Biomedical subjects

Jun Song

Publications and source records attributed to Jun Song.

At least 19 recordsLinked to original sources

PubMed2006

Cyclophilin a protects Peg3 from hypermethylation and inactive histone modification.

Imprinted genes are expressed from only one of the parental alleles and are marked epigenetically by DNA methylation and histone modifications. Disruption of normal imprinting leads to abnormal embryogenesis, certain inherited diseases, and is associated with various cancers. In the context of screening for the gene(s) responsible for the alteration of phenotype in cyclophilin A knockdown (CypA-KD) P19 cells, we observed a silent paternally expressed gene, Peg3. Treatment of CypA-KD P19 cells with the DNA demethylating agent 5-aza-dC reversed the silencing of Peg3 biallelically. Genomic bisulfite sequencing and methylation-specific PCR revealed DNA hypermethylation in CypA-KD P19 cells, as the normally unmethylated paternal allele acquired methylation that resulted in biallelic methylation of Peg3. Chromatin immunoprecipitation assays indicated a loss of acetylation and a gain of lysine 9 trimethylation in histone 3, as well as enhanced DNA methyltransferase 1 and MBD2 binding on the cytosine-guanine dinucleotide (CpG) islands of Peg3. Our results indicate that DNA hypermethylation on the paternal allele and allele-specific acquisition of histone methylation leads to silencing of Peg3 in CypA-KD P19 cells. This study is the first demonstration of the epigenetic function of CypA in protecting the paternal allele of Peg3 from DNA methylation and inactive histone modifications.

Alleles↗

PubMed2006

Genome-wide analysis of estrogen receptor binding sites.

The estrogen receptor is the master transcriptional regulator of breast cancer phenotype and the archetype of a molecular therapeutic target. We mapped all estrogen receptor and RNA polymerase II binding sites on a genome-wide scale, identifying the authentic cis binding sites and target genes, in breast cancer cells. Combining this unique resource with gene expression data demonstrates distinct temporal mechanisms of estrogen-mediated gene regulation, particularly in the case of estrogen-suppressed genes. Furthermore, this resource has allowed the identification of cis-regulatory sites in previously unexplored regions of the genome and the cooperating transcription factors underlying estrogen signaling in breast cancer.

Adaptor Proteins, Signal Transducing↗

PubMed2006

gp120-independent HIV infection of cells derived from the female reproductive tract, brain, and colon.

The infection of CD4 cells may have significant involvement in the transmission and long-term persistency of HIV. Using HIV clones carrying the enhanced green fluorescent protein (EGFP), we infected epithelial and glioneuronal cell lines derived from the female reproductive tract, brain, colon, and intestine. HIV infection was quantified by counting EGFP-positive cells. Infection was quantified in cell lines from the female reproductive tract, brain tissue, and colon tissue (0.36%-3.15%). Virus replicated in the infected cells and the progeny virus were infectious for CD4 cells, HeLa-CD4, and CEM T lymphocytes. Furthermore, we found that infection of these epithelial and brain cell lines is independent of gp120. The results from the infection of CD4 epithelial cells suggest that HIV can traverse epithelial cell layers by infecting them through a gp120-independent mechanism. Infection of glial and neuronal cell lines suggests that HIV infection of these cells is a probable mechanism for HIV pathogenicity in the brain and a possible cause for persistent infection in patients.

Brain↗

PubMed2006

IGF-1 protects intestinal epithelial cells from oxidative stress-induced apoptosis.

BACKGROUND: Reactive oxygen species (ROS) are involved in the pathogenesis of necrotizing enterocolitis (NEC) in premature infants. We have recently found that activation of multiple cellular signaling transduction pathways occurs during ROS-induced intestinal cell apoptosis; the phosphatidylinositol 3-kinase (PI3-K) pathway plays an anti-apoptotic role during this process. Insulin-like growth factor (IGF)-1 activates PI3-K pathway to promote cell survival; however, the effects of IGF-1 treatment during gut injury are not clearly defined. The purpose of this study was to determine whether IGF-1 protects intestinal cells from ROS-induced apoptosis. MATERIALS AND METHODS: Rat intestinal epithelial (RIE)-1 cells were treated with either IGF-1 (100 nm), hydrogen peroxide (H2O2; 500 microm), or combination. Western blotting was performed to assess phosphorylation of Akt, a downstream effector of PI3-K. Cell Death Detection ELISA, DCHF, and JC-1 assays were performed to demonstrate protective effects of IGF-1. Wortmannin, an inhibitor of PI3-K, was used to show PI3-K-dependent mechanism of action for IGF-1. RESULTS: H2O2 treatment resulted in increased intestinal epithelial cell apoptosis with intracellular ROS generation and mitochondrial membrane depolarization; IGF-1 pre-treatment attenuated this response without affecting ROS production. H2O2-induced phosphorylation of Akt was further increased with IGF-1 treatment; wortmannin abolished these effects in RIE-1 cells. CONCLUSIONS: PI3-K pathway is activated during ROS-induced intestinal epithelial cell injury; IGF-1 exerted an anti-apoptotic effect during this response by PI3-K activation. A better understanding of the exact role of IGF-1-mediated activation of PI3-K may allow us to facilitate the development of novel therapy against NEC.

Animals↗

PubMed2006

CEAS: cis-regulatory element annotation system.

The recent availability of high-density human genome tiling arrays enables biologists to conduct ChIP-chip experiments to locate the in vivo-binding sites of transcription factors in the human genome and explore the regulatory mechanisms. Once genomic regions enriched by transcription factor ChIP-chip are located, genome-scale downstream analyses are crucial but difficult for biologists without strong bioinformatics support. We designed and implemented the first web server to streamline the ChIP-chip downstream analyses. Given genome-scale ChIP regions, the cis-regulatory element annotation system (CEAS) retrieves repeat-masked genomic sequences, calculates GC content, plots evolutionary conservation, maps nearby genes and identifies enriched transcription factor-binding motifs. Biologists can utilize CEAS to retrieve useful information for ChIP-chip validation, assemble important knowledge to include in their publication and generate novel hypotheses (e.g. transcription factor cooperative partner) for further study. CEAS helps the adoption of ChIP-chip in mammalian systems and provides insights towards a more comprehensive understanding of transcriptional regulatory mechanisms. The URL of the server is http://ceas.cbi.pku.edu.cn.

Binding Sites↗

PubMed2006

Asymmetric Friedel-crafts reaction of indoles with imines by an organic catalyst.

In this communication, we report an asymmetric Friedel-Crafts reaction of indoles with imines catalyzed by a bifunctional cinchona alkaloid catalyst. This is the first efficient organocatalytic asymmetric Friedel-Crafts reaction of indoles with imines. This reaction is operationally simple and, unprecedentedly, affords high enantioselectivity for a wide range of indoles and both aryl and alkyl imines. This establishes a direct, convergent, and versatile approach to optically active 3-indolyl methanamines, a structural motif embedded in numerous indole alkaloids and synthetic indole derivatives.

Catalysis↗

PubMed2006

The Mannich reaction of malonates with simple imines catalyzed by bifunctional cinchona alkaloids: enantioselective synthesis of beta-amino acids.

We describe the first efficient, direct asymmetric Mannich reactions with malonates and N-Boc aryl and alkyl imines by cooperative hydrogen-bonding catalysis with a cinchona alkaloid bearing a thiourea functionality. We have also extended the scope of this reaction to beta-ketoesters. The synthetic value of this new reaction is demonstrated in the establishment of a convergent enantioselective route toward the biologically important beta-amino acids under mild and air- and moisture-tolerant conditions.

Amino Acids↗

PubMed2006

Protein kinase D protects against oxidative stress-induced intestinal epithelial cell injury via Rho/ROK/PKC-delta pathway activation.

Protein kinase D (PKD) is a novel protein serine kinase that has recently been implicated in diverse cellular functions, including apoptosis and cell proliferation. The purpose of our present study was 1) to define the activation of PKD in intestinal epithelial cells treated with H2O2, an agent that induces oxidative stress, and 2) to delineate the upstream signaling mechanisms mediating the activation of PKD. We found that the activation of PKD is induced by H2O2 in both a dose- and time-dependent fashion. PKD phosphorylation was attenuated by rottlerin, a selective PKC-delta inhibitor, and by small interfering RNA (siRNA) directed against PKC-delta, suggesting the regulation of PKD activity by upstream PKC-delta. Activation of PKD was also blocked by a Rho kinase (ROK)-specific inhibitor, Y-27632, as well as by C3, a Rho protein inhibitor, demonstrating that the Rho/ROK pathway also mediates PKD activity in intestinal cells. In addition, H2O2-induced PKC-delta phosphorylation was inhibited by C3 treatment, further suggesting that PKC-delta is downstream of Rho/ROK. Interestingly, H2O2-induced intestinal cell apoptosis was enhanced by PKD siRNA. Together, these results clearly demonstrate that oxidative stress induces PKD activation in intestinal epithelial cells and that this activation is regulated by upstream PKC-delta and Rho/ROK pathways. Importantly, our findings suggest that PKD activation protects intestinal epithelial cells from oxidative stress-induced apoptosis. These findings have potential clinical implications for intestinal injury associated with oxidative stress (e.g., necrotizing enterocolitis in infants).

Animals↗

PubMed2006

A simple protocol for protein extraction of recalcitrant fruit tissues suitable for 2-DE and MS analysis.

Fruit tissues are considered recalcitrant plant tissue for proteomic analysis. Three phenol-free protein extraction procedures for 2-DE were compared and evaluated on apple fruit proteins. Incorporation of hot SDS buffer, extraction with TCA/acetone precipitation was found to be the most effective protocol. The results from SDS-PAGE and 2-DE analysis showed high quality proteins. More than 500 apple polypeptides were separated on a small scale 2-DE gel. The successful protocol was further tested on banana fruit, in which 504 and 386 proteins were detected in peel and flesh tissues, respectively. To demonstrate the quality of the extracted proteins, several protein spots from apple and banana peels were cut from 2-DE gels, analyzed by MS and have been tentatively identified. The protocol described in this study is a simple procedure which could be routinely used in proteomic studies of many types of recalcitrant fruit tissues.

Amino Acid Sequence↗

PubMed2006

Caught in the act? Prevalence, predictors, and consequences of physician detection of unannounced standardized patients.

Objective. To examine the prevalence, predictors, and consequences of physician detection of unannounced standardized patients (SPs) in a study of the impact of direct-to-consumer advertising on treatment for depression. Data Sources. Eighteen trained SPs were randomly assigned to conduct 298 unannounced audio-recorded visits with 152 primary care physicians in three U.S. cities between May 2003 and May 2004. Study Design. Randomized controlled trial using SPs. SPs portrayed six roles, created by crossing two clinical conditions (major depression or adjustment disorder) with three medication request scripts (brand-specific request, general request for an antidepressant, or no request). Data Collection. Within 2 weeks following the visit, physicians completed a form asking whether they "suspected" conducting an office visit with an SP during the past 2 weeks; 296 (99 percent) detection forms were returned. Physicians provided contextual data, a Clinician Background Questionnaire. SPs filled in a Standardized Patient Reporting Form for each visit and returned all written prescriptions and medication samples to the laboratory. Principal Findings. Depending on the definition, detection rates ranged from 5 percent (unambiguous detection) to 23.6 percent (any degree of suspicion) of SP visits. In 12.8 percent of encounters, physicians accurately detected the SP before or during the visit but they only rarely believed their suspicions affected their clinical behavior. In random effects logistic regression analyses controlling for role, actor, physician, and practice factors, suspected visits occurred less frequently in HMO settings than in solo practice settings (p<.05). Physicians more frequently referred SPs to mental health professionals when visits aroused high suspicion (p<.05). Conclusions. Trained actors portrayed patient roles conveying mood disorders at low levels of detection. There was some evidence for differential treatment of detected standardized patients by physicians with regard to referrals but not antidepressant prescribing or follow-up recommendations. Systematic assessment of detection is recommended when SPs are used in studies of clinical process and quality of care.

Adjustment Disorders↗

PubMed2006

Dynamic IMRT treatments of sinus region tumors: comparison of Monte Carlo calculations with treatment planning system calculations and ion chamber measurements.

Results are presented comparing Monte Carlo (MC) calculations for dynamic IMRT treatments of tumors in the sinus region with Eclipse treatment planning system dose calculations, and ion chamber measurements. The EGS4nrc MC code, BEAMnrc, was commissioned to simulate a Varian 21Ex Linac for both open and IMRT fields. The accuracy of the simulation for IMRT plans was evaluated using a head phantom by comparing MC, Eclipse, TLD results, and ion chamber in solid water phantom measurements. The MC code was then used to simulate dose distributions for five patients who were treated using dynamic IMRT for tumors in the sinus region. The results were compared with absolute and relative dose distributions calculated using Eclipse (pencil beam, modified-Batho inhomogeneity correction). Absolute dose differences were also compared with ion chamber results. Comparison of the doses calculated on the head phantom using MC, compared with Eclipse, ion chamber, and TLD measurements showed differences of -3.9%, -1.4%, and -2.0%, respectively (MC is colder). Relative dose distributions for the patient plans calculated using MC agreed well with those calculated using Eclipse with respect to targets and critical organs, indicating the modified-Batho correction is adequate. Average agreement for mean absolute target doses between MC and Eclipse was -3.0 +/-; 2.3% (1 s.d.). Agreement between ion chamber and Eclipse for these patients was -2.2 +/- 1.9%, compared with 0.2 +/- 2.0% for all head and neck IMRT patients. When Eclipse doses were corrected based on ion chamber results, agreement between MC and Eclipse was -0.7 +/- 2.0%, indicating a small systematic uncertainty in the doses calculated using the treatment planning system for this subset of patients.

Head and Neck Neoplasms↗

PubMed2006

Effects of surface roughness on the performance of an etched diffraction grating demultiplexer.

The fabrication tolerance of surface roughness on the performance [such as the insertion loss, the polarization-dependent loss (PDL), and the chromatic dispersion] of an etched diffraction grating demultiplexer is analyzed by using an accurate method of moments. The results show that both the insertion loss and the chromatic dispersion rapidly increase as the roughness of the grating facets increases. Appropriate residual roughness of the shaded facets can reduce the PDL of the demultiplexer, and the mechanism for the existence of an optimal residual roughness is explained.

Journal Article↗

PubMed2006

Sidelobe suppression design of etched diffraction grating demultiplexers using optimized air trenches in front of each output waveguide.

An etched diffraction grating (EDG) demultiplexer with high sidelobe suppression is designed. Sidelobes resulting from two adjacent wavelengths are suppressed by etching two optimized rectangular air trenches in front of each output waveguide that can induce large resonance loss in the adjacent wavelength but have little influence on the operational wavelength. The designed EDG demultiplexer can suppress crosstalk to less than 50 dB in theory.

Journal Article↗

PubMed2006

[Set clinical therapeutic guideline in traditional medicine urgently].

Traditional medicine (TM) has been practiced in China for several thousand years. To better standardize the behaviors of medical staff of TM, rapidly improve their professional level, effectively and reasonably distribute TM resources, decrease the unnecessary application of medical care and suppress the rapidly increasing medical expenses, it is necessary to urgently set clinical therapeutic guideline in TM under the direction of evidence based medicine (EBM). The article also discusses the main existing problems and their solutions in setting clinical therapeutic guideline in TM.

China↗

PubMed2005

Involvement of claudin-7 in HIV infection of CD4(-) cells.

BACKGROUND: Human immunodeficiency virus (HIV) infection of CD4(-) cells has been demonstrated, and this may be an important mechanism for HIV transmission. RESULTS: We demonstrated that a membrane protein, claudin-7 (CLDN-7), is involved in HIV infection of CD4(-) cells. A significant increase in HIV susceptibility (2- to 100-fold) was demonstrated when CLDN-7 was transfected into a CD4(-) cell line, 293T. In addition, antibodies against CLDN-7 significantly decreased HIV infection of CD4(-) cells. Furthermore, HIV virions expressing CLDN-7 on their envelopes had a much higher infectivity for 293T CD4(-) cells than the parental HIV with no CLDN-7. RT-PCR results demonstrated that CLDN-7 is expressed in both macrophages and stimulated peripheral blood leukocytes, suggesting that most HIV virions generated in infected individuals have CLDN-7 on their envelopes. We also found that CLDN-7 is highly expressed in urogenital and gastrointestinal tissues. CONCLUSION: Together these results suggest that CLDN-7 may play an important role in HIV infection of CD4(-) cells.

Cell Line↗

PubMed2005

Catalytic enantioselective C-C bond forming conjugate additions with vinyl sulfones.

In this communication, we describe the development of the first highly enantioselective catalytic conjugate addition to vinyl sulfones. Promoted by readily accessible organocatalysts derived from C6'-OH cinchona alkaloid derivatives and under mild, air- and moisture-tolerant conditions, conjugate additions of a wide range of alpha-cyanoacetates bearing either an alpha-aryl or an alpha-alkyl substituent to vinyl sulfones proceeded in excellent enantioselectivity and high yield. Consequently, this efficient and operationally simple enantioselective C-C bond forming conjugate addition provides a new and useful approach for the enantioselective construction of all-carbon quaternary stereocenters.

Carbon↗

PubMed2005

Molecular cloning of cDNA for SPase, a monkey cathepsin L orthologue.

SPase is a cysteine protease isolated from an African green monkey kidney cell line, CV-1, and has selective cleavage activity toward transcription factor SP-1 and retinoblastoma susceptibility gene product RB. In this study, a cDNA encoding SPase was cloned from a cDNA library prepared from CV-1 cells. The cDNA clone encodes 333 amino acids and is 96.5% identical to human cathepsin L at the nucleotide and amino acid sequence levels. SPase appears to be translated as a preproenzyme based on the comparison between the deduced amino acid sequence and the N-terminal sequence of the purified enzyme. Northern blot analysis exhibited the considerably higher expression of SPase in CV-1 cells compared with COS-1 cells, showing a good correlation with enzymatic activity in these cell lines. Bacterially expressed SPase protein exhibited proteolytic activity toward SP-1 and RB proteins. These observations suggest that SPase is a monkey cathepsin L orthologue.

Amino Acid Sequence↗

PubMed2005

The impact of pediatric intensive care unit volume on mortality: a hierarchical instrumental variable analysis.

OBJECTIVE: To evaluate the relation between annual pediatric intensive care unit (PICU) admission volume and mortality. DESIGN: Nonconcurrent cohort design. SETTING: Pediatric patients included in the most currently available research database from the Pediatric Intensive Care Unit Evaluations (PICUEs). PATIENTS: A total of 34,880 consecutive pediatric admissions to a contemporary volunteer sample of 15 U.S. PICUs. MEASUREMENTS AND MAIN RESULTS: We conducted an instrumental variable analysis and adjusted for similarities between patients admitted to different PICUs using mixed-effects, hierarchical techniques. Case mix and severity of illness was adjusted for using patient-level data and the Pediatric Risk of Mortality, version III (PRISM III). On average, admission to higher-volume PICUs was associated with lower severity-adjusted mortality (odds ratio = 0.68 per 100 patient increase in volume; 95% confidence interval: 0.52-0.89) when volume was analyzed as a linear term; however, when PICU volume was analyzed as a quadratic term, we found the lowest severity-adjusted mortality rates among PICUs with annual admission volumes between 992 and 1,491. Furthermore, lower severity-adjusted mortality rates were primarily found among patients with less than a 10% PRISM III predicted risk of mortality. CONCLUSIONS: Although there is an association between lower severity-adjusted mortality among higher volume PICUs, our data suggest that best outcomes are among mid- to large-sized PICUs. These data support minimum annual admission criteria for PICUs but raise the concern that PICUs with very high annual admission volumes may operate beyond an ideal capacity.

Child↗