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Articles by K. Wang
Total Records ( 3 ) for K. Wang
  L. Y Wu , H. A Chipman , S. B Bull , L Briollais and K. Wang
 

Motivation: Efficient and accurate ascertainment of copy number variations (CNVs) at the population level is essential to understand the evolutionary process and population genetics, and to apply CNVs in population-based genome-wide association studies for complex human diseases. We propose a novel Bayesian segmentation approach to identify CNVs in a defined population of any size. It is computationally efficient and provides statistical evidence for the detected CNVs through the Bayes factor. This approach has the unique feature of carrying out segmentation and assigning copy number status simultaneously—a desirable property that current segmentation methods do not share.

Results: In comparisons with popular two-step segmentation methods for a single individual using benchmark simulation studies, we find the new approach to perform competitively with respect to false discovery rate and sensitivity in breakpoint detection. In a simulation study of multiple samples with recurrent copy numbers, the new approach outperforms two leading single sample methods. We further demonstrate the effectiveness of our approach in population-level analysis of previously published HapMap data. We also apply our approach in studying population genetics of CNVs.

  J. A Weber , D. H Baxter , S Zhang , D. Y Huang , K How Huang , M Jen Lee , D. J Galas and K. Wang
  BACKGROUND:

MicroRNAs (miRNAs) are small, noncoding RNAs that play an important role in regulating various biological processes through their interaction with cellular messenger RNAs. Extracellular miRNAs in serum, plasma, saliva, and urine have recently been shown to be associated with various pathological conditions including cancer.

METHODS:

With the goal of assessing the distribution of miRNAs and demonstrating the potential use of miRNAs as biomarkers, we examined the presence of miRNAs in 12 human body fluids and urine samples from women in different stages of pregnancy or patients with different urothelial cancers. Using quantitative PCR, we conducted a global survey of the miRNA distribution in these fluids.

RESULTS:

miRNAs were present in all fluids tested and showed distinct compositions in different fluid types. Several of the highly abundant miRNAs in these fluids were common among multiple fluid types, and some of the miRNAs were enriched in specific fluids. We also observed distinct miRNA patterns in the urine samples obtained from individuals with different physiopathological conditions.

CONCLUSIONS:

MicroRNAs are ubiquitous in all the body fluid types tested. Fluid type–specific miRNAs may have functional roles associated with the surrounding tissues. In addition, the changes in miRNA spectra observed in the urine samples from patients with different urothelial conditions demonstrates the potential for using concentrations of specific miRNAs in body fluids as biomarkers for detecting and monitoring various physiopathological conditions.

  C. Zhu , H. Xu , J. Zhang , K. Wang and P. Zhu
  Suppressor of cytokine signaling (SOCS) molecules belong to intracellular proteins that inhibit Janus kinase as well as signal transduction and activators of transcription pathways. In this study, we investigated whether SOCS-1–silenced dendritic cells (DCs) prolonged allograft survival in rat intestinal transplantation. Donor bone marrow–derived DCs were genetically transfected with SOCS-1 siRNA using liposomes. The level of SOCS-1 expression was quantitated by Western blots. DC function was assessed by MTT in mixed leukocyte reactions. We injected donor-derived SOCS-1 silenced DCs 7 days before heterotopic intestinal transplantation between SD donors and Wistar recipients. We compared untransfected DCs and silenced DCs to suppress allogeneic mixed leukocyte reactions. Recipients pretreated with SOCS-1–silenced DCs showed moderate survival prolongation with a mean allograft survival of 18.3 ± 5.3 days (P < .05), compared with 6.4 ± 2.0 days in the control group and 7.2 ± 2.1 days in a control siRNA transfection DC group. The difference between untreated DCs group and the control group was not significant. In summary, SOCS-1 silenced DCs induced allogeneic T-cell hyporesponsiveness in vitro, promoting allograft survival in rat intestinal transplantation.
 
 
 
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