Biomedical subjects

Jing Chen

Publications and source records attributed to Jing Chen.

At least 37 records · Page 2Linked to original sources

PubMed2006

Identification of unique genetic markers in Rv0927c among Mycobacterium tuberculosis W-Beijing strains.

Fifty-six clinical isolates of Mycobacterium tuberculosis were analyzed by spoligotyping to determine the prevalence of W-Beijing strains. Forty-nine of the 56 isolates belonged to W-Beijing strains and 7 isolates were non-Beijing strains. Comparative two-dimensional gel electrophoresis analysis of protein patterns between the W-Beijing and non-Beijing strains identified a unique protein Rv0927c that is absent in the former but present in the latter and the reference strain M. tuberculosis H37Rv. Compared with 7 non-Beijing clinical isolates and H37Rv, all 49 W-Beijing strains had two characteristic mutations, a deletion of AGC at nucleotide position 421 of Rv0927c gene encoding a putative short dehydrogenase/reductase, causing deletion of serine codon at amino acid position 141 and a -127 G-->A mutation in Rv0927c-pstS3 intergenic region, resulting in failure to express Rv0927c. Western blot analysis indicated that polyclonal antibody raised against H37Rv Rv0927c overexpressed in Escherichia coli reacted with non-Beijing strains and H37Rv but not W-Beijing strains. Characteristic mutations of Rv0927c that are present in W-Beijing strains can be used as a novel genetic marker for rapid molecular typing of M. tuberculosis W-Beijing strains.

Antibodies, Bacterial↗

PubMed2006

GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs.

Transcriptional cis-regulatory control regions frequently are found within non-coding DNA segments conserved across multi-species gene orthologs. Adopting a systematic gene-centric pipeline approach, we report here the development of a web-accessible database resource--GenomeTraFac (http://genometrafac.cchmc.org)--that allows genome-wide detection and characterization of compositionally similar cis-clusters that occur in gene orthologs between any two genomes for both microRNA genes as well as conventional RNA-encoding genes. Each ortholog gene pair can be scanned to visualize overall conserved sequence regions, and within these, the relative density of conserved cis-element motif clusters form graph peak structures. The results of these analyses can be mined en masse to identify most frequently represented cis-motifs in a list of genes. The system also provides a method for rapid evaluation and visualization of gene model-consistency between orthologs, and facilitates consideration of the potential impact of sequence variation in conserved non-coding regions to impact complex cis-element structures. Using the mouse and human genomes via the NCBI Reference Sequence database and the Sanger Institute miRBase, the system demonstrated the ability to identify validated transcription factor targets within promoter and distal genomic regulatory regions of both conventional and microRNA genes.

Animals↗

PubMed2006

Radiation quality of tritium.

Tritium occurs from both natural and manufactured processes. In the environment, tritium can exist in the form of tritiated water (HTO) and in an organic form known as organically-bound tritium (OBT). Although, the concentrations of environmental OBT are relatively low, there is concern that current risk factors may underestimate the risk from OBT. Because tritium poses an internal hazard at cellular levels, microdosimetric techniques provide suitable tools for the study of radiation quality of tritium. In this study, microdosimetric simulations are performed for tritium uniformly distributed in a medium, and for tritium bound to biologically critical sites of dimensions from 10 nm to 2 microm. Results of local energy density are different for these two cases in microscopic regions. Based on the spatial distribution of energy deposition, dose mean lineal energies are calculated for tritium in forms of HTO and OBT. The dose mean lineal energies of OBT are about a factor of 1.7 higher than those of HTO in a wide range of target dimensions of biological interest. The results are consistent with radiobiological findings that OBT is about twice as effective as that of HTO.

Half-Life↗

PubMed2006

Proximity functions for electrons from 100 eV to 10 MeV.

The objective of this study is to provide a set of proximity functions for electrons from 100 eV to 10 MeV. Numerical results of differential proximity functions are given graphically. The complete data set is available electronically upon request from the authors. The results can serve as a convenient database for anyone performing microdosimetric calculations in radiation fields of electrons. For mixed fields of electrons, the proximity functions can easily be derived from the proximity functions of monoenergetic electrons presented here.

Computer Simulation↗

PubMed2006

Parallel screening approach to identify solubility-enhancing formulations for improved bioavailability of a poorly water-soluble compound using milligram quantities of material.

In this article, we present a parallel experimentation approach to rapidly identify a solubility-enhancing formulation that improved the bioavailability of a poorly water-soluble compound using milligrams of material. The lead compound and a panel of excipients were dissolved in n-propanol and dispensed into the wells of a 96-well microtiter plate by a TECAN robot. Following solvent evaporation, the neat formulations were diluted with an aqueous buffer, and incubated for 24h. The solubilization capacity of the excipients for the compound at 24h (SC(24h)), was determined by HPLC, and compared with its solubility in the corresponding neat formulations determined by a bench-scale method. The ranking order of solubilization capacity of the five tested formulations for this compound by this microscreening assay is same as the ranking order of the compound solubility in the neat formulations. Several formulations that achieved the target aqueous solubility were identified using the screening method. One of the top formulations, an aqueous solution of the compound containing 20% Tween 80 by weight, increased the compound solubility from less than 2 microg/mL to at least 10mg/mL. In a rat pharmacokinetic (PK) study, the Tween 80 formulation achieved 26.6% of bioavailability, a significant improvement over 3.4% of bioavailability for the aqueous Methocel formulation (p<0.01). The results in the study suggest that this parallel screening assay can be potentially used to rapidly identify solubility-enhancing formulations for an improved bioavailability of poorly water-soluble compounds using milligram quantities of material.

Animals↗

PubMed2006

PolyDoms: a whole genome database for the identification of non-synonymous coding SNPs with the potential to impact disease.

As knowledge of human genetic polymorphisms grows, so does the opportunity and challenge of identifying those polymorphisms that may impact the health or disease risk of an individual person. A critical need is to organize large-scale polymorphism analyses and to prioritize candidate non-synonymous coding SNPs (nsSNPs) that should be tested in experimental and epidemiological studies to establish their context-specific impacts on protein function. In addition, with emerging high-resolution clinical genetics testing, new polymorphisms must be analyzed in the context of all available protein feature knowledge including other known mutations and polymorphisms. To approach this, we developed PolyDoms (http://polydoms.cchmc.org/) as a database to integrate the results of multiple algorithmic procedures and functional criteria applied to the entire Entrez dbSNP dataset. In addition to predicting structural and functional impacts of all nsSNPs, filtering functions enable group-based identification of potentially harmful nsSNPs among multiple genes associated with specific diseases, anatomies, mammalian phenotypes, gene ontologies, pathways or protein domains. PolyDoms, thus, provides a means to derive a list of candidate SNPs to be evaluated in experimental or epidemiological studies for impact on protein functions and disease risk associations. PolyDoms will continue to be curated to improve its usefulness.

Databases, Nucleic Acid↗

PubMed2006

Saturation effect and forward-dominant second-harmonic generation in single-defect photonic crystals with dual localizations.

We study the forward-dominant output of second-harmonic generation (SHG) in single-defect and dual-localized photonic crystals within the saturation limit. We propose that an asymmetric structure can be used to improve the performance of the enhanced SHG. We get two empirical expressions for the total saturation SHG efficiency and the forward factor and provide a reasonable explanation. The theoretical results predict a nearly 100% conversion efficiency and a nearly 100% forward output. Our work is very valuable for designing nonlinear photonic devices. As a test, a practical asymmetrical structure is presented.

Journal Article↗

PubMed2006

Effect of compressed CO2 on the critical micelle concentration and aggregation number of AOT reverse micelles in isooctane.

The effect of compressed CO2 on the critical micelle concentration (cmc) and aggregation number of sodium bis-2-ethylhexylsulfosuccinate (AOT) reverse micelles in isooctane solution was studied by UV/Vis and fluorescence spectroscopy methods in the temperature range of 303.2-318.2 K and at different pressures or mole fractions of CO2 (X(CO2)). The capacity of the reverse micelles to solubilize water was also determined by direct observation. The standard Gibbs free energy (DeltaGo(m)), standard enthalpy (DeltaHo(m)), and standard entropy (DeltaSo(m)) for the formation of the reverse micelles were calculated by using the cmc data determined. It was discovered that the cmc versus X(CO2) curve and the DeltaGo(m) versus X(CO2) curve for a fixed temperature have a minimum, and the aggregation number and water-solubilization capacity of the reverse micelles reach a maximum at the X(CO2) value corresponding to that minimum. These results indicate that CO2 at a suitable concentration favors the formation of and can stabilize AOT reverse micelles. A detailed thermodynamic study showed that the driving force for the formation of the reverse micelles is entropy.

Journal Article↗

PubMed2006

Interleukin-6 facilitates lipopolysaccharide-induced disruption in working memory and expression of other proinflammatory cytokines in hippocampal neuronal cell layers.

Proinflammatory cytokines inhibit learning and memory but the significance of interleukin-6 (IL-6) in acute cognitive deficits induced by the peripheral innate immune system is not known. To examine the functional role of IL-6 in hippocampus-mediated cognitive impairments associated with peripheral infections, C57BL6/J (IL-6(+/+)) and IL-6 knock-out (IL-6(-/-)) mice were trained in a matching-to-place version of the water maze. After an acquisition phase, IL-6(+/+) mice injected intraperitoneally with lipopolysaccharide (LPS) exhibited deficits in working memory. However, IL-6(-/-) mice were refractory to the LPS-induced impairment in working memory. To determine the mechanism by which IL-6 deficiency conferred protection from disruption in working memory, plasma IL-1beta and tumor necrosis factor alpha (TNFalpha), c-Fos immunoreactivity in the nucleus of the solitary tract (NTS), and steady-state levels of IL-1beta and TNFalpha mRNA in neuronal layers of the hippocampus were determined in IL-6(+/+) and IL-6(-/-) mice after injection of LPS. Plasma IL-1beta and TNFalpha and c-Fos immunoreactivity in the NTS were increased similarly in IL-6(+/+) and IL-6(-/-) mice after LPS, indicating high circulating levels of IL-1beta and TNFalpha and activation of vagal afferent pathways were not sufficient to disrupt working memory in the absence of IL-6. However, the LPS-induced upregulation of IL-1beta and TNFalpha mRNA that was evident in hippocampal tissue of IL-6(+/+) mice was greatly attenuated or entirely absent in IL-6(-/-) mice. Collectively, these data suggest that humoral and neural immune-to-brain communication pathways are intact in IL-6-deficient mice but that, in the absence of IL-6, the central cytokine compartment is hyporesponsive.

Animals↗

PubMed2006

Prohibitin suppresses renal interstitial fibroblasts proliferation and phenotypic change induced by transforming growth factor-beta1.

Prohibitin (PHB), a potential tumor suppressor, has been shown to inhibit cell proliferation by repressing E2F-mediated transcription. But little is known about the role of PHB involved in tubulointerstitial fibrosis (TIF). Here, for the first time, we found PHB protein was positively expressed at normal renal tissues, strongly down-regulated in renal biopsy specimens, and negatively correlated with the expression of alpha-smooth-muscle actin (alpha-SMA) and with the degrees of tubulointerstitial lesions. Transforming growth factor-beta1 (TGF-beta1) is the most important profibrotic cytokine in the process of TIF and capable of inducing cell phenotypic change of interstitial fibroblasts characterized by the de novo expression of alpha-SMA. Confocal microscopy showed majority of PHB is located at cytoplasm as well as at nucleus in rat kidney fibroblasts cell (NRK-49F). As we found that PHB protein and mRNA expression were down-regulated in NRK-49F cells following TGF-beta1 stimulation. We used transient transfection to over-express PHB protein and found that cells with increased PHB levels had a significant reduction in the percentage entering cell cycle and abolished de novo expression of alpha-SMA following TGF-beta1 stimulation. Therefore, over-expression of PHB suppresses renal interstitial fibroblasts proliferation and cell phenotypic change induced by TGF-beta1, which indicates PHB as a potential therapeutic target to halt the progression of TIF.

Actins↗

PubMed2006

Variants in mitochondrial tRNAGlu, tRNAArg, and tRNAThr may influence the phenotypic manifestation of deafness-associated 12S rRNA A1555G mutation in three Han Chinese families with hearing loss.

We report here on the clinical, genetic, and molecular characterization of three Han Chinese pedigrees with aminoglycoside-induced and nonsyndromic hearing loss. Clinical evaluation revealed the variable phenotype of hearing loss including severity, age-at-onset, audiometric configuration in these subjects. Penetrances of hearing loss in BJ107, BJ108, and BJ109 pedigrees are 35%, 63%, and 67%, respectively. Mutational analysis of the complete mitochondrial genomes in these pedigrees showed the identical homoplasmic A1555G mutation and distinct sets of mitochondrial DNA (mtDNA) variants belonging to haplogroups N, F, and M, respectively. Of these variants, the A14693G mutation in the tRNA(Glu), the T15908C mutation in the tRNA(Thr), and the T10454C mutation in the tRNA(Arg) are of special interest as these mutations occur at positions which are highly evolutionarily conserved nucleotides of corresponding tRNAs. These homoplasmic mtDNA mutations were absent among 156 unrelated Chinese controls. The A14693G and T10454C mutations occur at the highly conserved bases of the TpsiC-loop of tRNA(Glu) and tRNA(Arg), respectively. Furthermore, the T15908C mutation in the tRNA(Thr) disrupts a highly conserved A-U base-pairing at the D-stem of this tRNA. The alteration of structure of these tRNAs by these mtDNA mutations may lead to a failure in tRNA metabolism, thereby causing impairment of mitochondrial translation. Thus, mitochondrial dysfunctions, caused by the A1555G mutation, would be worsened by these mtDNA mutations. Therefore, these mtDNA mutations may have a potential modifier role in increasing the penetrance and expressivity of the deafness-associated 12S rRNA A1555G mutation in those Chinese pedigrees.

Base Pairing↗

PubMed2006

Carboxyl terminus of severe acute respiratory syndrome coronavirus nucleocapsid protein: self-association analysis and nucleic acid binding characterization.

Coronavirus nucleocapsid (N) protein envelops the genomic RNA to form long helical nucleocapsid during virion assembly. Since N protein oligomerization is usually a crucial step in this process, characterization of such an oligomerization will help in the understanding of the possible mechanisms for nucleocapsid formation. The N protein of severe acute respiratory syndrome coronavirus (SARS-CoV) was recently discovered to self-associate by its carboxyl terminus. In this study, to further address the detailed understanding of the association feature of this C-terminus, its oligomerization was systematically investigated by size exclusion chromatography and chemical cross-linking assays. Our results clearly indicated that the C-terminal domain of SARS-CoV N protein could form not only dimers but also trimers, tetramers, and hexamers. Further analyses against six deletion mutants showed that residues 343-402 were necessary and sufficient for this C-terminus oligomerization. Although this segment contains many charged residues, differences in ionic strength have no effects on its oligomerization, indicating the absence of electrostatic force in SARS-CoV N protein C-terminus self-association. Gel shift assay results revealed that the SARS-CoV N protein C-terminus is also able to associate with nucleic acids and residues 363-382 are the responsible interaction partner, demonstrating that this fragment might involve genomic RNA binding sites. The fact that nucleic acid binding could promote the SARS-CoV N protein C-terminus to form high-order oligomers implies that the oligomeric SARS-CoV N protein probably combines with the viral genomic RNA in triggering long nucleocapsid formation.

Amino Acid Sequence↗

PubMed2006

SHP-2 phosphatase is required for hematopoietic cell transformation by Bcr-Abl.

SHP-2 phosphatase forms a stable protein complex with and is heavily tyrosine-phosphorylated by the oncogenic tyrosine kinase Bcr-Abl. However, the role of SHP-2 in Bcr-Abl-mediated leukemogenesis is unclear. In the present report, we provide evidence that SHP-2 is required for hematopoietic cell transformation by Bcr-Abl. In vitro biological effects of Bcr-Abl transduction were diminished in SHP-2Delta/Delta hematopoietic cells, and the leukemic potential of Bcr-Abl-transduced SHP-2Delta/Delta cells in recipient animals was compromised. Further analyses showed that Bcr-Abl protein (p210) was degraded, and its oncogenic signaling was greatly decreased in SHP-2Delta/Delta cells. Treatment with proteasome inhibitors or reintroduction of SHP-2 restored p210 level in Bcr-Abl-transduced SHP-2Delta/Delta cells. Subsequent investigation revealed that SHP-2 interacted with heat shock protein 90, an important chaperone protein protecting p210 from proteasome-mediated degradation. The role of SHP-2 in the stability of p210 is independent of its catalytic activity. Blockade of SHP-2 expression in p210-expressing cells by antisense or small-interfering RNA approaches decreased p210 level, causing cell death. Inhibition of SHP-2 enzymatic activity by overexpression of catalytically inactive SHP-2 mutant did not destabilize p210 but enhanced serum starvation-induced apoptosis, suggesting that SHP-2 also plays an important role in downstream signaling of p210 kinase. These studies identified a novel function of SHP-2 and suggest that SHP-2 might be a useful target for controlling Bcr-Abl-positive leukemias.

Animals↗

PubMed2006

Increased visfatin messenger ribonucleic acid and protein levels in adipose tissue and adipocytes in women with polycystic ovary syndrome: parallel increase in plasma visfatin.

CONTEXT: Polycystic ovary syndrome (PCOS) is a multifaceted metabolic disease linked with insulin resistance (IR) and obesity. Recent studies have shown that plasma levels of the insulin-mimetic adipokine visfatin increase with obesity. Currently, no data exist on the relative expression of visfatin in either plasma or adipose tissue of PCOS women. OBJECTIVES: We investigated the mRNA expression of visfatin from sc and omental (om) adipose tissue and sc adipocytes in women with PCOS compared with matched normal women, as well as visfatin protein in adipose tissue; plasma visfatin was also assessed. DESIGN: Real-time RT-PCR and Western blotting were used to assess the relative mRNA and protein expression of visfatin. Biochemical measurements were performed. RESULTS: There was significant up-regulation of visfatin mRNA in both sc (P < 0.05) and om (P < 0.05) adipose tissue of PCOS women, when compared with normal controls; these findings were also reflected in isolated sc adipocytes (PCOS > controls; P < 0.05). In addition to elevated plasma visfatin levels in women with PCOS (mean +/- sd, 30.2 +/- 10.4 vs. 11.2 +/- 6.2 ng/ml; P < 0.01) when compared with normal controls, visfatin protein levels were significantly greater in both sc and om adipose tissue of PCOS women (P < 0.05 and P < 0.01, respectively). CONCLUSIONS: The precise reason for the up-regulation of visfatin seen in women with PCOS, a proinflammatory state, is unknown. Additional studies are needed to clarify the potential role of visfatin in the pathophysiology of PCOS.

Adipocytes↗

PubMed2006

Identification of two novel DSRAD mutations in two Chinese families with dyschromatosis symmetrica hereditaria.

Dyschromatosis symmetrica hereditaria (DSH) is a hereditary skin disease characterized by the presence of hyperpigmented and hypopigmented macules on face and dorsal aspects of the extremities that appear in infancy or early childhood. Genetic studies have identified mutations in the double-stranded RNA-specific adenosine deaminase (DSRAD) gene, encoding double-stranded RNA-specific adenosine deaminase, to be responsible for this disorder. Here, we report two novel mutations c.2116 G > A (E706K) and c.2848 C > T (Q950X) in the DSRAD gene identified in two Chinese pedigrees with DSH. This study should be useful for genetic counseling and prenatal diagnosis for affected families and in expanding the database on DSRAD gene mutations in DSH.

Adenosine Deaminase↗

PubMed2006

Helicobacter pylori acyl carrier protein: expression, purification, and its interaction with beta-hydroxyacyl-ACP dehydratase.

Acyl carrier protein (ACP) is an essential component in the type II fatty acid biosynthesis (FAS II) process and is responsible for the acyl group transfer within a series of related enzymes. In this work, the ACP from Helicobacter pylori strain SS1 was cloned and the gene sequence of Hpacp was deposited in the GenBank database (Accession No.: AY904356). Two forms of HpACP (apo, holo) were successfully purified and characterized. The thermal stability of these two forms was quantitatively investigated by CD spectral analyses. The results revealed that the holo-HpACP was more stable than apo-HpACP according to the transition midpoint temperature(Tm). Moreover, the interaction of HpACP with the related enzyme (beta-hydroxyacyl-ACP dehydratase, HpFabZ) was determined by GST-pull down assay and surface plasmon resonance (SPR) technique in vitro, the results showed that HpACP displays a strong binding affinity to HpFabZ (KD=1.2 x 10(-8)M). This current work is hoped to supply useful information for better understanding the ACP features of Helicobacter pylori SS1 strain.

Acyl Carrier Protein↗

PubMed2006

Adsorption of polycyclic aromatic hydrocarbons at the air-water interface: molecular dynamics simulations and experimental atmospheric observations.

Adsorption of benzene, naphthalene, anthracene, and phenanthrene at the aqueous surface is investigated by means of molecular dynamics simulations. Potentials of mean force, i.e., free energy profiles obtained when moving the studied molecules across an aqueous slab were evaluated. In all cases, deep surface free energy minima, corresponding to orders of magnitude of surface enhancement of the aromatic molecule, were located. This enhancement, which increases with the size of the solute, points to the importance of the aqueous surface for the chemistry of polycyclic aromatic hydrocarbons (PAHs). Supporting evidence in the atmospheric environment related to the heterogeneous chemistry of PAHs on water droplets and planar surfaces is summarized. There is good agreement between the hydration free energies computed from MD calculations and the experimentally determined values. Data pertaining to the importance of the air-water interface in the adsorption and transport of PAHs on micron sized water droplets are described. The relevant data on adsorption and reaction (ozonation and photochemical) at the air-water interface of planar surfaces and droplets are also summarized.

Adsorption↗

PubMed2006

A family of diverse Cul4-Ddb1-interacting proteins includes Cdt2, which is required for S phase destruction of the replication factor Cdt1.

Cul4 E3 ubiquitin ligases contain the cullin 4 scaffold and the triple beta propeller Ddb1 adaptor protein, but few substrate receptors have been identified. Here, we identify 18 Ddb1- and Cul4-associated factors (DCAFs), including 14 containing WD40 repeats. DCAFs interact with multiple surfaces on Ddb1, and the interaction of WD40-containing DCAFs with Ddb1 requires a conserved "WDXR" motif. DCAF2/Cdt2, which is related to S. pombe Cdt2, functions in Xenopus egg extracts and human cells to destroy the replication licensing protein Cdt1 in S phase and after DNA damage. Depletion of human Cdt2 causes rereplication and checkpoint activation. In Xenopus, Cdt2 is recruited to replication forks via Cdt1 and PCNA, where Cdt1 ubiquitylation occurs. These studies uncover diverse substrate receptors for Cul4 and identify Cdt2 as a conserved component of the Cul4-Ddb1 E3 that is essential to destroy Cdt1 and ensure proper cell cycle regulation of DNA replication.

Adaptor Proteins, Signal Transducing↗