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Zhen Zhang

Publications and source records attributed to Zhen Zhang.

At least 91 records · Page 5Linked to original sources
PubMed2004

Dissecting the protein-protein interface between beta-lactamase inhibitory protein and class A beta-lactamases.

beta-Lactamase inhibitory protein (BLIP) binds and inhibits a diverse collection of class A beta-lactamases at a wide range of affinities. Alanine-scanning mutagenesis was previously performed to identify the amino acid sequence requirements of BLIP for inhibiting TEM-1 beta-lactamase and SME-1 beta-lactamase. Two hotspots of binding energy, one from each domain of BLIP, were identified (Zhang, Z., and Palzkill, T. (2003) J. Biol. Chem. 278, 45706-45712). This study has been extended to examine the amino acid sequence requirements of BLIP for binding to the SHV-1 beta-lactamase, which is a poor binding substrate (Ki= 1.1 microm), and the Bacillus anthracis Bla1 enzyme (Ki= 2.5 nm). The two hotspots previously identified as important for binding TEM-1 and SME-1 beta-lactamase were also found to be important for binding Bla1. The hotspot from the second domain of BLIP, however, does not make substantial contributions to SHV-1 binding. This may explain why BLIP binds to SHV-1 beta-lactamase with much weaker affinity than to the other three enzymes. Three regions, including two loops that insert into the active pocket of TEM-1 beta-lactamase and the Glu-73-Lys-74 buried charge motif, exhibit strikingly different effects on the binding affinity of BLIP toward the various enzymes when mutated and, therefore, act as specificity determinants. Analysis of double mutants of BLIP that combine specificity-determining residues suggests that these residues contribute to the poor affinity between the second domain of BLIP and SHV-1 beta-lactamase.

Alanine↗
PubMed2004

Serum diagnosis of pancreatic adenocarcinoma using surface-enhanced laser desorption and ionization mass spectrometry.

PURPOSE: Each year in the United States, approximately 30,000 people die from pancreatic cancer. Fewer than 5% of patients survive >5 years after diagnosis, because most patients present with advanced disease. Early diagnosis may improve the prognosis of patients with pancreatic cancer. EXPERIMENTAL DESIGN: In an attempt to improve on current approaches to the serological diagnosis of pancreatic cancer, we analyzed serum samples from patients with and without pancreatic cancer using surface-enhanced laser desorption and ionization (SELDI) protein chip mass spectrometry. Using a case-control study design, serum samples from 60 patients with resectable pancreatic adenocarcinoma were compared with samples from 60 age- and sex-matched patients with nonmalignant pancreatic diseases, as well as 60 age- and sex-matched healthy controls. To increase the number of proteins potentially identifiable, serum was fractionated using anion exchange and profiled on two ProteinChip surfaces (metal affinity capture and weak cation exchange). RESULTS: We determined a minimum set of protein peaks able to discriminate between patient groups and used the unified maximum separability algorithm to compare the performance of the individual marker panels alone or in conjunction with CA19-9. Among the peaks identified by SELDI profiling that had the ability to distinguish between patient groups, the 2 most discriminating protein peaks could differentiate patients with pancreatic cancer from healthy controls with a sensitivity of 78% and specificity of 97%. These 2 markers performed significantly better than the current standard serum marker, CA19-9 (P < 0.05). The diagnostic accuracy of the 2 markers was improved by using them in combination with CA 19-9. Similarly, a combination of 3 SELDI markers and CA19-9 was superior to CA19-9 alone in distinguishing individuals with pancreatic cancer from the combined pancreatic disease controls and healthy subject groups (P = 0.078). SELDI markers were also better than CA19-9 in distinguishing patients with pancreatic cancer from those with pancreatitis. CONCLUSION: SELDI profiling of serum can be used to accurately differentiate patients with pancreatic cancer from those with other pancreatic diseases and from healthy controls.

Adenocarcinoma↗
PubMed2004

Transport, location, and quantal release monitoring of single cells on a microfluidic device.

A novel microfluidic device has been developed for on-chip transport, location, and quantal release monitoring of single cells. The microfluidic device consists of a plate of PDMS containing channels for introducing cells and stimulants and a glass substrate into which a cell micro-chamber was etched. The two tightly reversibly sealed plates can be separated for respective cleaning, which significantly extends the lifetime of the microchip that is frequently clogged in cell analysis experiments. Using hydraulic pressure, single cells were transported and located on the microfluidic chip. After location of a single PC12 cell on the microfluidic chip, the cell was stimulated by nicotine that was also introduced through the micro-channels, and the quantum release of dopamine from the cell was amperometricly detected with our designed carbon fiber microelectrode. The results have demonstrated the convenience and efficiency of using the microfluidic chip for monitoring of quantal release from single cells and have offered a facile method for the analysis of single cells on microfluidic devices.

Journal Article↗
PubMed2004

Bioinformatics strategies for proteomic profiling.

Clinical proteomics is an emerging field that involves the analysis of protein expression profiles of clinical samples for de novo discovery of disease-associated biomarkers and for gaining insight into the biology of disease processes. Mass spectrometry represents an important set of technologies for protein expression measurement. Among them, surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI TOF-MS), because of its high throughput and on-chip sample processing capability, has become a popular tool for clinical proteomics. Bioinformatics plays a critical role in the analysis of SELDI data, and therefore, it is important to understand the issues associated with the analysis of clinical proteomic data. In this review, we discuss such issues and the bioinformatics strategies used for proteomic profiling.

Computational Biology↗
PubMed2004

Detection of prostate cancer using serum proteomics pattern in a histologically confirmed population.

PURPOSE: We retrospectively identified a panel of serum proteins that can discriminate between men with prostate cancer (clinically organ confined) and men with benign prostate disease. MATERIALS AND METHODS: A contemporary set of 345 men who had an archival serum sample available were included in this study. The cancer group consisted of 246 men who underwent radical prostatectomy at the Johns Hopkins Hospital between March 1999 and April 2001. The noncancer group included 99 men with no histological evidence of prostate cancer on biopsy between April 1997 and April 2001 at the same institution. Serum proteomics mass spectra of these patients were generated using ProteinChip arrays and a ProteinChip Biomarker System II surface enhanced laser desorption/ionization time of flight mass spectrometer (Ciphergen Biosystems, Inc., Fremont, California). The cases and controls were randomly split into training and testing groups by a stratified sampling procedure. A combination of bioinformatics tools including ProPeak (3Z Informatics, Charleston, South Carolina) was used to reveal the optimal panel of biomarkers for maximum separation of the prostate cancer and the benign prostate disease cohorts. RESULTS: A panel of 3 proteins (PC-1, PC-2 and PC-3) was selected using the training data. Performance of each of the protein markers and a linear regression derived composite index (PC-com3) were evaluated on the testing data. The area under the curve for prostate specific antigen (PSA), PC-1, PC-2, PC-3 and PC-com3 was 0.542, 0.585, 0.600, 0.636 and 0.643, respectively. Improvement of PC-com3 compared to PSA is observed at specificity range 30% to 80%. At a selected specificity of 45% the sensitivity of PC-com3 is 76%, significantly better than the PSA sensitivity of 57% (p <0.0001). CONCLUSIONS: Serum proteomics patterns may potentially aid in the early detection of prostate cancer.

Diagnosis, Differential↗
PubMed2004

[Application of enzyme histochemistry in evaluation of in vitro and in vivo biocompatibility of HA/TCP].

In order to explore the possibility of applying enzyme histochemistry in biocompatibility evaluation, we investigated the effect of biomaterials on the activities of intracellular enzymes in this experiment. It was found that there was no obvious difference in morphology between osteoblasts co-cultured with HA/TCP and with Ti-alloy. However, transient down-regulation of NADH, SDH, LDH and CCO of the osteoblasts co-cultured with HA/TCP was detected by enzyme histochemistry, but these enzymes of osteoblasts the co-cultured with Ti-alloy were not down-regulated. It was indicated that something extracted from HA/TCP injured the co-cultured osteoblasts slightly. Similar early acute inflammatory reactions were observed after HA/TCP and Ti-alloy were separately implanted into the dorsal muscle of rabbit. There was also no obvious difference between the tissue response to HA/TCP and that to Ti-alloy. Activities of enzymes in tissues around implanted materials were down-regulated at the early injury period and recovered gradually within 30 days post-operation. But the mild toxicity of extracts from HA/TCP was demonstrated by the fact that the recovery period of HA/TCP group was longer than that of Ti-alloy group. It was proved that enzyme histochemistry is more sensitive than tissue morphology analysis in detecting the cell or tissue responses to biomaterials. Therefore, it is possible to use enzyme histochemistry in biocompatibility evaluation.

Alloys↗
PubMed2004

[Quantitative determination of aqueous flare and cells in the eyes of patients with inflammation of anterior uvea].

OBJECTIVE: To quantify aqueous flare and cells in the eyes of patients with inflammation of anterior uvea by FC-2000 laser flare cell meter (LFCM), and to compare these results with those obtained with slit lamp microscopy. METHODS: Aqueous flare and cells of 194 eyes of 110 patients with inflammation of anterior uvea and 52 eyes of 52 healthy subjects were graded into 0, 1+, 2+, 3+ and 4 + scale based on a previously described system using slit lamp microscopy. LFCM was also used for evaluation of aqueous flare and cells. RESULTS: All eyes in normal individuals were graded as "0" scale of both flare and cells by silt lamp microscopy. Flare of grade 0, 1+ and 2+ were noted in 74, 98 and 18 eyes, and cell of grade 0, 1+, 2+, 3+ and 4+ were noted in 124, 26, 19, 14 and 11 eyes in uveitis patients, respectively. LFCM examination revealed that the mean flare values in uveitis eyes with flare of grade 0, 1+ and 2+ were 7.9, 29.5 and 189.0 photon count/ms, respectively. In patients with flare of grade 3+ and 4+, LFCM readings were unreliable because of increased background noise. There was significant correlation between slit lamp examination and the laser flare measurement for flare of grade 0, 1+ and 2+ (r = 0.75, P < 0.001). The mean flare values were significantly higher in patients with flare of grade 0, 1+ and 2+ than that in normal controls (5.3 pc/ms) (t = 5.872, P < 0.05). The mean cell numbers in the eyes with cell of grade 0, 1+, 2+, 3+ and 4+ were 1.5, 12.1, 33.9, 84.9 and 193.1 count/0.5 mm(3), respectively. The results of slit lamp examination showed significant correlation with laser cell counts measurement (r = 0.72, P < 0.001). The mean cell numbers were significantly higher in uveitis patients than that in normal controls (0.9 count/0.5 mm(3)) (t = 7.351, P < 0.05). CONCLUSIONS: Our results indicate that LFCM is able to evaluate precisely the mild and moderate breakdown of blood aqueous barrier and inflammation of the anterior uvea tract, therefore it provides an important parameter for the treatment of anterior uveitis.

Adolescent↗
PubMed2004

[Study on the risk factors related to severe acute respiratory syndrome among close contactors in Beijing].

OBJECTIVE: To understand the risk factors on severe acute respiratory syndrome (SARS) among their contacts and to develop effective strategy for its control. METHODS: Available epidemiological data of SARS cases and close contacts were reviewed and analyzed by SPSS. RESULTS: Out of the 2195 close contacts, 138 (6.3%) were diagnosed as SARS. Among colleagues and classmates of SARS patients, the infection rate was 0.36% versus 31.71% in contacts among families and hospitals, 0.77% in schools. No one was infected among 459 close contacts to SARS in the working unit. CONCLUSIONS: Among close contacts, factors that facilitating transmission would include: time, extent, frequency and place of contact to the patients, as well as factors related to close contacts as way, time of isolation and age. One of the epidemiological characteristics was that SARS were as clustered in the family among those close contacts. It is important to control the spread of SARS through supervision on the close contacts to patients.

Adult↗
PubMed2004

[Determination of double bond position in conjugated dienes in sex pheromones of Dendrolimus spp].

The dienophile 4-methyl-1,2,4-triazoline-3,5-dione (MTAD) adducts of conjugated diene compounds were used to locate the position of the conjugated double bonds in the parent compounds by high-resolution gas chromatography and electron impact mass spectrometry. Their mass spectra are marked by recognizable molecular ions and abundant diagnostic ions that allow the determination of the diene position. With the identification of the sex pheromone gland extracts of Yunnan pine caterpillar moth Dendrolimus houi as an example, the characteristics of reaction of (E, Z)-5,7-dodecadien-1-ol (E5, Z7-12: OH) and its corresponding aldehyde and acetate with MTAD are discussed. Potential problems in gas chromatographic analysis are also discussed.

Animals↗
PubMed2004

[Preliminary study on the applying value of two measurements for bone age in the cases of minors].

OBJECTIVE: To research the connection of the minor's bone age and chronological age and age for penal responsibility, to discuss the application of Gu's Atlas and Li Guozhen's Percent Numeration to measure the bone age in the cases of immature criminals and the applying value. METHODS: 33 healthy youths, 12-19 years old, were selected, whose left wrists were photographed with X-rays. According to the radiographic appearance of the maturity indicators, the bone age of every person was determined respectively by the Gu's Atlas and Li Guozhen's Percent Numeration, and then compared with his/her chronological age. CMH test and Pearson test were used to evaluate precision and accuracy on concluding the immature age for penal responsibility. RESULTS: Li Guozhen's Percent Numeration was more precise than Gu's Atlas on extrapolating the chronological age of the youth, P<0.005. On extrapolating the age for penal responsibility, the accuracy of the former was 90.91%, and the latter was 78.79%, but the statistic result did not show significant difference (P>0.1). CONCLUSION: Both measurements can apply in determining the criminal cases of immature youths.

Adolescent↗
PubMed2004

[Suppression of apple polyphenol oxidase by double-stranded RNA (RNAi)].

Antisense and sense gene fragments (710 base pairs) of apple polyphenol oxidase (APPO) gene were obtained by RT-PCR amplification, using the total RNAs isolated from ripen apple fruit as the template. These two fragments were ligated with a 1000 bp spacer, YYT (crtW+crtY fusion) gene, which is relative to carotenoid synthesization in subcocci. The full-length 2446 bp-target gene was then inserted into plant binary vector pYPX145 to generate the recombinant plasmid pYF7704, which carried the expression unit, of APPO dsRNA. pYF7704 was transformed to apple (Malus x domestica) var. Red Fuji via agrobacterium tumefaciens mediated leaf disc transformation. With the selection of Karamycin and GUS detection assays, transgenic shoots of A PPO dsRNA were obtained. The results of FQ-RT-PCR indicated that APPO mRNA level was suppressed to 91.69% in transgenic shoots compared to wide shoots. The data suggested that dsRNAi technology on apple polyphenol oxidase is feasible to be utilized in transgenic shoots.

Agrobacterium tumefaciens↗
PubMed2003

Determinants of binding affinity and specificity for the interaction of TEM-1 and SME-1 beta-lactamase with beta-lactamase inhibitory protein.

The hydrolysis of beta-lactam antibiotics by class A beta-lactamases is a common cause of bacterial resistance to these agents. The beta-lactamase inhibitory protein (BLIP) is able to bind and inhibit several class A beta-lactamases, including TEM-1 beta-lactamase and SME-1 beta-lactamase. Although the TEM-1 and SME-1 enzymes share 33% amino acid sequence identity and a similar fold, they differ substantially in surface electrostatic properties and the conformation of a loop-helix region that BLIP binds. Alanine-scanning mutagenesis was performed to identify the residues on BLIP that contribute to its binding affinity for each of these enzymes. The results indicate that the sequence requirements for binding are similar for both enzymes with most of the binding free energy provided by two patches of aromatic residues on the surface of BLIP. Polar residues such as several serines in the interface do not make significant contributions to affinity for either enzyme. In addition, the specificity of binding is significantly altered by mutation of two charged residues, Glu73 and Lys74, that are buried in the structure of the TEM-1.BLIP complex as well as by residues located on two loops that insert into the active site pocket. Based on the results, a E73A/Y50A double mutant was constructed that exhibited a 220,000-fold change in binding specificity for the TEM-1 versus SME-1 enzymes.

Alanine↗
PubMed2003

Identifying tumor origin using a gene expression-based classification map.

Identifying the primary site in cases of metastatic carcinoma of unknown origin has profound clinical importance in managing cancer patients. Although transcriptional profiling promises molecular solutions to this clinical challenge, simpler and more reliable methods for this purpose are needed. A training set of 11 serial analysis of gene expression (SAGE) libraries was analyzed using a combination of supervised and unsupervised computational methods to select a small group of candidate genes with maximal power to discriminate carcinomas of different tissue origins. Quantitative real-time PCR was used to measure their expression levels in an independent validation set of 62 samples of ovarian, breast, colon, and pancreatic adenocarcinomas and normal ovarian surface epithelial controls. The diagnostic power of this set of genes was evaluated using unsupervised cluster analysis methods. From the training set of 21,321 unique SAGE transcript tags derived from 11 libraries, five genes were identified with expression patterns that distinguished four types of adenocarcinomas. Quantitative real-time PCR expression data obtained from the validation set clustered tumor samples in an unsupervised manner, generating a self-organized map with distinctive tumor site-specific domains. Eighty-one percent (50 of 62) of the carcinomas were correctly allocated in their corresponding diagnostic regions. Metastases clustered tightly with their corresponding primary tumors. A classification map diagnostic of tumor types was generated based on expression patterns of five genes selected from the SAGE database. This expression map analysis may provide a reliable and practical approach to determine tumor type in cases of metastatic carcinoma of clinically unknown origin.

Adenocarcinoma↗
PubMed2003

Pentanucleotide TTTTA repeat polymorphism of apolipoprotein(a) gene and plasma lipoprotein(a) are associated with ischemic and hemorrhagic stroke in Chinese: a multicenter case-control study in China.

BACKGROUND AND PURPOSE: It is still inconclusive whether high plasma lipoprotein(a) [Lp(a)] level is a risk factor for stroke. Small sample size and different ethnic groups and methodologies might be contributors to the conflicts in study results. The purpose of the present study was to investigate the association between plasma Lp(a) levels, pentanucleotide TTTTA repeat (PNTR) polymorphism of the apolipoprotein(a) [apo(a)] gene, and Chinese stroke in a case-control study. METHODS: We recruited 1825 cases with stroke (44.3% cerebral atherothrombosis, 28.3% lacunar infarction, and 27.3% intracerebral hemorrhage) and 1817 controls from 7 centers in China. Lp(a) concentrations were quantified by enzyme-linked immunosorbent assay. The PNTR polymorphism of the apo(a) gene was determined by polymerase chain reaction-polyacrylamide gel electrophoresis. Conditional multivariate logistic regression analysis was used to identify independent risk factors for stroke and its subtypes. RESULTS: Lp(a) levels were significantly higher in cases than in controls (median, 28.5 versus 23.1 mg/dL; P<0.001), leading to a 1.97-fold (95% CI, 1.64 to 2.37) increase in risk for overall stroke, 2.0-fold (95% CI, 1.59 to 2.52) increase for atherothrombotic type, 2.05-fold increase (95% CI, 1.59 to 2.63) for lacunar type, and 1.64-fold increase (95% CI, 1.21 to 2.21) for hemorrhagic type. The number of PNTR negatively correlated with Lp(a) levels. Low-number repeats (sum of both alleles <16) of apo(a) PNTR were associated with both atherothrombotic stroke (odds ratio, 1.41; 95% CI, 1.04 to 1.91) and hemorrhagic stroke (odds ratio, 1.62; 95% CI, 1.09 to 2.37). CONCLUSIONS: Our results indicate for the first time that low numbers of apo(a) PNTR and plasma Lp(a) levels are independently associated with both ischemic and hemorrhagic stroke in Chinese.

5' Untranslated Regions↗
PubMed2003

Subcellular localization of yeast ribonucleotide reductase regulated by the DNA replication and damage checkpoint pathways.

The fidelity of DNA replication and repair processes is critical for maintenance of genomic stability. Ribonucleotide reductase (RNR) catalyzes the rate-limiting step in dNTP production and thus plays an essential role in DNA synthesis. The level and activity of RNR are highly regulated by the cell cycle and DNA damage checkpoints, which maintain optimal dNTP pools required for genetic fidelity. RNRs are composed of a large subunit that binds the nucleoside diphosphate substrates and allosteric effectors and a small subunit that houses the di-iron tyrosyl radical cofactor essential for the reduction process. In Saccharomyces cerevisiae, there are two large subunits (Rnr1 and Rnr3) and two small subunits (Rnr2 and Rnr4). Here we report the subcellular localization of Rnr1-4 during normal cell growth and the redistribution of Rnr2 and Rnr4 in response to DNA damage and replicational stress. During the normal cell cycle, Rnr1 and Rnr3 are predominantly localized to the cytoplasm and Rnr2 and Rnr4 are predominantly present in the nucleus. Under genotoxic stress, Rnr2 and Rnr4 become redistributed to the cytoplasm in a checkpoint-dependent manner. Subcellular redistribution of Rnr2 and Rnr4 can occur in the absence of the transcriptional induction of the RNR genes after DNA damage and likely represents a posttranslational event. These results suggest a mechanism by which DNA damage checkpoint modulates RNR activity through the temporal and spatial regulation of its subunits.

DNA Damage↗
PubMed2003

Cloning, expression, and genomic structure of a novel human Rap2 interacting gene (RPIP9).

During a large-scale screen of a human fetal brain cDNA library, a full-length cDNA encoding a novel Rap2 interacting protein was isolated and sequenced. The cDNA is 3397bp long and has a predicted open reading frame encoding a protein of 329 aa. The predicted protein shows high homology to mouse and human RPIP8, and has a RUN domain near its C-terminus. The gene was mapped to human chromosome 7q21-7q22 and has 9 exons and 8 introns. The expression pattern was also detected by cycle-limited reverse polymerase chain reaction (RT-PCR).

Amino Acid Sequence↗