Mast cells (MC) are stem cell factor-dependent tissue-based hematopoietic cells with substantial functional heterogeneity. Cord blood-derived human MC (hMC) express functional receptors for IL-5, and IL-5 mediates stem cell factor-dependent comitogenesis of hMC in vitro. Although IL-5 is not required for normal hMC development, we considered that it might prime hMC for their high-affinity Fc re...

The formation of differentiated cell types from pluripotent progenitors involves epigenetic regulation of gene expression. DNA hydroxymethylation results from the enzymatic oxidation of 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC) by the ten-eleven translocation (TET) 5-mC dioxygenase enzymes. Previous work has mapped changes in 5-mC during differentiation of intestinal stem cells...

To improve the epigenomic analysis of tissues rich in 5-hydroxymethylcytosine (hmC), we developed a novel protocol called TAB-Methyl-SEQ, which allows for single base resolution profiling of both hmC and 5-methylcytosine by targeted next-generation sequencing. TAB-Methyl-SEQ data were extensively validated by a set of five methodologically different protocols. Importantly, these extensive cross...

Accumulating evidences suggest that large-scale loss of 5-hydroxymethylcytosine (5-hmC) is an epigenetic hallmark in different cancers. However, the levels of 5-hmC in laryngeal squamous cell carcinoma (LSCC) and its prognostic value in this cancer remain largely unknown. Using dot-blot and quantitative RT-PCR assays, we investigate 5-hmC levels and expression of TET-1, -2 and -3 in LSCCs and e...

DNA methylation is an important epigenetic modification and is frequently altered in cancer. Convert of 5-methylcytosine (5 mC) to 5-hydroxymethylcytosine (5 hmC) by ten-eleven translocation (TET) family enzymes plays important biological functions in embryonic stem cells, development, aging and disease. Recent reports showed that level of 5 hmC was altered in various types of cancers. However,...

DNA methylation is an important epigenetic modification as a hallmark in cancer. Conversion of 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC) by ten-eleven translocation (TET) family enzymes plays an important biological role in embryonic stem cells, development, aging and disease. Lymphoid specific helicase (LSH), a chromatin remodeling factor, is regarded as a reader of 5-hmC. Rec...

This paper presents a fully non-Gaussian version of the Hamiltonian Monte Carlo (HMC) sampling filter. The Gaussian prior assumption in the original HMC filter is relaxed. Specifically, a clustering step is introduced after the forecast phase of the filter, and the prior density function is estimated by fitting a Gaussian Mixture Model (GMM) to the prior ensemble. Using the data likelihood func...

Limousin-cross steers (n=135; 258+/-26 kg) were used to compare forage vs grain feeding on carcass composition and palatability attributes of beef when time on feed was controlled. Diets included a 95% alfalfa silage ration (AS) or a 68% high-moisture corn, 25% alfalfa silage ration (HMC). These were incorporated into six treatments to allow comparisons of end points based on similar days on fe...

The Hybrid Monte Carlo (HMC) algorithm[1] is now the standard method to simulate dynamical fermions. However the cost of the algorithm is substantial. It is therefore desirable to improve the efficiency of the HMC algorithm. First, we examine the possibility of changing the step size adaptively[2,3]. Second, we implement the HMC algorithm with approximate Hamiltonians. Lastly, we precondition t...

Prior to 2009, 5-methylcytosine (5-mC) was thought to be the only biologically significant cytosine modification in mammalian DNA. With the discovery of the TET enzymes, which convert 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC), however, intense interest has emerged in determining the biological function of 5-hmC. Here, we review the techniques used to study 5-hmC and evidence th...