Biomedical subjects

Jing Wang

Publications and source records attributed to Jing Wang.

At least 253 records · Page 14Linked to original sources

PubMed2005

Influence of switch region length on immunoglobulin class switch recombination.

The class and effector functions of antibodies are modulated through the process of Ig heavy chain class switch recombination (CSR). CSR occurs between switch (S) regions that lie upstream of the various Ig heavy chain constant region exons. Molecular analyses of S-region functions have been hampered by their large size and repetitive nature. To test potential relationships between S-region size and efficiency of CSR, we generated normal B lymphocytes in which the 12-kb S region flanking the Cgamma1 exons (Sgamma1) was replaced with synthetic or endogenous S regions of various lengths. Replacement of Sgamma1 with 1- and 2-kb synthetic sequences representing the Sgamma1 core repeats or a 4-kb portion of the core endogenous Sgamma1 region supported CSR frequencies that directly correlated with S-region length. These findings indicate that S-region size is an important factor in determining endogenous CSR efficiency. Moreover, these results also will allow the development of a systematic system to test the function of various S-region motifs by replacing endogenous S regions with synthetic S regions controlled for size effects.

Animals↗

PubMed2005

Comprehensive global energy minimum modeling of the sarin-serine adduct.

DFT-based molecular dynamics and quantum chemistry theory approaches are combined to investigate the various conformers of sarin-serine adduct. Twenty different conformers have been located as the local minima on the potential energy surface. They are categorized into five classes based on the relative orientation of sarin moiety. The energy properties of the twenty sarin-serine conformers revealed in the present study suggest that at least four of the conformers (1-1, 4-1, 4-2, and 5-1) are expected to have crucial contributions to the phosphonylation and dealkylation reactions of the sarin-serine adduct at low temperature. Among them, the 1-1 conformer which has both the lowest energy and the highest Boltzman distribution relative probability is expected to be the most important. However, as the temperature rises, the 4-1 conformer plays a more important role than 1-1 in the sarin-serine adductation reactions. Under the relatively high temperatures, the contribution of conformer 5-1 decreases in the phosphonylation and dealkylation reactions while at least eight other conformers (1-2, 1-3, 3-1, 3-4, 3-7, 4-2, 4-3, and 4-4) are expected to have larger contributions in these reactions.

Computer Simulation↗

PubMed2005

Conditional MLL-CBP targets GMP and models therapy-related myeloproliferative disease.

Chromosomal translocations that fuse the mixed lineage leukemia (MLL) gene with multiple partners typify acute leukemias of infancy as well as therapy-related leukemias. We utilized a conditional knockin strategy to bypass the embryonic lethality caused by MLL-CBP expression and to assess the immediate effects of induced MLL-CBP expression on hematopoiesis. Within days of activating MLL-CBP, the fusion protein selectively expanded granulocyte/macrophage progenitors (GMP) and enhanced their self-renewal/proliferation. MLL-CBP altered the gene expression program of GMP, upregulating a subset of genes including Hox a9. Inhibition of Hox a9 expression by RNA interference demonstrated that MLL-CBP required Hox a9 for its enhanced cell expansion. Following exposure to sublethal gamma-irradiation or N-ethyl-N-nitrosourea (ENU), MLL-CBP mice developed myelomonocytic hyperplasia and progressed to fatal myeloproliferative disorders. These represented the spectrum of therapy-induced acute myelomonocytic leukemia/chronic myelomonocytic leukemia/myelodysplastic/myeloproliferative disorder similar to that seen in humans possessing the t(11;16). This model of MLL-CBP therapy-related myeloproliferative disease demonstrates the selectivity of this MLL fusion for GMP cells and its ability to initiate leukemogenesis in conjunction with cooperating mutations.

Animals↗

PubMed2005

ChickVD: a sequence variation database for the chicken genome.

Working in parallel with the efforts to sequence the chicken (Gallus gallus) genome, the Beijing Genomics Institute led an international team of scientists from China, USA, UK, Sweden, The Netherlands and Germany to map extensive DNA sequence variation throughout the chicken genome by sampling DNA from domestic breeds. Using the Red Jungle Fowl genome sequence as a reference, we identified 3.1 million non-redundant DNA sequence variants. To facilitate the application of our data to avian genetics and to provide a foundation for functional and evolutionary studies, we created the 'Chicken Variation Database' (ChickVD). A graphical MapView shows variants mapped onto the chicken genome in the context of gene annotations and other features, including genetic markers, trait loci, cDNAs, chicken orthologs of human disease genes and raw sequence traces. ChickVD also stores information on quantitative trait loci using data from collaborating institutions and public resources. Our data can be queried by search engine and homology-based BLAST searches. ChickVD is publicly accessible at http://chicken.genomics.org.cn.

Animals↗

PubMed2005

SilkDB: a knowledgebase for silkworm biology and genomics.

The Silkworm Knowledgebase (SilkDB) is a web-based repository for the curation, integration and study of silkworm genetic and genomic data. With the recent accomplishment of a approximately 6X draft genome sequence of the domestic silkworm (Bombyx mori), SilkDB provides an integrated representation of the large-scale, genome-wide sequence assembly, cDNAs, clusters of expressed sequence tags (ESTs), transposable elements (TEs), mutants, single nucleotide polymorphisms (SNPs) and functional annotations of genes with assignments to InterPro domains and Gene Ontology (GO) terms. SilkDB also hosts a set of ESTs from Bombyx mandarina, a wild progenitor of B.mori, and a collection of genes from other Lepidoptera. Comparative analysis results between the domestic and wild silkworm, between B.mori and other Lepidoptera, and between B.mori and the two sequenced insects, fruitfly and mosquito, are displayed by using B.mori genome sequence as a reference framework. Designed as a basic platform, SilkDB strives to provide a comprehensive knowledgebase about the silkworm and present the silkworm genome and related information in systematic and graphical ways for the convenience of in-depth comparative studies. SilkDB is publicly accessible at http://silkworm.genomics.org.cn.

Animals↗

PubMed2005

Glycolytic enzymes can modulate cellular life span.

An unbiased screen for genes that can immortalize mouse embryonic fibroblasts identified the glycolytic enzyme phosphoglycerate mutase (PGM). A 2-fold increase in PGM activity enhances glycolytic flux, allows indefinite proliferation, and renders cells resistant to ras-induced arrest. Glucosephosphate isomerase, another glycolytic enzyme, displays similar activity and, conversely, depletion of PGM or glucosephosphate isomerase with short interfering RNA triggers premature senescence. Immortalized mouse embryonic fibroblasts and mouse embryonic stem cells display higher glycolytic flux and more resistance to oxidative damage than senescent cells. Because wild-type p53 down-regulates PGM, mutation of p53 can facilitate immortalization via effects on PGM levels and glycolysis.

Animals↗

PubMed2005

Paraneoplastic pemphigus associated with Castleman tumor: a commonly reported subtype of paraneoplastic pemphigus in China.

BACKGROUND: Castleman tumor, a rare lymphoproliferative disorder, is one of the associated tumors in paraneoplastic pemphigus. We analyzed the characteristics of a group of patients with Castleman tumor to clearly understand and to improve the prognosis of the disease. OBSERVATIONS: Ten cases of paraneoplastic pemphigus associated with Castleman tumor treated in the Department of Dermatology, Peking University First Hospital, Beijing, China, from May 1, 1999, to March 31, 2004, were analyzed for clinical aspects, characteristics and histologic features of the tumors, and computed tomographic findings. Literature was reviewed and data were compared with our cases. Castleman tumor was a frequently reported neoplasm in association with paraneoplastic pemphigus in China. The disease was found to be caused by an autoimmune reaction originating from the B lymphocytes in the Castleman tumor. CONCLUSIONS: Castleman tumor in association with paraneoplastic pemphigus is a commonly reported subtype of paraneoplastic pemphigus in China. Early detection and removal of the Castleman tumor are crucial for the treatment of this tumor-associated autoimmune disease.

Adolescent↗

PubMed2005

OPA1 R445H mutation in optic atrophy associated with sensorineural deafness.

The heterozygous R445H mutation in OPA1 was found in five patients with optic atrophy and deafness. Audiometry suggested that the sensorineural deafness resulted from auditory neuropathy. Skin fibroblasts showed hyperfragmentation of the mitochondrial network, decreased mitochondrial membrane potential, and adenosine triphosphate synthesis defect. In addition, OPA1 was found to be widely expressed in the sensory and neural cochlear cells of the guinea pig. Thus, optic atrophy and deafness may be related to energy defects due to a fragmented mitochondrial network.

Adolescent↗

PubMed2005

Evaluation of right ventricular volume and systolic function by realtime three-dimensional echocardiography.

The optimal plane for measurement of the right ventricular (RV) volumes by real-time three-dimensional echocardiography (RT3DE) was determined and the feasibility and accuracy of RT3DE in studying RV systolic function was assessed. RV "Full volume" images were acquired by RT3DE in 22 healthy subjects. RV end-diastolic volumes (RVEDV) and end-systolic volumes (RVESV) were outlined using apical biplane, 4-plane, 8-plane, 16-plane offline separately. RVSV and RVEF were calculated. Meanwhile tricuspid annual systolic excursion (TASE) was measured by M-mode echo. LVSV was outlined by 2-D echo according to the biplane Simpson's rule. The results showed: (1) There was a good correlation between RVSV measured from series planes and LVSV from 2-D echo (r = 0.73; r = 0.69; r = 0.63; r = 0.66, P < O. 25-0. 0025); (2) There were significant differences between RVEDV in biplane and those in 4-, 8-, 16-plane (P < 0.001). There was also difference between RV volume in 4-plane and that in 8-plane (P < 0.05), but there was no significant difference between RV volume in 8-plane and that in 16-plane (P > 0.05); (3) Inter-observers and intro-observers variability analysis showed that there were close agreements and relations for RV volumes (r = 0.986, P < 0.001; r = 0.93, P < 0.001); (4) There was a significantly positive correlation of TASE to RVSV and RVEF from RT3DE (r = 0.83; r = 0.90). So RV volume measures with RT3DE are rapid, accurate and reproducible. In view of RV's complex shape, apical 8-plane method is better in clinical use. It may allow early detection of RV systolic function.

Adult↗

PubMed2005

Applications of the double-barreled data in whole-genome shotgun sequence assembly and analysis.

Double-barreled (DB) data have been widely used for the assembly of large genomes. Based on the experience of building the whole-genome working draft of Oryza sativa L. ssp. Indica, we present here the prevailing and improved uses of DB data in the assembly procedure and report on novel applications during the following data-mining processes such as acquiring precise insert fragment information of each clone across the genome, and a new kind of low-cost whole-genome microarray. With the increasing number of organisms being sequenced, we believe that DB data will play an important role both in other assembly procedures and in future genomic studies.

Cloning, Molecular↗

PubMed2005

Self-actuated, thermo-responsive hydrogel valves for lab on a chip.

An easy to fabricate, thermally-actuated, self-regulated hydrogel valve for flow control in pneumatically driven, microfluidic systems is described. This microvalve takes advantage of the properties of the hydrogel, poly(N-isopropylacrylamide), as well as the aqueous fluid itself to realize flow control. The valve was designed for use in a diagnostic system fabricated with polycarbonate and aimed at the detection of pathogens in oral fluids at the location of the sample collection. The paper describes the construction and characterization of the hydrogel valves and their application for flow control, sample and reagent metering, sample distribution into multiple analysis paths, and the sealing of a polymerase chain reaction (PCR) reactor to suppress bubble formation. The hydrogel-based flow control is electronically addressable, does not require any moving parts, introduces minimal dead volume, is leakage and contaminant free, and is biocompatible.

Acrylic Resins↗

PubMed2005

cDNA cloning, functional expression and antifungal activities of a dimeric plant defensin SPE10 from Pachyrrhizus erosus seeds.

SPE10 is an antifungal protein isolated from the seeds of Pachyrrhizus erosus. cDNA encoding a 47 amino acid peptide was cloned by RT-PCR and the gene sequence proved SPE10 to be a new member of plant defensin family. The synthetic cDNA with codons preferred in yeast was cloned into the pPIC9 plasmid directly in-frame with the secretion signal alpha-mating factor, and highly expressed in methylotrophic Pichia pastoris. Activity assays showed the recombinant SPE10 inhibited specifically the growth of several pathogenic fungi as native SPE10. Circular dichroism and fluorescence spectroscopy analysis indicated that the native and recombinant protein should have same folding, though there are eight cystein residues in the sequence. Several evidence suggested SPE10 should be the first dimeric plant defensin reported so far.

Amino Acid Sequence↗

PubMed2005

Recovery of protein from poultry processing wastewater using membrane ultrafiltration.

The feasibility of using ultrafiltration (UF) to recover protein from poultry processing wastewater (PPW) after primary treatment was investigated. By using polysulfone membrane with 30,000 molecular-weight-cut-off, almost all crude proteins in PPW were retained, subsequently reducing the chemical oxygen demand (COD) in the effluent to less than 200 mg L(-1). Similar to the processing of proteinaceous materials, the average fluxes reached only 100 Lm(-2) h(-1). By identifying the optimal values of key operation parameters, including pH, volumetric flow rate, and transmembrane pressure (6.74, 683 mL min(-1) and 14 psi, respectively) using response surface methodology (RSM), the flux was improved to higher than 200 Lm(-2) h(-1). Although severe membrane fouling was still inevitable after processing, flushing the membrane with a cleaning reagent was found capable of effectively restoring membrane performance.

Animals↗

PubMed2005

Characteristics of the beta myosin heavy chain gene Ala26Val mutation in a Chinese family with hypertrophic cardiomyopathy.

BACKGROUND: Genotype-phenotype studies have suggested that some mutations of genes encoding various components of the cardiac sarcomere cause hypertrophic cardiomyopathy (HCM) and are associated with the prognosis of patients with HCM. The aims of this study were to investigate the gene mutations of exons in the cardiac beta myosin heavy chain (MYH7) gene, the troponin T (TNNT2) gene, and the brain natriuretic peptide (BNP) gene, as well as to assess the effect of these mutations on the clinical features of Chinese patients with HCM. METHODS: Five unrelated Chinese families with HCM were studied. Exons 3 and 18 in the MYH7 gene, exon 9 in the TNNT2 gene, and all three exons in the BNP gene were screened with the polymerase chain reaction (PCR) for genomic DNA amplification. Further study included purification of PCR products and direct sequencing of PCR fragments by fluorescent end labeling. RESULTS: A C-to-T transition in codon 26 of exon 3 in the MYH7 gene was found in one family (including four patients and five carriers), resulting in an amino acid substitution of valine (Val) for alanine (Ala). The Ala26Val mutation was of incomplete dominance (penetrance 44%). This mutation was not seen in the other four families or in the control group. Moreover, the association between the gene mutations of exon 18 in MYH7, of exon 9 of TNNT2, and of all three exons in BNP and HCM was not found in the populations we studied. CONCLUSIONS: The missense mutation Ala26Val found in this one Chinese family was associated with a mild phenotype of HCM. The genetic and phenotypic heterogeneity of HCM exists in the Chinese population. It suggests that genetic and environmental factors may be involved in the pathogenesis of HCM.

Journal Article↗

PubMed2005

Purification and characterization of a single-chain chimeric anti-p185 antibody expressed by CHO-GS system.

Monoclonal antibody A21 reacts specifically with the extracellular domain of p185c-erbB-2 oncoprotein, a member of the epidermal growth factor receptor family. In a previous study, we constructed a single-chain chimeric antibody, assembled using an A21 single-chain Fv antibody and a human IgG1 Fc fragment. In this study, we expressed this chimeric antibody using a CHO-GS system, and developed a simple and efficient method for its purification. After only one step using affinity purification, the recovery rate and purity of the antibody attained was 60 and 91%, respectively. After a second step, using reverse phase HPLC purification, the purity was above 99%. The high purity of the recombinant antibody allowed us to identify a number of its intrinsic molecular properties, including antigen binding activity, measurement of affinity constant, N-terminal sequencing, and mass spectrometer analysis. These results further augment the potential of this recombinant antibody to be a drug candidate for cancer therapy.

Amino Acid Sequence↗

PubMed2005

Use of Ssp dnaB derived mini-intein as a fusion partner for production of recombinant human brain natriuretic peptide in Escherichia coli.

To prevent in vivo degradation, small peptides are usually expressed in fusion proteins from which target peptides can be released by proteolytic or chemical reagents. In this report, a modified Ssp dnaB mini-intein linked with a chitin binding domain tag was used as a fusion partner for production of human brain natriuretic peptide (hBNP), a hormone for the treatment of congestive heart failure. The fusion protein was expressed as an inclusion body in Escherichia coli. After refolding, the fusion protein was purified with a chitin affinity column, and dnaB mini-intein mediated peptide-bond hydrolysis was triggered by shifting the pH in the chitin column to 7.0 at 25 degrees C for 16 h, which led to the release and separation of hBNP from its fusion partner. The hBNP sample was further purified with reverse phase HPLC and its biological activity was assayed in vitro. It was found that hBNP had a potent vasodilatory effect on rabbit aortic strips with an EC(50) of (1.24+/-0.32)x10(-6)mg/ml, which was similar to that of the synthetic BNP standard. The expression strategy described here promises to produce small peptides without use of proteolytic or chemical reagents.

Adenosine Triphosphatases↗

PubMed2005

Biological validation of differentially expressed genes in chronic lymphocytic leukemia identified by applying multiple statistical methods to oligonucleotide microarrays.

Oligonucleotide microarrays are a powerful tool for profiling the expression levels of thousands of genes. Different statistical methods for identifying differentially expressed genes can yield different results. To our knowledge, no experimental test has been performed to decide which method best identifies genes that are truly differentially expressed. We applied three statistical methods (dChip, t-test on log-transformed data, and Wilcoxon test) to identify differentially expressed genes in previously untreated patients with chronic lymphocytic leukemia (CLL). We used a training set of Affymetrix Hu133A microarray data from 11 patients with unmutated immunoglobulin (Ig) heavy chain variable region (VH) genes and 8 patients with mutated Ig VH genes. Differential expression was validated using semiquantitative real-time polymerase chain reaction assays and by validating models to predict the somatic mutation status of an independent test set of nine CLL samples. The methods identified 144 genes that were differentially expressed between cases of CLL with unmutated compared with mutated Ig VH genes. Eighty genes were identified by Wilcoxon test, 60 by t-test, and 65 by dChip, but only 11 were identified by all three methods. Greater agreement was found between the t-test and the Wilcoxon test. Differential expression was validated by semiquantitative real-time polymerase chain reaction assays for 83% of individual genes, regardless of the statistical method. However, the Wilcoxon test gave the most accurate predictions on new samples, and dChip, the least accurate. We found that all three methods were equally good for finding differentially expressed genes, but they found different genes. The genes selected by the nonparametric Wilcoxon test are the most robust for predicting the status of new cases. A comprehensive list of all differentially expressed genes can only be obtained by combining the results of multiple statistical tests.

Algorithms↗

PubMed2005

Comparison of the predictive accuracy of DNA array-based multigene classifiers across cDNA arrays and Affymetrix GeneChips.

We examined how well differentially expressed genes and multigene outcome classifiers retain their class-discriminating values when tested on data generated by different transcriptional profiling platforms. RNA from 33 stage I-III breast cancers was hybridized to both Affymetrix GeneChip and Millennium Pharmaceuticals cDNA arrays. Only 30% of all corresponding gene expression measurements on the two platforms had Pearson correlation coefficient r >or= 0.7 when UniGene was used to match probes. There was substantial variation in correlation between different Affymetrix probe sets matched to the same cDNA probe. When cDNA and Affymetrix probes were matched by basic local alignment tool (BLAST) sequence identity, the correlation increased substantially. We identified 182 genes in the Affymetrix and 45 in the cDNA data (including 17 common genes) that accurately separated 91% of cases in supervised hierarchical clustering in each data set. Cross-platform testing of these informative genes resulted in lower clustering accuracy of 45 and 79%, respectively. Several sets of accurate five-gene classifiers were developed on each platform using linear discriminant analysis. The best 100 classifiers showed average misclassification error rate of 2% on the original data that rose to 19.5% when tested on data from the other platform. Random five-gene classifiers showed misclassification error rate of 33%. We conclude that multigene predictors optimized for one platform lose accuracy when applied to data from another platform due to missing genes and sequence differences in probes that result in differing measurements for the same gene.

Adult↗