Biomedical subjects

Yan Wang

Publications and source records attributed to Yan Wang.

At least 55 records · Page 3Linked to original sources

PubMed2006

Phase II trial of sequential gefitinib after minor response or partial response to chemotherapy in Chinese patients with advanced non-small-cell lung cancer.

BACKGROUND: Basic research of gefitinib (Iressa, ZD1839) has demonstrated the combination effects of gefitinib and chemotherapy were sequence-dependent. To evaluate the efficacy of sequential administration of gefitinib following a minor response or partial response to two to three cycles of chemotherapy, a phase II clinical trial was done in Chinese patients with advanced non-small-cell lung cancer (NSCLC). METHODS: Thirty-three consecutive patients with advanced NSCLC that had been pretreated with at least one chemotherapeutic regimen and were responding to chemotherapy following 2 to 3 cycles of treatment, entered the trial from May 2004 to February 2006. Patients received gefitinib at an oral dose of 250 mg once daily for 4 weeks. RESULTS: Thirty-three patients were evaluable for response and toxicity. The objective response rate was 24.2% (8 of 33) (95% CI, 11% to 42%). The symptom improvement rate was 54.5% (18 of 33) (95% CI, 41% to 69%). The median duration of response was 7 months (95%CI, 4.0 to 13.2 months). The median time to disease progression (TTP) was 6.5 months (95%CI, 0.7 to 16.6 months). The median overall survival time (OS) was 9.8 months (range, 2.1 to 18.0 months), and the actuarial 1-year survival was 36.4%. Toxicity was relatively mild and included only one patient (3.0%) with grade 4 diarrhea, 1 (3.0%) with grade 3 rash, 1 (3.0%) with grade 3 nausea, and 1 with grade 3 vomiting (3.0%). CONCLUSION: Preliminary results suggest that sequential administration of gefitinib following a response to chemotherapy may be beneficial for Chinese patients with advanced NSCLC. Further randomized clinical trials are needed.

Adenocarcinoma↗

PubMed2006

Appropriate range of quality control limit for wet deposition monitoring.

Precipitation chemistry programs in different regions of the world have different quality control limits for ion balance parameter IPD in wet deposition monitoring (R). The range of R values was calculated by assuming sample rainwater models in this paper. It was found that R was influenced by the inorganic ion types, total ion concentrations (IS) and the accuracy of the measurements (a(i)). R was defined and calculated as a function of a(i) and ion concentration C(i). R values of different types of wet deposition (including ocean type, continent type and combined oceanic and continental deposition) were different. There were also differences between the samples of the same type if the samples had different total ion concentrations. When IS>100 microeq/L, the ranges of R of ocean type deposition, continent type deposition and combined oceanic and continental deposition were 5 approximately 7%, 5 approximately 9% and 5 approximately 11%, respectively. When IS<50 microeq/L, if a(i) was 100%, the range of R was 33 approximately 71% because of the lower accuracy. It was also found that R of each criterion was in the range of R as calculated in this paper when IS>or=50 microeq/L, but when IS<50 microeq/L, the criteria varied greatly in their R values.

Quality Control↗

PubMed2006

Effect of RNA interference targeting human telomerase reverse transcriptase on telomerase and its related protein expression in nasopharyngeal carcinoma cells.

OBJECTIVE: Analysis of the correlation between telomerase and the expression of its related proteins may provide insight into the molecular mechanism of nasopharyngeal carcinogenesis. We investigated the effect of short hair pin ribonucleic acid (RNA) specific for human telomerase reverse transcriptase messenger RNA on the expression of the proteins c-myc (the transcription factor c-myc is a shortlived nuclear phospho-protein involved in cell proliferation and differentiation, belongs to the myc family), proliferating cell nuclear antigen and Caspase-3 in nasopharyngeal carcinoma cells. METHODS: Short hairpin RNA expression vectors targeting the messenger RNA of human telomerase reverse transcriptase were constructed. Cells were treated with the short hairpin RNA expression vectors targeting human telomerase reverse transcriptase or vectors that included mismatched short hairpin RNA, and telomerase activity was measured by telomeric repeat amplification enzyme-linked immunosorbent assay. Cell viability was examined using the 3-(4,5-dimethyl thizol-2-yl) 2,5-diphenyl tetrazolium bromide assay. The expression of the three proteins (c-myc, proliferating cell nuclear antigen and Caspase-3) was determined by Western blotting. RESULTS: Short hairpin RNA specific for human telomerase reverse transcriptase messenger RNA significantly inhibited telomerase activity. In addition, the expression of and proliferating cell nuclear antigen were both inhibited, while the expression of Caspase-3 was up-regulated. CONCLUSIONS: Our results suggest that short hairpin RNA directed against human telomerase reverse transcriptase inhibits cell viability by regulating telomerase activity and its related proteins expression in nasopharyngeal carcinoma cells. Therefore, RNA interference technology may be a promising strategy for the treatment of nasopharyngeal cancer.

Carcinoma, Squamous Cell↗

PubMed2006

Relation between plasma oxLDL antibodies and oxLDL in the circulation.

OBJECTIVES: To investigate the possible relationship between circulating oxLDL and oxLDL Ab concentrations in order to better understand the role of oxLDL Ab in atherosclerosis. DESIGN: In a cross-sectional study of 86 patients undergoing ultrasonographic scanning of the carotid artery, concentration of circulating oxLDL and oxLDL Ab were determined by ELISA. For multivariate analysis, we also measured many conventional cardiovascular risk factors. Spearman's rank correlation test and chi-square test were used to evaluate the correlation between circulating oxLDL and oxLDL Ab. A stepwise multiple regression analysis and Logistic regression analysis were used to study the influencing factors. RESULTS: There was no linear correlation between circulating oxLDL and oxLDL Ab. Circulating oxLDL was influenced by HDL, systolic blood pressure and body mass index, while only TC was independent factor associating with oxLDL Ab. CONCLUSIONS: The present study showed that oxLDL was present at a low concentration in the circulation, and that plasma oxLDL had no linear correlation with oxLDL antibodies. However, the issue still needs further study.

Adult↗

PubMed2006

Increased brachial-ankle pulse wave velocity is associated with impaired endothelial function in patients with coronary artery disease.

BACKGROUND: Pulse wave velocity and flow-mediated vasodilation (FMD) are widely used as noninvasive modalities for evaluating atherosclerosis. However, it is not known whether pulse wave velocity is related to FMD in patients with coronary artery disease (CAD). Therefore, the present study was designed to investigate the alteration in brachial-ankle pulse wave velocity (baPWV) and endothelial function in CAD patients. METHODS: Thirty-three patients with CAD and thirty control subjects were recruited for this study. baPWV was measured non-invasively using a VP 1000 automated PWV/ABI analyzer (PWV/ABI, Colin Co. Ltd., Komaki, Japan). Endothelial function as reflected by FMD in the brachial artery was assessed with a high-resolution ultrasound device. RESULTS: baPWV was increased in CAD patients compared with control subjects [(1756.1 +/- 253.1) cm/s vs (1495.3 +/- 202.3) cm/s, P < 0.01]. FMD was significantly reduced in CAD patients compared with control subjects [(5.2 +/- 2.1)% vs (11.1 +/- 4.4)%, P < 0.01]. baPWV correlated with FMD (r = -0.68, P < 0.001). The endothelium-independent vasodilation induced by sublingual nitroglycerin in the brachial artery was similar in the CAD group compared with the control group. CONCLUSIONS: CAD is associated with increased baPWV and endothelial dysfunction. Increased baPWV parallels diminished endothelial function. Our data therefore suggest that baPWV can be used as a noninvasive surrogate index in clinical evaluation of endothelial function.

Aged↗

PubMed2006

Fragile X mental retardation protein controls trailer hitch expression and cleavage furrow formation in Drosophila embryos.

During the cleavage stage of animal embryogenesis, cell numbers increase dramatically without growth, and a shift from maternal to zygotic genetic control occurs called the midblastula transition. Although these processes are fundamental to animal development, the molecular mechanisms controlling them are poorly understood. Here, we demonstrate that Drosophila fragile X mental retardation protein (dFMRP) is required for cleavage furrow formation and functions within dynamic cytoplasmic ribonucleoprotein (RNP) bodies during the midblastula transition. dFMRP is observed to colocalize with the cytoplasmic RNP body components Maternal expression at 31B (ME31B) and Trailer Hitch (TRAL) in a punctate pattern throughout the cytoplasm of cleavage-stage embryos. Complementary biochemistry demonstrates that dFMRP does not associate with polyribosomes, consistent with their reported exclusion from many cytoplasmic RNP bodies. By using a conditional mutation in small bristles (sbr), which encodes an mRNA nuclear export factor, to disrupt the normal cytoplasmic accumulation of zygotic transcripts at the midblastula transition, we observe the formation of giant dFMRP/TRAL-associated structures, suggesting that dFMRP and TRAL dynamically regulate RNA metabolism at the midblastula transition. Furthermore, we show that dFMRP associates with endogenous tral mRNA and is required for normal TRAL protein expression and localization, revealing it as a previously undescribed target of dFMRP control. We also show genetically that tral itself is required for cleavage furrow formation. Together, these data suggest that in cleavage-stage Drosophila embryos, dFMRP affects protein expression by controlling the availability and/or competency of specific transcripts to be translated.

Animals↗

PubMed2006

Silencing stathmin gene expression by survivin promoter-driven siRNA vector to reverse malignant phenotype of tumor cells.

Stathmin gene overexpression has been shown to play an important role in maintenance of malignant phenotype in tumor cells, and the blocking efficacy and tumor specificity of this target has been concerned in clinical trails. In this report, we designed survivin promoter-driven siRNA eukaryotic expression vector that expressed the small interfering RNA targeting stathmin gene to selectively knock down the stathmin gene expression in two different kinds of tumor cell lines while sparing normal cell lines. The therapeutic potential of this recombinant vector was tested in human cervical cancer Hela cells and osteosarcoma SSOP-9607 cells, and in human umbilical vein endothelial cell line ECV304 cells as control. The siRNA vector- transfected Hela cells and SSOP-9607 cells revealed marked inhibition of stathmin expression and a dramatic growth inhibition comparing with ECV304 cells, parental-vector transfected cells and untransfected cells. Cell cycle analysis of siRNA vector transfected tumor cells by Flow Cytometry showed G(2)/M phase block, while morphologic analysis by TURNEL staining method showed marked increase of apoptosis. Our study indicates that survivin gene promoter-driven stathmin siRNA expression vector may have potential use in tumor gene therapy with targeted tumor gene silencing effect.

Apoptosis↗

PubMed2006

Clinical report of cervical arthroplasty in management of spondylotic myelopathy in Chinese.

OBJECTIVES: To investigate clinical effects and manual operational point of Bryan cervical disc prosthesis in Chinese, to observe the stability and range of movement (ROM) post-operatively. METHODS AND MATERIALS: From 2003,12 to 2005,12, Bryan disc prosthesis replacement applied in 83 cases (102 levels) of cervical spondylotic myelopathy (CSM) after anterior decompression in our hospital. Clinical (JOA grade and Odom's scale) and radiological (X-ray of flexion, extension; left and right bending position) follow-up was performed. Systemic radiographic study about stability and ROM of replaced level post operationally were measured. CT or MRI scans were applied in all cases to evaluate the signs of the prosthesis deflexion and hetero-ossification in the replaced levels. RESULTS: At least 12 months follow-up were done in 65/83 of these patients. All of 83 patients were improved according to Odsm's scale. JOA score increased from average 8.7 to 15.5. There was no prosthesis subsidence. Replaced segment achieved stability and restored partial of normal ROM 4.73 degrees (3.7 degrees -5.9 degrees ) early postoperation and 8.12 degrees (5.8 degrees -13.6 degrees ) more than 12 months postoperation in flex and extension position. No obvious loss of lordosis was found. CT or MRI follow-up shows position deflexion of the prosthesis metal endplates (<1.5 mm) in 14/77 levels and (1.5-3 mm) in 4/77. heter-ossification was found in the replaced levels only in 2 cases. CONCLUSION: Byran cervical disc prosthesis restored motion to the level of the intact segment in flexion-extension and lateral bending in post-operative images. At the same time, it can achieve good anterior decompression treatment effect and immediate stability in replaced 1 or 2 levels, and which is a new choice for the treatment of CSM.

Journal Article↗

PubMed2006

Simultaneous determination of eight components in Radix Tinosporae by high-performance liquid chromatography coupled with diode array detector and electrospray tandem mass spectrometry.

High-performance liquid chromatography (HPLC) coupled with electrospray tandem mass spectrometry (ESI-MS-MS) and diode array detection (DAD) was used to identify and simultaneously determine eight major ingredients in Radix Tinosporae. The assay was performed on a Diamonsil C(18) analytical column with a gradient solvent system of A (water containing 0.2% formic acid, 20mM ammonium acetate) and B (methanol/acetonitrile=1/1, v/v). The 217, 248, 270 and 347 nm, respectively, were chosen as the monitoring wavelengths to determine four structural types of components, say columbin, phytoecdysteroids (including 20-hydroxyecdysone, 2-deoxy-20-hydroxyecdysone 3-O-beta-d-glucopyranoside and 2-deoxy-20-hydroxyecdysone), menisperine and protoberberine alkaloids (including columbamine, jatrorrhizine and palmatine). This method was validated in respect to precision, repeatability and accuracy, and was successfully applied to quantify the eight components in 39 batches of R. Tinosporae for quality control purpose. The results indicated that the proposed method could be readily utilized as a quality control method for traditional Chinese medicine (TCM).

Calibration↗

PubMed2006

Chitosan nanoparticle as gene therapy vector via gastrointestinal mucosa administration: results of an in vitro and in vivo study.

This study was designed to investigate the in vitro and in vivo transfection efficiency of chitosan nanoparticles used as vectors for gene therapy. Three types of chitosan nanoparticles [quaternized chitosan -60% trimethylated chitosan oligomer (TMCO-60%), C(43-45 KDa, 87%), and C(230 KDa, 90%)] were used to encapsulate plasmid DNA (pDNA) encoding green fluorescent protein (GFP) using the complex coacervation technique. The morphology, optimal chitosan-pDNA binding ratio and conditions for maximal in vitro transfection were studied. The in vivo transfection was conducted by feeding the chitosan/pDNA nanoparticles to 12 BALB/C-nu/nu nude mice. Both conventional and TMCO-60% could form stable nanoparticles with pDNA. The in vitro study showed the transfection efficiency to be in the following descending order: TMCO-60%>C(43-45 KDa, 87%)>C(230 KDa, 90%). TMCO-60% proved to be the most efficient and the optimal chitosan/pDNA ratio being 3.2:1. In vivo study showed most prominent GPF expression in the gastric and upper intestinal mucosa. GFP expression in the mucosa of the stomach and duodenum, jejunum, ileum, and large intestine were found, respectively, in 100%, 88.9%, 77.8% and 66.7% of the nude mice examined. TMCO-60%/pDNA nanoparticles had better in vitro and in vivo transfection activity than the other two, and with minimal toxicity, which made it a desirable non-viral vector for gene therapy via oral administration.

Administration, Oral↗

PubMed2006

Deletion of JAM-A causes morphological defects in the corneal epithelium.

Junctional adhesion molecule-A (JAM-A, JAM-1, F11R) is an Ig domain containing transmembrane protein that has been proposed to function in diverse processes including platelet activation and adhesion, leukocyte transmigration, angiogenesis, epithelial cell shape and endothelial cell migration although its function in vivo is less well established. In the mouse eye, JAM-A protein expression is first detected at 12.5 dpc in the blood vessels of the tunica vasculosa, while it is first detected in both the corneal epithelium and lens between 13.5 and 14.5 dpc. In the corneal epithelium, JAM-A levels remain appreciable throughout life, while JAM-A immunostaining becomes stronger in the lens as the animals age. Both the cornea and lens of mice lacking an intact JAM-A gene are transparent until at least a year of age, although the cells of the JAM-A null corneal epithelium are irregularly shaped. In wild-type mice, JAM-A protein is found at the leading edge of repairing corneal epithelial wounds, however, corneal epithelial wound repair was qualitatively normal in JAM-A null animals. In summary, JAM-A is expressed in the corneal epithelium where it appears to regulate cell shape.

Animals↗

PubMed2006

The mechanism of apoptosis induced by a novel thioredoxin reductase inhibitor in A549 cells: possible involvement of nuclear factor-kappaB-dependent pathway.

1,2-[bis(1,2-benzisoselenazolone-3(2H)-ketone)]ethane (BBSKE, PCT: CN02/00412), a novel thioredoxin reductase inhibitor previously synthesized in our lab, has been demonstrated to inhibit the growth of a variety of human cancer cells and to induce apoptosis. Here we report on the potential molecular mechanism of apoptosis induced by BBSKE in A549 cells. The treatment of BBSKE reduced the protein levels of Bcl-2, Bcl-xL, procaspase-9 and procaspase-3, and caused the release of cytochrome C from the mitochondria to the cytosol in a dose-dependent manner, suggesting the onset of mitochondria-dependent apoptosis. Through electrophoretic mobility shift assay (EMSA), the DNA-binding activity of nuclear factor-kappaB (NF-kappaB) was found to be attenuated after BBSKE treatment, accompanied by the diminution of the immunoprecipitated complex of thioredoxin and NF-kappaB in co-immunoprecipitation experiments. Meanwhile, the ratio of pIkappaB-alpha to IkappaB-alpha and the subcellular localization of p65 between cytoplasm and nucleus were not significantly altered by BBSKE treatment, as demonstrated in western analysis and immunocytochemistry assay. Furthermore, the mRNA levels of the NF-kappaB regulated anti-apoptosis genes Bcl-2, Bcl-xL, cIAP-2 and XIAP were decreased in a dose-dependent manner after BBSKE treatment. All the above observations suggest that BBSKE induce mitochondria-dependent apoptosis in A549 cells probably through suppressing the thioredoxin reductase-thioredoxin-NF-kappaB pathway.

Antineoplastic Agents↗

PubMed2006

Survey of the patients with cleft lip and palate in China who were funded for surgery by the Smile Train Program from 2000 to 2002.

BACKGROUND: Cleft lip (CL) and cleft palate (CP) are two of the most frequent congenital malformations. Many epidemiologic studies on this deformity have been conducted worldwide, often producing inconsistent results. This study assessed epidemiology and some genetic aspects of cleft lip and palate in a Chinese sample from the Smile Train Program and to compare with other methodologically sound surveys. METHODS: The general information, family history, classification of cleft and associated malformations of 8000 CL and CP surgery patients were analyzed. RESULTS: Of the 8000 cases, 7812 had complete data. The distribution of cleft types is 17.04% with CP, 23.39% with CL and 59.58% with cleft lip and palate (CLP). Unilateral clefts were more common than bilateral, with unilateral to bilateral ratios being 10.4:1 for CL, and 3.42:1 for CLP. The overall male:female ratio was 2.01:1. Left sided defects were more common than right sided regardless of sex, 1.90:1 for CL and 1.96:1 for CLP. CLP and CL were more common in males than in females with sex ratios (SR) of 2.88:1 and 1.85:1 respectively, whereas CP was more common in females with SR of 0.76:1. Associated malformations (2.89%), involved 29 CP cases, 41 CL and 156 CLP. The frequency of associated malformations in CLP (3.35%) was higher than CL (2.24%) and CP (2.22%) (P < 0.05). Patients with CP or CLP were born less often in the winter than in the summer (P < 0.05). A history of family members having clefts occurred in 6.84% of patients. The proportion of CLP cases (7.56%) was significantly higher than that of CL cases (5.64%) (P < 0.05). CONCLUSIONS: The different types of clefts appeared in the highest proportion in CLP and lowest proportion in CP. Males are more common with CL and CLP and less common with CP. These characteristics are the same as those of other Chinese surveys but different from some European reports.

China↗

PubMed2006

Essential role of RBP-Jkappa in activation of the K8 delayed-early promoter of Kaposi's sarcoma-associated herpesvirus by ORF50/RTA.

KSHV K8 gene is activated by virally encoded transactivator RTA in delayed-early stage of viral reactivation. Three RTA-responsive elements (RREs) were identified in the promoter. Among them, RRE-II was found to be the most critical cis-acting element for RTA transactivation. In this report, the mechanism underlying RTA-mediated activation of the K8 delayed-early promoter was investigated. A DNA affinity purification study demonstrated that RRE-II was bound by cellular protein RBP-Jkappa, a sequence-specific DNA binding protein and a primary target of the Notch signaling pathway. Inspection of the RRE-II sequence revealed a potential recognition sequence for RBP-Jkappa (GTGAGAA) between the nucleotides -102 and -108 relative to the transcription initial site. Removal or mutation of the motif abolished RBP-Jkappa binding to the K8 promoter and as a consequence, RTA failed to bind to and activate the promoter. An essential role of RBP-Jkappa in the transcription of the K8 promoter was demonstrated by diminishment of the promoter activity in RBP-Jkappa-null murine embryonic fibroblasts. Taken together, RTA activates the K8 promoter through an indirect binding mechanism, i.e. being recruited to the K8 promoter through interaction with RBP-Jkappa bound to an RBP-Jkappa motif in the promoter.

Animals↗

PubMed2006

[Expression of connective tissue growth factor and low density lipoprotein receptor related protein induced by transforming growth factor beta 1 in human pulmonary fibroblasts-1].

OBJECTIVE: To investigate the tendency and correlation between connective tissue growth factor (CTGF) and low density lipoprotein receptor-related protein (LRP) in human pulmonary fibroblasts-1 (HPF-1) induced by transforming growth factor beta1 (TGF-beta1) at different times. METHODS: After the HPF-1 cells were stimulated with TGF-beta1 (5 microg/L) at different times (0 h, 3 h, 6 h,12 h and 24 h),CTGF and LRP mRNA expressions were analyzed by RT-PCR. The same preparation steps of cell culture were repeated, then, the protein expressions were determined by Western Blot, co-immunoprecipitation Western Blot and immunocytochemistry. RESULTS: The expressions of CTGF and LRP mRNA had similar tendency, and LRP (224.87 +/- 7.00) correlated with CTGF (131.53 +/- 2.86) positively (r = 0.8402, P < 0.05). Furthermore, the protein expression levels had significant difference between 0 h (190.85 +/- 2.86) and 3 h (222.45 +/- 3.66) groups (F = 18.06, P < 0.01),and by immunoprecipitation, it was discovered that the quantity of CTGF bounded to LRP changes, which was similar to the result of LRP western blot. The analysis of immunocytochemistry disclosed the like results as well (3 h: 88.66 +/- 15.72, 0 h: 27.56 +/- 6.72, F = 244.36, P < 0.01). CONCLUSION: The expression of LRP coincides with that of CTGF at the same stimulated time point of TGF-beta1. It suggests that LRP may be involved in the biological process of CTGF. And further research about LRP may provide a new direction to pulmonary fibrosis therapy.

Blotting, Western↗

PubMed2006

Kaposi's sarcoma-associated herpesvirus ori-Lyt-dependent DNA replication: dual role of replication and transcription activator.

Lytic replication of Kaposi's sarcoma-associated herpesvirus (KSHV) is essential for viral propagation and pathogenicity. In Kaposi's sarcoma lesions, constant lytic replication plays a role in sustaining the population of latently infected cells that otherwise are quickly lost by segregation of latent viral episomes as spindle cells divide. Lytic DNA replication initiates from an origin (ori-Lyt) and requires trans-acting elements. Two functional ori-Lyts have been identified in the KSHV genome. Some cis-acting and trans-acting elements for ori-Lyt-dependent DNA replication have been found. Among these, K8 binding sites, a cluster of C/EBP binding motifs, and a replication and transcription activator (RTA) responsive element (RRE) are crucial cis-acting elements. Binding of K8 and RTA proteins to these motifs in ori-Lyt DNA was demonstrated to be absolutely essential for DNA replication. In the present study, functional roles of RTA in ori-Lyt-dependent DNA replication have been investigated. Two distinct functions of RTA were revealed. First, RTA activates an ori-Lyt promoter and initiates transcription across GC-rich tandem repeats. This RTA-mediated transcription is indispensable for DNA replication. Second, RTA is a component of the replication compartment, where RTA interacts with prereplication complexes composed of at least six core machinery proteins and K8. The prereplication complexes are recruited to ori-Lyt DNA through RTA, which interacts with the RRE, as well as K8, which binds to a cluster of C/EBP binding motifs with the aid of C/EBP alpha. The revelation of these two functions of RTA, together with its role in initiation of a transcriptional cascade that leads to transcription of all viral lytic genes, shows that RTA is a critical initiator and regulator of KSHV lytic DNA replication and viral propagation.

Amino Acid Sequence↗

PubMed2006

Better prediction of the location of alpha-turns in proteins with support vector machine.

We have developed a novel method named AlphaTurn to predict alpha-turns in proteins based on the support vector machine (SVM). The prediction was done on a data set of 469 nonhomologous proteins containing 967 alpha-turns. A great improvement in prediction performance was achieved by using multiple sequence alignment generated by PSI-BLAST as input instead of the single amino acid sequence. The introduction of secondary structure information predicted by PSIPRED also improved the prediction performance. Moreover, we handled the very uneven data set by combining the cost factor j with the "state-shifting" rule. This further promoted the prediction quality of our method. The final SVM model yielded a Matthews correlation coefficient (MCC) of 0.25 by a 10-fold cross-validation. To our knowledge, this MCC value is the highest obtained so far for predicting alpha-turns. An online Web server based on this method has been developed and can be freely accessed at http://bmc.hust.edu.cn/bioinformatics/ or http://210.42.106.80/.

Amino Acid Sequence↗

PubMed2006

Bisulfite modification of immobilized DNAs for methylation detection.

We have developed a novel method for detecting DNA methylation status of multiple samples, in which the DNA samples were firstly immobilized on the slide and treated with bisulfite directly on the chip. In this experiment, DNAs of pUC19 plasmid were restricted by the enzymes, and ligated with a linker bearing 5'-terminal acrylamide group at the sticky ends. Using universal acrylamide gel polymerization technique, a large amount of DNAs could be immobilized on the slide. The immobilized DNAs were converted by soaking the chip in bisulfite reaction mixtures for 16 h. The probes for detection of the methylation patterns of CpG sites hybridized with the converted DNAs on the microarray, and non-specifically bound probes were cleaned by electrophoresis. We have optimized the experimental conditions of both bisulfite treatment and electrophoresis to increase sensitivity and specificity. The results were further validated by bisulfite DNA sequencing. The experiments show that the method can simplify the experimental processes and increase the efficiency of the bisulfite treatment. This novel method could be used as a convenient tool to detect the methylation status of the multiple genes for a large amount of samples in the future.

Adsorption↗