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Biomedical subjects

Jie Qin

Publications and source records attributed to Jie Qin.

At least 19 recordsLinked to original sources
PubMed2006

Isolation and expression analysis of a GDSL-like lipase gene from Brassica napus L.

As lipolytic enzymes, GDSL lipases play an important role in plant growth and development. In order to identify their functions and roles, the full-length cDNA of a GDSL lipase gene, designated BnLIP2, was isolated from Brassica napus L. BnLIP2 was 1,300 bp long, with 1,122 bp open reading frame (ORF) encoding 373 amino acid residues. Sequence analysis indicated that BnLIP2 belonged to GDSL family. Southern blot analysis indicated that BnLIP2 belonged to a small gene family in rapeseed genome. RT-PCR analysis revealed that BnLIP2 was a tissue-specific expressing gene during reproductive growth and strongly expressed during seed germination. BnLIP2 expression could not be detected until three days after germination, and it subsequently became stronger. The transcript of this gene was deficient in root of seedlings growing at different stages. When juvenile seedlings were treated by methyl jasmonate (MeJ), salicylic acid (SA) and naphthalene acetic acid (NAA), BnLIP2 expression could not be induced in root. Our study implicates that BnLIP2 probably plays an important role in rapeseed germination, morphogenesis, flowering, but independent of root growth and development.

Amino Acid Sequence↗
PubMed2006

Structures of thiolate- and carboxylate-ligated ferric H93G myoglobin: models for cytochrome P450 and for oxyanion-bound heme proteins.

Crystal structures of the ferric H93G myoglobin (Mb) cavity mutant containing either an anionic proximal thiolate sulfur donor or a carboxylate oxygen donor ligand are reported at 1.7 and 1.4 A resolution, respectively. The crystal structure and magnetic circular dichroism spectra of the H93G Mb beta-mercaptoethanol (BME) thiolate adduct reveal a high-spin, five-coordinate complex. Furthermore, the bound BME appears to have an intramolecular hydrogen bond involving the alcohol proton and the ligated thiolate sulfur, mimicking one of the three proximal N-H...S hydrogen bonds in cytochrome P450. The Fe is displaced from the porphyrin plane by 0.5 A and forms a 2.41 A Fe-S bond. The Fe(3+)-S-C angle is 111 degrees , indicative of a covalent Fe-S bond with sp(3)-hybridized sulfur. Therefore, the H93G Mb.BME complex provides an excellent protein-derived structural model for high-spin ferric P450. In particular, the Fe-S bond in high-spin ferric P450-CAM has essentially the same geometry despite the constraints imposed by covalent linkage of the cysteine to the protein backbone. This suggests that evolution led to the geometric optimization of the proximal Fe-S(cysteinate) bond in P450. The crystal structure and spectral properties of the H93G Mb acetate adduct reveal a high-spin, six-coordinate complex with proximal acetate and distal water axial ligands. The distal His-64 forms a hydrogen bond with the bound water. The Fe-acetate bonding geometry is inconsistent with an electron pair along the Fe-O bond as the Fe-O-C angle is 152 degrees and the Fe is far from the plane of the acetate. Thus, the Fe-O bonding is ionic. The H93G Mb cavity mutant has already been shown to be a versatile model system for the study of ligand binding to heme proteins; this investigation affords the first structural evidence that nonimidazole exogenous ligands bind in the proximal ligation site.

Binding Sites↗
PubMed2006

Arsenic detoxification and evolution of trimethylarsine gas by a microbial arsenite S-adenosylmethionine methyltransferase.

In this article, a mechanism of arsenite [As(III)]resistance through methylation and subsequent volatization is described. Heterologous expression of arsM from Rhodopseudomonas palustris was shown to confer As(III) resistance to an arsenic-sensitive strain of Escherichia coli. ArsM catalyzes the formation of a number of methylated intermediates from As(III), with trimethylarsine as the end product. The net result is loss of arsenic, from both the medium and the cells. Because ArsM homologues are widespread in nature, this microbial-mediated transformation is proposed to have an important impact on the global arsenic cycle.

Arsenic↗
PubMed2006

Fluoride inhibition of enolase: crystal structure and thermodynamics.

Enolase is a dimeric metal-activated metalloenzyme which uses two magnesium ions per subunit: the strongly bound conformational ion and the catalytic ion that binds to the enzyme-substrate complex inducing catalysis. The crystal structure of the human neuronal enolase-Mg2F2P(i) complex (enolase fluoride/phosphate inhibitory complex, EFPIC) determined at 1.36 A resolution shows that the combination of anions effectively mimics an intermediate state in catalysis. The phosphate ion binds in the same site as the phosphate group of the substrate/product, 2-phospho-D-glycerate/phosphoenolpyruvate, and induces binding of the catalytic Mg2+ ion. One fluoride ion bridges the structural and catalytic magnesium ions while the other interacts with the structural magnesium ion and the ammonio groups of Lys 342 and Lys 393. These fluoride ion positions correspond closely to the positions of the oxygen atoms of the substrate's carboxylate moiety. To relate structural changes resulting from fluoride, phosphate, and magnesium ions binding to those that are induced by phosphate and magnesium ions alone, we also determined the structure of the human neuronal enolase-Mg2P(i) complex (enolase phosphate inhibitory complex, EPIC) at 1.92 A resolution. It shows the closed conformation in one subunit and a mixture of open and semiclosed conformations in the other. The EPFIC dimer is essentially symmetric while the EPIC dimer is asymmetric. Isothermal titration calorimetry data confirmed binding of four fluoride ions per dimer and yielded Kb values of 7.5 x 10(5) +/- 1.3 x 10(5), 1.2 x 10(5) +/- 0.2 x 10(5), 8.6 x 10(4) +/- 1.6 x 10(4), and 1.6 x 10(4) +/- 0.7 x 10(4) M(-1). The different binding constants indicate negative cooperativity between the subunits; the asymmetry of EPIC supports such an interpretation.

Binding Sites↗
PubMed2006

Prediction of protein structural class with Rough Sets.

BACKGROUND: A new method for the prediction of protein structural classes is constructed based on Rough Sets algorithm, which is a rule-based data mining method. Amino acid compositions and 8 physicochemical properties data are used as conditional attributes for the construction of decision system. After reducing the decision system, decision rules are generated, which can be used to classify new objects. RESULTS: In this study, self-consistency and jackknife tests on the datasets constructed by G.P. Zhou (Journal of Protein Chemistry, 1998, 17: 729-738) are used to verify the performance of this method, and are compared with some of prior works. The results showed that the rough sets approach is very promising and may play a complementary role to the existing powerful approaches, such as the component-coupled, neural network, SVM, and LogitBoost approaches. CONCLUSION: The results with high success rates indicate that the rough sets approach as proposed in this paper might hold a high potential to become a useful tool in bioinformatics.

Algorithms↗
PubMed2006

Overexpression of GbERF confers alteration of ethylene-responsive gene expression and enhanced resistance to Pseudomonas syringae in transgenic tobacco.

GbERF belongs to the ERF (ethylene responsive factor) family of transcription factors and regulates the GCC-box containing pathogen-related (PR) genes in the ethylene signal transduction pathway. To study the function of GbERF in the process of biotic stress, transgenic tobacco plants expressing GbERF were generated. Overexpression of GbERF did not change transgenic plant's phenotype and endogenous ethylene level. However, the expression profile of some ethylene-inducible GCC-box and non-GCC-box containing genes was altered, such as PR1b, PR2, PR3, PR4, Osmotin, CHN50, ACC oxidase and ACC synthase genes. These data indicate that the cotton GbERF could act as a transcriptional activator or repressor to regulate the differential expression of ethylene-inducible genes via GCC and non-GCC cis-elements. Moreover, the constitutive expression of GbERF in transgenic tobacco enhanced the plant's resistance to Pseudomonas syringae pv tabaci infection. In conclusion, GbERF mediates the expression of a wide array of PR and ethylene-responsive genes and plays an important role in the plant's response to biotic stress.

Base Sequence↗
PubMed2006

Hg(II) sequestration and protection by the MerR metal-binding domain (MBD).

MerR, the metalloregulator of the bacterial mercury resistance (mer) operon, binds Hg(II) with high affinity. To study the mechanism of metal-induced activation, a small protein was previously engineered embodying in a single polypeptide the metal-binding domain (MBD) ordinarily formed between two monomers of MerR. Here the physiological and biochemical properties of MBD expressed on the cell surface or in the cytosol were examined, to better understand the environments in which specific metal binding can occur with this small derivative. Over 20 000 surface copies of MBD were expressed per Escherichia coli cell, with metal stoichiometries of approximately 1.0 Hg(II) per MBD monomer. Cells expressing MBD on their surface in rich medium bound 6.1-fold more Hg(II) than those not expressing MBD. Although in nature cells use the entire mer operon to detoxify mercury, it was interesting to note that cells expressing only MBD survived Hg(II) challenge and recovered more quickly than cells without MBD. Cell-surface-expressed MBD bound Hg(II) preferentially even in the presence of a 22-fold molar excess of Zn(II) and when exposed to equimolar Cd(II) in addition. MBD expressed in the cystosol also afforded improved survival from Hg(II) exposure for E. coli and for the completely unrelated bacterium Deinococcus radiodurans.

Bacterial Proteins↗
PubMed2006

Role of PI3-kinase/Akt signalling pathway in renal function and cell proliferation after renal ischaemia/reperfusion injury in mice.

BACKGROUND: PI3K/Akt pathway has been shown to play a critical role in the regulation of mitogenic signalling, apoptosis, cell proliferation and survival in a variety of cells and tissues. The aim of the present study was to investigate the role of PI3K/Akt pathway in the renal ischaemia/reperfusion. METHODS: Four experimental groups, sham-operative mice, vehicle-delivered and wortmannin-treated ischaemic/reperfusion injury mice, wortmannin-treated normal mice were designed to examined serum blood urea nitrogen level, renal injury, proliferating cell nuclear antigen protein and Akt phosphorylation status at 30 min, 90 min, 24 h, 48 h of reperfusion after ischaemic treatment. Wortmannin or its vehicle was given intraperitoneally at 4 h before surgery. Blood urea nitrogen was measured, and immunohistochemistry and western blotting were used to detect the components of PI3K/Akt pathway in the ischaemic/reperfusion injury kidney. RESULTS: PI3-kinase inhibitor wortmannin imposes a deleterious effect on serum blood urea nitrogen level, renal function after renal ischaemia/reperfusion injury in mice. The renal cell proliferation increased after ischaemia/reperfusion injury in mouse, which could be inhibited by wortmannin. Phosphorylation of Akt was increased after ischaemia/reperfusion in the mouse kidney, and reduced by wortmannin administration. CONCLUSION: This primary study suggests that PI3-kinase/Akt signalling pathway play an important role in the regulation of the renal repair after ischaemia/reperfusion injury.

Animals↗
PubMed2006

Distributional gradient of amino acid repeats in plant proteins.

A computer-based analysis was conducted to assess the characteristics of amino acid repeats in Arabidopsis and rice. Our analysis showed a negative gradient in amino acid repeat distribution along the direction of translation in plants. Repeat occurrences are obviously associated with position in plant proteins but are not consistent with the corresponding amino acid contents. These repeats are encoded by the mixed synonymous codons rather than the uninterrupted reiterations of a single codon, and both Arabidopsis and rice have gradients in their distribution. Functional investigation showed that these repeat-containing proteins are preferentially involved in transcription regulation and protein ubiquitination but significantly underrepresented in the processes of DNA recombination and DNA replication. These data reveal that the direction-related mutation bias and functional selection have influenced the distribution of amino acid repeats in plants.

Arabidopsis↗
PubMed2006

[Distribution features of Gleason score and its relationship with clinical stages in 346 prostate cancer patients].

OBJECTIVE: To analyze the distribution features of Gleason score and evaluate the relationship between Gleason score and clinical stages in patients with prostate cancer. METHODS: Surveys were made of the inpatients with prostate cancer diagnosed by pathology from January 1992 to June 2005 in our hospital. Gleason score and clinical stages were determined on the basis of pathological examination and clinical data of the prostate cancer patients. The patients were divided into three groups (1992-1999, 2000-2002 and 2003-2005). The Chi-square test was used to evaluate the distribution and differences of Gleason score among the three groups. Spearman rank correlation was applied to the evaluation of the relationship between Gleason score and clinical stages. RESULTS: We found a statistically significant shift in the distribution of Gleason score (chi2 = 17.703, P < 0.01), and a slight increase in the mean Gleason score. The proportion of moderately differentiated tumor increased (chi2 = 10.736, P < 0.01). There was little change in the proportion of Gleason score 7, 8, 9 and 10 (chi2 = 4.038, P > 0.05). Gleason score had a significant positive correlation with clinical stages in the 346 cases of prostate cancer (r = 0.452, P < 0.01). Significant difference was observed between Gleason score 2-6 and 7 or 8-10 (chi2 = 8.786, P < 0.01, chi2 = 22.956, P < 0.01), but not between the latter 2 groups (chi2 = 0.787, P > 0.05) in prediction of organ-confined disease. CONCLUSIONS: Gleason score 7 shows the similar value to Gleason score 8-10 in predicting the progression of the disease. Gleason score was significantly correlated with clinical stages, which suggests that Gleason score is also an important indicator for the prognosis of prostate cancer.

Adult↗
PubMed2005

Transcriptional and behavioral interaction between 22q11.2 orthologs modulates schizophrenia-related phenotypes in mice.

Microdeletions of 22q11.2 represent one of the highest known genetic risk factors for schizophrenia. It is likely that more than one gene contributes to the marked risk associated with this locus. Two of the candidate risk genes encode the enzymes proline dehydrogenase (PRODH) and catechol-O-methyltransferase (COMT), which modulate the levels of a putative neuromodulator (L-proline) and the neurotransmitter dopamine, respectively. Mice that model the state of PRODH deficiency observed in humans with schizophrenia show increased neurotransmitter release at glutamatergic synapses as well as deficits in associative learning and response to psychomimetic drugs. Transcriptional profiling and pharmacological manipulations identified a transcriptional and behavioral interaction between the Prodh and Comt genes that is likely to represent a homeostatic response to enhanced dopaminergic signaling in the frontal cortex. This interaction modulates a number of schizophrenia-related phenotypes, providing a framework for understanding the high disease risk associated with this locus, the expression of the phenotype, or both.

Animals↗
PubMed2005

[Hand-assisted laparoscopic renal surgery: report of 45 cases].

OBJECTIVE: To evaluate the effect and clinical application of hand-assisted laparoscopic renal surgery. METHODS: Forty-five patients with urologic diseases underwent hand-assisted laparoscopic renal surgery: radical nephrectomy was performed on 23 cases, simple nephrectomy on 9 cases, nephroureterectomy on 8 cases, excision of cysts of kidney on 3 cases, partial nephrectomy on 1 case, and upper pole heminephrectomy in duplex kidney on 1 case. The operation was performed by transperitoneal approach in 38 cases and by underwent and by retroperitoneal approach in 7 cases. RESULTS: Hand-assisted laparoscopic renal surgery were performed successfully on all patients. The mean operation time was 154.7 minutes (40 approximately 300 min), and the mean estimated blood loss was 100.4 ml (15 approximately 300 ml). CONCLUSION: With the advantages of minimal invasion, less blood loss, faster recovery, hand-assisted laparoscopic renal surgery is worth popularizing in urologic clinical practice.

Adolescent↗
PubMed2005

[Chemoprevention of prostate cancer].

In the western world, prostate cancer is a most common malignant neoplasm in human males. In recent years, its incidence has been rising dramatically in China. Prevention of this disease would have a positive impact on the disease-related cost, morbidity, and mortality for a large portion of the population. Cancer chemoprevention is defined as the use of natural, synthetic or biologic chemical agents to reverse, suppress, or prevent carcinogenic progression to invasive cancer. This article reviews the progress in chemoprevention of prostate cancer.

Aged↗
PubMed2005

[Age and pathological features of 481 prostate cancer patients].

OBJECTIVE: To investigate the age and pathological features of prostate cancer patients in recent years. METHODS: An analysis was made of the age and pathological features of 481 cases of prostate cancer pathologically diagnosed from January 1998 to April 2004, 39 cases in 1998, 69 in 1999, 73 in 2000, 68 in 2001, 72 in 2002, 121 in 2003, and 39 in the first four months of 2004. RESULTS: The patients ranged in age from 40 to 91 years, averaging 72, 95% between 55 and 84, and 84.2% over 65 years. Pathologically, 14 cases were well, 29 moderately, and 83 poorly differentiated according to the three-grade system (WHO, the Mostofi system), with 355 cases ungraded. Forty cases (8.3%) were microcarcinoma (< 1 cm), and 20 cases (4.2%) incidental carcinoma. Of the total number, 473 cases (98.1%) were pathologically diagnosed as adenocarcinoma, 1 endometrioid adenocarcinoma, 1 squamous cell carcinoma, 1 signet ring cell carcinoma, 1 adenosquamous cell carcinoma, 1 small cell carcinoma, 1 mucinous adenocarcinoma, 1 adenoid cystic carcinoma, and 1 transitional cell carcinoma. CONCLUSION: Prostate cancer commonly develops in men over 65 years, and adenocarcinoma is the most common histological type. The disease has become a major malignant tumor to endanger elderly males.

Adenocarcinoma↗
PubMed2004

Using the gene ontology for microarray data mining: a comparison of methods and application to age effects in human prefrontal cortex.

One of the challenges in the analysis of gene expression data is placing the results in the context of other data available about genes and their relationships to each other. Here, we approach this problem in the study of gene expression changes associated with age in two areas of the human prefrontal cortex, comparing two computational methods. The first method, "overrepresentation analysis" (ORA), is based on statistically evaluating the fraction of genes in a particular gene ontology class found among the set of genes showing age-related changes in expression. The second method, "functional class scoring" (FCS), examines the statistical distribution of individual gene scores among all genes in the gene ontology class and does not involve an initial gene selection step. We find that FCS yields more consistent results than ORA, and the results of ORA depended strongly on the gene selection threshold. Our findings highlight the utility of functional class scoring for the analysis of complex expression data sets and emphasize the advantage of considering all available genomic information rather than sets of genes that pass a predetermined "threshold of significance."

Adolescent↗
PubMed2004

Coexpression analysis of human genes across many microarray data sets.

We present a large-scale analysis of mRNA coexpression based on 60 large human data sets containing a total of 3924 microarrays. We sought pairs of genes that were reliably coexpressed (based on the correlation of their expression profiles) in multiple data sets, establishing a high-confidence network of 8805 genes connected by 220,649 "coexpression links" that are observed in at least three data sets. Confirmed positive correlations between genes were much more common than confirmed negative correlations. We show that confirmation of coexpression in multiple data sets is correlated with functional relatedness, and show how cluster analysis of the network can reveal functionally coherent groups of genes. Our findings demonstrate how the large body of accumulated microarray data can be exploited to increase the reliability of inferences about gene function.

Cluster Analysis↗
PubMed2004

Gene expression signatures in chronic and aggressive periodontitis: a pilot study.

This pilot study examined gene expression signatures in pathological gingival tissues of subjects with chronic or aggressive periodontitis, and explored whether new subclasses of periodontitis can be identified based on gene expression profiles. A total of 14 patients, seven with chronic and seven with aggressive periodontitis, were examined with respect to clinical periodontal status, composition of subgingival bacterial plaque assessed by checkerboard hybridizations, and levels of serum IgG antibodies to periodontal bacteria assayed by checkerboard immunoblotting. In addition, at least two pathological pockets/patient were biopsied, processed for RNA extraction, amplification and labeling, and used to study gene expression using Affymetrix U-133 A arrays. Based on a total of 35 microarrays, no significantly different gene expression profiles appeared to emerge between chronic and aggressive periodontitis. However, a de novo grouping of the 14 subjects into two fairly robust clusters was possible based on similarities in gene expression. These two groups had similar clinical periodontal status and subgingival bacterial profiles, but differed significantly with respect to serum IgG levels against the important periodontal pathogens Porphyromonas gingivalis, Tannerella forsythensis and Campylobacter rectus. These early data point to the usefulness of gene expression profiling techniques in the identification of subclasses of periodontitis with common pathobiology.

Acute Disease↗