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Biomedical subjects

Z Deng

Publications and source records attributed to Z Deng.

At least 19 recordsLinked to original sources
PubMed2001

Stimulation of CREB binding protein nucleosomal histone acetyltransferase activity by a class of transcriptional activators.

The transcriptional coactivator CREB binding protein (CBP) possesses intrinsic histone acetyltransferase (HAT) activity that is important for gene regulation. CBP binds to and cooperates with numerous nuclear factors to stimulate transcription, but it is unclear if these factors modulate CBP HAT activity. Our previous work showed that CBP interacts with the Epstein-Barr virus-encoded basic region zipper (b-zip) protein, Zta, and augments its transcriptional activity. Here we report that Zta strongly enhances CBP-mediated acetylation of nucleosomal histones. Zta stimulated the HAT activity of CBP that had been partially purified or immunoprecipitated from mammalian cells as well as from affinity-purified, baculovirus expressed CBP. Stimulation of nucleosome acetylation required the CBP HAT domain, the Zta DNA binding and transcription activation domain, and nucleosomal DNA. In addition to Zta, we found that two other b-zip proteins, NF-E2 and C/EBPalpha, strongly stimulated nucleosomal HAT activity. In contrast, several CBP-binding proteins, including phospho-CREB, JUN/FOS, GATA-1, Pit-1, and EKLF, failed to stimulate HAT activity. These results demonstrate that a subset of transcriptional activators enhance the nucleosome-directed HAT activity of CBP and suggest that nuclear factors may regulate transcription by altering substrate recognition and/or the enzymatic activity of chromatin modifying coactivators.

Acetylation↗
PubMed2000

Site-directed mutagenesis of the fructose 6-phosphate binding site of the pyrophosphate-dependent phosphofructokinase of Entamoeba histolytica.

Attempts to define the active site of pyrophosphate-dependent phosphofructokinase (PPi-PFK) using homology modeling based on the three-dimensional structure of the ATP-dependent PFKs from bacteria have been frustrated by low sequence identity between PPi- and ATP-PFKs in their carboxyl terminal halves. In the current study, alanine scanning mutagenesis of residues in the carboxyl terminal half of the PPi-PFK of Entamoeba histolytica coupled with comparative sequence analysis and computational modeling is used to identify residues that contribute to fructose 6-phosphate (fructose 6-P) binding. Of seven alanine mutants that were generated by site-directed mutagenesis, Arg377, Ser392, Arg405, Lys408, His415, His416, and Arg423, only the last mutant, Arg423Ala, was found to have dramatically lower affinity for fructose 6-P. Mutation of Arg 423 decreased k(cat) by 10,000-fold and decreased apparent affinity for fructose 6-P by 126-fold, while the K(m) for PPi increased only 4-fold. The second greatest effect was seen with Arg377Ala, which had a nearly 10-fold decrease in apparent affinity and an approximate 60-fold decrease in maximal activity. Another residue, Tyr420, was chosen for mutagenesis by its complete identity in all other PPi-PFK. This residue and its homologue in Escherichia coli ATP-PFK, His249, were mutated and shown to be very important for substrate binding in both enzymes.

Alanine↗
PubMed2000

Familial primary pulmonary hypertension (gene PPH1) is caused by mutations in the bone morphogenetic protein receptor-II gene.

Familial primary pulmonary hypertension is a rare autosomal dominant disorder that has reduced penetrance and that has been mapped to a 3-cM region on chromosome 2q33 (locus PPH1). The phenotype is characterized by monoclonal plexiform lesions of proliferating endothelial cells in pulmonary arterioles. These lesions lead to elevated pulmonary-artery pressures, right-ventricular failure, and death. Although primary pulmonary hypertension is rare, cases secondary to known etiologies are more common and include those associated with the appetite-suppressant drugs, including phentermine-fenfluramine. We genotyped 35 multiplex families with the disorder, using 27 microsatellite markers; we constructed disease haplotypes; and we looked for evidence of haplotype sharing across families, using the program TRANSMIT. Suggestive evidence of sharing was observed with markers GGAA19e07 and D2S307, and three nearby candidate genes were examined by denaturing high-performance liquid chromatography on individuals from 19 families. One of these genes (BMPR2), which encodes bone morphogenetic protein receptor type II, was found to contain five mutations that predict premature termination of the protein product and two missense mutations. These mutations were not observed in 196 control chromosomes. These findings indicate that the bone morphogenetic protein-signaling pathway is defective in patients with primary pulmonary hypertension and may implicate the pathway in the nonfamilial forms of the disease.

Amino Acid Sequence↗
PubMed2000

The genome sequence of Drosophila melanogaster.

The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans. We have determined the nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map. Efforts are under way to close the remaining gaps; however, the sequence is of sufficient accuracy and contiguity to be declared substantially complete and to support an initial analysis of genome structure and preliminary gene annotation and interpretation. The genome encodes approximately 13,600 genes, somewhat fewer than the smaller Caenorhabditis elegans genome, but with comparable functional diversity.

Animals↗
PubMed2000

Population-based, case-control study of HER2 genetic polymorphism and breast cancer risk.

BACKGROUND: Alterations of the HER2 (also known as erbB-2 or neu) proto-oncogene have been implicated in the carcinogenesis and prognosis of breast cancer. A polymorphism at codon 655 (GTC/valine to ATC /isoleucine [Val(655)Ile]) in the transmembrane domain-coding region of this gene has been identified and may be associated with the risk of breast cancer. We evaluated this hypothesis in a subgroup of women who participated in a large-scale, population-based, case-control study of breast cancer in Shanghai, China. METHODS: Genomic DNA from 339 patients with breast cancer and 361 healthy control subjects was examined for the Val(655)Ile polymorphism with a polymerase chain reaction-restriction fragment-length polymorphism-based assay. All study subjects completed a structured questionnaire during an in-person interview. All P values are from two-sided tests. RESULTS: We found that 25.1% of the case patients and 21.7% of the control subjects were heterozygous for the Val allele and 3.2% of the case patients and 0. 3% of the control subjects were homozygous for this allele (P =.005). Compared with women with the Ile/Ile genotype, women who had the Ile/Val or Val/Val genotype had an elevated risk of breast cancer (odds ratio [OR] = 1.4; 95% confidence interval [CI] = 1.0-2.0; P =. 05) after adjustment for age, educational level, study period, history of breast fibroadenoma, leisure physical activity, and age at first live birth. The risk was elevated even more among women who were homozygous for the Val allele (OR = 14.1; 95% CI = 1.8-113.4). The association was more pronounced among younger women (</=45 years) than among older women (>45 years). The adjusted OR associated with the Val allele was 1.7 (95% CI = 1.1-2.6) for younger women and 1.0 (95% CI = 0.5-1.9) for older women. CONCLUSIONS: Results of this study suggest that polymorphisms of the HER2 gene may be important susceptibility biomarkers for breast cancer risk, particularly among younger women.

Adult↗
PubMed2000

Potential panic disorder syndrome: clinical and genetic linkage evidence.

This paper reports evidence for a possible "chromosome 13 syndrome," which includes panic disorder, kidney or bladder problems, serious headaches, thyroid problems (usually hypothyroid), and/or mitral valve prolapse (MVP). In the course of a genetic linkage study of panic disorder, we noted these medical conditions in individual family members. (We were blind to family relationships and marker data.) We hypothesized that there may exist a subgroup of panic families with these medical conditions, which for simplicity we called it the "syndrome." Subsequently we reclassified the families as with or without the "syndrome" and extended the phenotype for analysis to include the above medical conditions. All these classifications were also done before the analysis and blind to marker data. We then examined our linkage results, looking for significant differences between families with and without the "syndrome" (using several definitions of the "syndrome")-i.e., testing for genetic heterogeneity. When the families with and without bladder/kidney problems were separated from each other, one marker-D13S779 (ATA26D07)-yielded a lod score of over 3 in the families with bladder/kidney problems. This lod score went up to 4.2 in these families when we diagnosed any individual with any one of the "syndrome" conditions as affected. These results were statistically significant even after applying an extremely overconservative Bonferroni correction for multiple tests. We present these results in order to alert other investigators working on panic disorder, for replication. If replicated, one may hypothesize that a candidate gene for the syndrome should be expressed in CNS, kidney, gut, thyroid, etc. We also noted that two independent studies report recent linkage findings between schizophrenia and the same region on chromosome 13. No connection between schizophrenia and panic disorder has ever been reported. Finally, we suggest that genetic studies of psychiatric disorders might prove more fruitful if phenotypes were expanded to include possible manifestations of the disorder in medical (non-mental) symptoms. Am. J. Med. Genet.(Neuropsychiatr. Genet.) 96:24-35, 2000.

Genetic Linkage↗
PubMed2000

Fine mapping of PPH1, a gene for familial primary pulmonary hypertension, to a 3-cM region on chromosome 2q33.

Familial primary pulmonary hypertension (PPH) is a rare autosomal dominant disease characterized by distinctive changes in pulmonary arterioles that lead to increased pulmonary artery pressures, right ventricular failure, and death. Our previous studies had mapped the disease locus, PPH1, to a 27-cM region on chromosome 2q31-q33, with a maximum multipoint logarithm of the odds favoring genetic linkage score of 3.87 with markers D2S350 and D2S364. To narrow the minimal genetic region for PPH, we physically mapped 33 highly polymorphic microsatellite markers and used them to genotype 44 affected individuals and 133 unaffected individuals from 17 families with PPH. We observed recombination events that substantially reduced the interval for PPH1 to the approximately 3-cM region that separates D2S311 and D2S1384. This entire region lies within chromosome 2q33. A maximum two-point lod score of 7.23 at a recombination fraction of zero was obtained for marker D2S307. A maximum multipoint lod score of 7.41 was observed close to marker D2S1367. The current minimal genetic region contains multiple candidate genes for PPH, including a locus thought to play a role in lung cancer.

Chromosome Aberrations↗
PubMed2000

Effects of acute and chronic coingestion of AlCl3 with citrate or polyphenolic acids on tissue retention and distribution of aluminum in rats.

Aluminum (Al) is toxic to certain biological systems and has been implicated as a neurotoxic agent in the pathogenesis of Alzheimer's disease. Intestinal absorption of Al is very low (0.1%), but many organic dietary components are potential chelators of Al and may enhance its absorption and tissue distribution. We examined the effects of acute and chronic coingestion of AlCl3 with different polyphenolic acids on Al retention and compared to citrate in rats. In experiment 1, animals fasted for 14 h were dosed orally with demineralized water, Al chloride, Al chloride plus sodium citrate, or Al chloride plus a polyphenol acid. Blood samples were taken before and 2 h after the gavage and animals were killed 6 h later. In experiment 2, the rats were adapted on a purified diet for 1 wk and received the following for 4 wk in their experimental diets: AlCl3, except group 1, plus citrate or a polyphenol acid, except groups 1 and 2. Animals were killed and blood and tissues were sampled. In experiment 1, citrate highly enhanced Al absorption and its tissue retention. Gallic and chlorogenic acids significantly increased tibia and kidney Al levels compared to the Al group. In experiment 2, Al levels in the urine were significantly increased in all the Al groups compared to the control group. Significantly higher Al levels in the tibia, kidney, and brain were observed in the citrate group and a significant increase in brain Al level was also noted in the chlorogenic acid group compared to AlCl3 group. This may suggest a possible relation structure-activity of polyphenol acids. However, further studies are necessary to better understand the influence of polyphenol acids on Al metabolism, in particular that of chlorogenic acid.

Aluminum↗
PubMed2000

Measurement and significance of oblique occipital frontal diameter and superior inferior diameter of hepatic left lobulus in patients with hepatic fibrosis.

OBJECTIVE: To study the changes and significance of oblique occipital frontal diameter (OFD) and superior inferior diameter (SID) of the hepatic left lobulus in different stages of hepatic fibrosis, and to evaluate the value of corresponding serological examination in the non-invasive diagnosis to hepatic fibrosis and cirrhosis. METHODS: Seventy-two patients with chronic hepatitis were confirmed by biopsy. OFD and SID of the hepatic left lobulus were measured by type B ultrasonic flaw detector. Serum levels of hyaluronic acid (HA), laminin (LN), type IV collagen (CIV) and type III procollagen (PCIII) were measured by radioimmunoassay. RESULTS: SID of the hepatic left lobulus in S(4) stage was 5.7cmA1.5cm, significantly shorter than the values of 7.7cmA1.4 cm in S(0) stage. OFD of the hepatic left lobulus was longer in S(4) stage than S(0) stage, but the difference didn't reach statistical significance. Serum levels of HA, LN,CIV, and PCIII elevated as the increase of fibrosis. HA and PCIII increased to 273.4mug/LA131.3mug/L and 167. 4mug/LA48.1mug/L in S3 stage from 66.2mug/LA35.0mug/L and 103. 4mug/LA23.8mug/L in S(0) stage. CONCLUSION: Changes in of SID and OFD of the hepatic left lobulus and serum levels of HA and PCIII may indicate indirectly mid-late hepatic fibrosis or early cirrhosis.

Adult↗
PubMed1999

Expression, characterization, and crystallization of the pyrophosphate-dependent phosphofructo-1-kinase of Borrelia burgdorferi.

The two genes for the putative pyrophosphate-dependent phosphofructokinases (PPi-PFKs) of Borrelia burgdorferi were cloned by PCR and expressed in Escherichia coli, and their protein products were purified to near homogeneity. The larger of the two gene products, a 62-kDa protein, is an active PPi-PFK and exists in solution as a dimer. It has apparent K(m) values for fructose 6-P and PPi of 109 and 15 microM, respectively, and a pH optimum of 6.4 to 7.2. The 62-kDa protein was crystallized and subjected to preliminary diffraction analysis. The smaller gene product, a 48-kDa protein, exists in solution as a higher polymer and shows no ATP- or PPi-dependent activity, despite having a secondary structure as estimated by circular dichroism that is not significantly different from that of other PFKs.

Animals↗
PubMed1999

Identification and characterization of a zinc finger gene (ZNF213) from 16p13.3.

During our search for the familial Mediterranean fever (FMF) gene, we identified by cDNA selection a 1.2 kb cDNA fragment representing a novel human gene that is expressed in a wide variety of tissues. This gene spans approx. 8.0 kb genomic DNA and has seven exons. Its 3' untranslated region contains a long tandem repeat that gives rise to a polymorphism with two alleles of approx. 1.1 kb and 1.0 kb, with the 1.1 kb allele in strong linkage disequilibrium with FMF in patients of different ethnic backgrounds. However, both genetic and mutational analyses have excluded this gene as the one responsible for FMF. The predicted 424 amino acid protein, designated ZNF213, contains three C2H2 zinc fingers, a Kruppel associated A box and a leucine rich motif (LeR domain/SCAN box), strongly suggestive of a transcription factor.

Amino Acid Sequence↗
PubMed1999

A productive NADP+ binding mode of ferredoxin-NADP + reductase revealed by protein engineering and crystallographic studies.

The flavoenzyme ferredoxin-NADP+ reductase (FNR) catalyzes the production of NADPH during photosynthesis. Whereas the structures of FNRs from spinach leaf and a cyanobacterium as well as many of their homologs have been solved, none of these studies has yielded a productive geometry of the flavin-nicotinamide interaction. Here, we show that this failure occurs because nicotinamide binding to wild type FNR involves the energetically unfavorable displacement of the C-terminal Tyr side chain. We used mutants of this residue (Tyr 308) of pea FNR to obtain the structures of productive NADP+ and NADPH complexes. These structures reveal a unique NADP+ binding mode in which the nicotinamide ring is not parallel to the flavin isoalloxazine ring, but lies against it at an angle of approximately 30 degrees, with the C4 atom 3 A from the flavin N5 atom.

Amino Acid Sequence↗
PubMed1999

Study on pathogenic mechanism of emotions in traditional Chinese medicine--an observation of hydrogen peroxide releasing function of celiac macrophages in rats under stress state.

The hydrogen peroxide releasing function of macrophages in rats under the stress state was observed with the animal model of "excessive anger impairing the liver". The results showed that the volume of hydrogen peroxide released from the macrophages in rats was decreased, while the corticosterone level in plasma increased after stress. It indicates that stimulation of harmful emotions could cause inhibition of immunoreaction of the organism, which might be related to the enhancement in excitability of the hypothalamus-pituitary-adrenal axis and hypersecretion of glucocorticoid hormone.

Animals↗
PubMed1999

Replacement vectors for localized gene cloning in the specified region of Streptomyces lividans 66 and model method for the screening of desired recombinants via counter-selection.

Two DNA fragments (3.5 kb and 3.8 kb in size) flanking both ends of the phi HAU3R gene in the genome of Streptomyces lividans 66 were determined and cloned in their natural relative orientations in pIJ653, a cosmid vector derived from the multi-copy Streptomyces plasmid pIJ101, resulting in pHZ806. After insertion of spectinomycin/streptomycin (spc/str) resistance gene into the pIJ101 replication region in pHZ806 and insertion of a hygromycin (hyg) resistance gene between 3.5 kb and 3.8 kb DNA fragments, a new vector with a non-functional Streptomyces replicon, pHZ808, was obtained. In principle, any DNA fragment cloned between 3.5 kb and 3.8 kb fragments of this vector can be stably integrated between the two corresponding regions after introduction into the wild-type S.lividans strains, with synchronous replacement of the DNA between the two regions of the chromosome within which phi HAU3R gene is located. The resultant recombinant strains will thus become phi HAU3-sensitive (phi HAU3S). This phenotype could serve as a good indication that the desired gene replacement has occurred. This principle was demonstrated to be successful using pHZ808 as vector. phi HAU3-resistance gene (phi HAU3R) from the genome of S.lividans 66 was substituted by the hygromycin resistance gene (hyg) from pHZ808. An additional advantage of using pHZ808 as the vector to clone foreign genes is that hyg could be served as a reportor gene to imply that foreign DNA fragment has been co-integrated with hyg. The recombinants will have both hygR and phi HAU3S.

Anti-Bacterial Agents↗
PubMed1998

Probing the function of the invariant glutamyl residue 312 in spinach ferredoxin-NADP+ reductase.

Ferredoxin-NADP+ reductase, the prototype of a large family of structurally related flavoenzymes, pairs single electrons carried by ferredoxin I and transfers them as a hydride to NADP+. Four mutants of the enzyme, in which Glu-312 was replaced with Asp, Gln, Leu, and Ala to probe the role of the residue charge, size, and polarity in the enzyme activity, have been heterologously expressed, purified, and characterized through steady-state, rapid kinetic studies, ligand-binding experiments, and three-dimensional structure determination by x-ray crystallography. The E312L mutant was the only one that was almost inactive (approximately 1%), whereas unexpectedly the E312A reductase was 10-100% active with the various acceptors tested. Rapid kinetic absorption spectroscopy studies demonstrated that flavin reduction by NADPH was impaired in the mutants. Furthermore, NADP(H) binding was partially perturbed. These functional and structural studies lead us to conclude that Glu-312 does not fulfil the role of proton donor during catalysis, but it is required for proper binding of the nicotinamide ring of NADP(H). In addition, its charge modulates the two one-electron redox potentials of the flavin to stabilize the semiquinone form.

Amino Acid Sequence↗
PubMed1998

On the active site of Old Yellow Enzyme. Role of histidine 191 and asparagine 194.

Old Yellow Enzyme (OYE) binds phenolic ligands forming long wavelength (500-800 nm) charge-transfer complexes. The enzyme is reduced by NADPH, and oxygen, quinones, and alpha,beta-unsaturated aldehydes and ketones can act as electron acceptors to complete catalytic turnover. Solution of the crystal structure of OYE1 from brewer's bottom yeast (Fox, K. M., and Karplus, P. A. (1994) Structure 2, 1089-1105) made it possible to identify histidine 191 and asparagine 194 as amino acid residues that hydrogen-bond with the phenolic ligands, stabilizing the anionic form involved in charge-transfer interaction with the FMN prosthetic group. His-191 and Asn-194 are also predicted to interact with the nicotinamide ring of NADPH in the active site. Mutations of His-191 to Asn, Asn-194 to His, and a double mutation, H191N/N194H, were made of OYE1. It was not possible to isolate the N191H mutant enzyme, but the other two mutant forms had the expected effect on phenolic ligand binding, i.e. decreased binding affinity and decreased charge-transfer absorbance. Reduction of the H191N mutant enzyme by NADPH was similar to that of OYE1, but the reduction rate constant for NADH was greatly decreased. The double mutant enzyme had an increased rate constant for reduction by NADPH, but the reduction rate constant with NADH was lower by a factor of 15. The reactivity of OYE1 and the mutant enzymes with oxygen was similar, but the reactivity of 2-cyclohexenone was greatly decreased by the mutations. The crystal structures of the two mutant forms showed only minor changes from that of the wild type enzyme.

Amino Acid Sequence↗
PubMed1998

Identification of two Krüppel-related zinc finger genes (ZNF200 and ZNF210) from human chromosome 16p13.3.

During the course of cloning the gene for familial Mediterranean fever (FMF), we identified a number of transcripts from a 275-kb genomic region on 16p13.3. Two of the transcripts were found to contain multiple C2H2-type zinc finger motifs in tandem arrays, indicating that they are members of the Krüppel-type family. One transcript was found to be an alternatively spliced form of a previously reported zinc finger gene, ZNF200. The other transcript, ZNF210, is 2017 bp and encodes an open reading frame of 504 aa. Northern blot analysis indicates that ZNF210 is expressed in all the tissues tested with the highest expression in heart, skeletal muscle, pancreas, prostate, ovary, and colon. On the other hand, the strongest expression of ZNF200 is in testis, with very low levels in all the other tissues tested. Sequence analysis reveals eight C2H2 zinc finger motifs at the C-terminus of ZNF210 and five in ZNF200. In addition, ZNF210 also possesses a Krüppel-associated box at its N-terminus, indicating that it might function as a transcription repressor. The intron-exon structures of both genes were determined and showed that ZNF210 has seven exons while the coding part of ZNF200 is distributed in four exons. The locations of ZNF200 and ZNF210 are 10 and 120 kb telomeric to the FMF gene, respectively.

Amino Acid Sequence↗