloning of the resultant construct in Escherichia coli BL21(DE3)pLysE gave transformants which expressed ACC oxidase at levels greater than 30% of soluble protein under optimized conditions. When induced by addition of isopropyl-beta-D-thiogalactopyranoside (IPTG) at 37 degrees C the ACC oxidase expressed was less soluble and less active than when induced at 27 degrees C. The enzyme was purified to near homogeneity by a three-step chromatographic procedure. The specific activity of the purified recombinant ACC oxidase was typically 1.3-1.9 mol of ethylene/mol of enzyme per min, higher than values reported for native enzyme. Like the native enzyme it displayed a requirement for ferrous iron and ascorbate, and CO2 was an activator. The ability to discriminate between racemic diastereomers of 1-amino-2-ethyl cyclopropane-1-carboxylic acid was demonstrated. The enzyme was found to have a loose specificity for ascorbate, showing apparent preference for D-ascorbate and 5,6-O-isopropylidene L-ascorbate rather than L-ascorbate. The addition of catalase, dithiothreitol and BSA to incubation mixtures all resulted in significant increases in activity. When treated with diethylpyrocarbonate (DEPC) under mildly acidic conditions, the enzyme rapidly lost activity. Comparison of the rate of inactivation with the increase in absorbance at 240 nm gave results consistent with the modification of two to three histidine residues at the active site, although the possibility of additional modification of other nucleophilic residues cannot be excluded. Inactivation was largely prevented by the addition of substrates and ferrous iron, implying that DEPC treatment results in the modification of active-site histidines, which act as ligands for ferrous iron. CO2 offered no protection against DEPC inactivation, either in the absence or presence of substrates and/or ferrous iron.

Amino Acid Oxidoreductases↗
PubMed1995

Lung congestion augments the responses of cells in the rapidly adapting receptor pathway to cigarette smoke in rabbit.

1. We examined the effects of cigarette smoke, inhaled alone and during mild pulmonary venous congestion, on the activity of fifty-three neurones in the nucleus tractus solitarii (NTS) that were excited by input from pulmonary rapidly adapting receptors (RAR). Ten neurones excited by slowly adapting stretch receptors (SAR) were also studied. 2. Extracellular recordings of RAR-activated neurones were recorded in alpha-chloralose anaesthetized rabbits. Smoke from low- and high-nicotine cigarettes was delivered through a ventilator. Mild pulmonary venous congestion was produced by inflating a balloon in the left atrium. 3. Inhalation of three breaths of smoke from low-nicotine cigarettes increased the activity of fifty-one out of fifty-three RAR-activated neurones from 5.9 +/- 1.0 to 14.4 +/- 2.1 spikes breath-1 (P < 0.05). 4. The responses of fifteen neurones were compared with smoke inhaled alone or during mild pulmonary venous congestion. Smoke alone increased unit activity from 6.8 +/- 2.3 to 12.6 +/- 3.7 spikes breath-1 (P < 0.05). Small increases in left atrial pressure (2.0 +/- 0.5 mmHg) had no effect on baseline unit activity (7.6 +/- 2.11 vs. 7.7 +/- 2.3 spikes breath-1; P > 0.05), but enhanced the responses to smoke, increasing the activity from 7.6 +/- 2.1 to 17.1 +/- 4.8 spikes breath-1 (P < 0.05). The response was greater than to smoke alone (P < 0.05). 5. Of ten SAR-activated neurones, seven failed to respond to inhaled cigarette smoke, two were excited and one was inhibited. Pulmonary venous congestion had no effect on the unit activity before and after smoke (n = 4 neurones). 6. We conclude that smoke-evoked excitation of RAR lower-order neurones is augmented by pulmonary venous congestion.

Animals↗
PubMed1995

Expression of activins and activin receptors in human retinoblastoma cell line Y-79.

Activin is a member of TGF beta family and is known to inhibit neuronal differentiation in certain tumor cell lines. In this study, the messenger RNA expression of activin subunits and activin receptors was characterized in retinoblastoma cell line Y-79 using the reverse transcription-polymerase chain reaction as well as in situ hybridization. The identity of the RT-PCR products was confirmed by DNA sequencing of PCR products. The activin protein production was determined by immunocytochemistry. We found that Y-79 cells transcribe mRNAs coding activin subunits and activin receptors and produce activin proteins. Our results imply that activin may have autocrine functions in these cells.

Activin Receptors↗
PubMed1995

Measurement of striatal H2O2 by microdialysis following global forebrain ischemia and reperfusion in the rat: correlation with the cytotoxic potential of H2O2 in vitro.

Toxic reactive oxygen species have been implicated as important mediators of tissue injury after reperfusion of ischemic organs. When rats are subject to 30 min global forebrain ischemia, 24 h following this insult, there is substantial loss of medium-sized neurones as revealed by histological sectioning of the striatal region of the forebrain. The goal of this study was to utilize microdialysis to directly measure one of the more stable intermediates of reduced molecular oxygen, H2O2 in the rat striatum following 4-vessel occlusion and reperfusion, and to correlate these levels with H2O2 toxicity to neurones grown in culture. A significant rise in striatal H2O2 levels was observed for about 1 h during reperfusion, amounting to an increase of approximately 100 microM at the peak. In control experiments where the dialysis probe was embedded in cortical regions surrounding the striatum (where there is no neuronal loss due to the ischemic episode), there was no measurable increase in tissue H2O2 levels. H2O2 has been previously shown to be neurotoxic to PC12 cells as well as rat primary hippocampal neurones at comparable concentrations striatal neurones experience during reperfusion. We demonstrate that H2O2 is also neurotoxic to the human cortical neuronal cell line, HCN-1A. These experiments establish an important link between oxidant generation and neuronal loss in this tissue following global forebrain ischemia.

Animals↗