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A novel DNA sequence periodicity decodes nucleosome positioning

There have been two types of well-characterized DNA sequence periodicities; both are found to be associated with important molecular mechanisms. One is a 3-nt periodicity corresponding to codon triplets, the other is a 10.5-nt periodicity related to the structure of DNA helixes. In the process of analyzing the genome and transcriptome of Trichomonas vaginalis, we observed a 120.9...

A Simple Spatial Working Memory and Attention Test on Paired Symbols Shows Developmental Deficits in Schizophrenia Patients

People with neuropsychiatric disorders such as schizophrenia often display deficits in spatial working memory and attention. Evaluating working memory and attention in schizophrenia patients is usually based on traditional tasks and the interviewer’s judgment. We developed a simple Spatial Working Memory and Attention Test on Paired Symbols (SWAPS). It takes only several minutes...

The Gene Regulatory Cascade Linking Proneural Specification with Differentiation in Drosophila Sensory Neurons

Temporal expression profiling of sensory precursor cells reveals how the atonal proneural transcription factor regulates a specialized neuronal differentiation pathway.

Defining the chromatin signature of inducible genes in T cells

Background Specific chromatin characteristics, especially the modification status of the core histone proteins, are associated with active and inactive genes. There is growing evidence that genes that respond to environmental or developmental signals may possess distinct chromatin marks. Using a T cell model and both genome-wide and gene-focused approaches, we examined the...

The transcription repressor, ZEB1, cooperates with CtBP2 and HDAC1 to suppress IL-2 gene activation in T cells

Activation of T cells leads to the induction of many cytokine genes that are required for appropriate immune responses, including IL-2, a key cytokine for T cell proliferation and homeostasis. The activating transcription factors such as nuclear factor of activated T cells, nuclear factor κB/Rel and activated protein-1 family members that regulate inducible IL-2 gene expression...

RiceWiki: a wiki-based database for community curation of rice genes

Rice is the most important staple food for a large part of the world’s human population and also a key model organism for biological studies of crops as well as other related plants. Here we present RiceWiki (http://ricewiki.big.ac.cn), a wiki-based, publicly editable and open-content platform for community curation of rice genes. Most existing related biological databases are...

Analysis of synonymous codon usage in Hepatitis A virus

Background Hepatitis A virus is the causative agent of type A viral hepatitis, which causes occasional acute hepatitis. Nevertheless, little information about synonymous codon usage pattern of HAV genome in the process of its evolution is available. In this study, the key genetic determinants of codon usage in HAV were examined. Results The overall extent of codon usage bias in...

An Integrated Analysis of miRNA and mRNA Expressions in Non-Small Cell Lung Cancers

Science and Technology of Zhoushan awarded to Professor Yongkui Zhang (20081059), and the Research Fund of Zhoushan Hospital awarded to Dr. Lina Ma, and the National Basic Research Program (973 Program

Plasticity of DNA methylation in mouse T cell activation and differentiation

Background Circulating CD4+ T helper cells are activated through interactions with antigen presenting cells and undergo differentiation into specific T helper cell subsets depending on the type of antigen encountered. In addition, the relative composition of the circulating CD4+ T cell population changes as animals mature with an increased percentage of the population being...

A quality evaluation strategy for Rhizoma coptidis from a variety of different sources using chromatographic fingerprinting combined with biological fingerprinting

Most of herbal medicines of different sources are used for the same treatment goal in clinic despite their tremendous differences of the quality. Because the clinical efficacy is closely related to the quality of medicines, the implementation of an effective quality control (QC) process is vital. Chemical methods based on content determination and chromatographic fingerprints...

Molecular logic computing model based on DNA self-assembly strand branch migration

In this study, the DNA logic computing model is established based on the methods of DNA self-assembly and strand branch migration. By adding the signal strands, the preprogrammed signals are released with the disintegrating of initial assembly structures. Then, the computing results are able to be detected by gel electrophoresis. The whole process is controlled automatically and...

A Role for the Budding Yeast Separase, Esp1, in Ty1 Element Retrotransposition

Separase/Esp1 is a protease required at the onset of anaphase to cleave cohesin and thereby enable sister chromatid separation. Esp1 also promotes release of the Cdc14 phosphatase from the nucleolus to enable mitotic exit. To uncover other potential roles for separase, we performed two complementary genome-wide genetic interaction screens with a strain carrying the budding yeast...

Ginkgolide B Reduces LOX-1 Expression by Inhibiting Akt Phosphorylation and Increasing Sirt1 Expression in Oxidized LDL-Stimulated Human Umbilical Vein Endothelial Cells

Oxidized low-density lipoprotein (ox-LDL) is an important risk factor in the development of atherosclerosis. LOX-1, a lectin-like receptor for ox-LDL, is present primarily on endothelial cells and upregulated by ox-LDL, tumor necrosis factor a, shear stress, and cytokines in atherosclerosis. Recent studies demonstrated that ginkgolide B, a platelet-activating factor receptor...

Dilatory is a Drosophila protein related to AZI1 (CEP131) that is located at the ciliary base and required for cilium formation

Lina Ma 0 Andrew P. Jarman () 0 0 Centre for Integrative Physiology, School of Biomedical Sciences, University of Edinburgh , George Square, Edinburgh EH8 9XD , UK Summary A significant number of

LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs

Long non-coding RNAs (lncRNAs) perform a diversity of functions in numerous important biological processes and are implicated in many human diseases. In this report we present lncRNAWiki (http://lncrna.big.ac.cn), a wiki-based platform that is open-content and publicly editable and aimed at community-based curation and collection of information on human lncRNAs. Current related...

Contamination of Phthalate Esters (PAEs) in Typical Wastewater-Irrigated Agricultural Soils in Hebei, North China

The Wangyang River (WYR) basin is a typical wastewater irrigation area in Hebei Province, North China. This study investigated the concentration and distribution of six priority phthalate esters (PAEs) in the agricultural soils in this area. Thirty-nine soil samples (0–20 cm) were collected along the WYR to assess the PAE residues in soils. Results showed that PAEs are ubiquitous...

Plasma Biomarker of Dietary Phytosterol Intake

Background Dietary phytosterols, plant sterols structurally similar to cholesterol, reduce intestinal cholesterol absorption and have many other potentially beneficial biological effects in humans. Due to limited information on phytosterol levels in foods, however, it is difficult to quantify habitual dietary phytosterol intake (DPI). Therefore, we sought to identify a plasma...

Global Analysis of a Model of Viral Infection with Latent Stage and Two Types of Target Cells

By introducing the probability function describing latency of infected cells, we unify some models of viral infection with latent stage. For the case that the probability function is a step function, which implies that the latency period of the infected cells is constant, the corresponding model is a delay differential system. The model with delay of latency and two types of...

Global Analysis of a Model of Viral Infection with Latent Stage and Two Types of Target Cells

By introducing the probability function describing latency of infected cells, we unify some models of viral infection with latent stage. For the case that the probability function is a step function, which implies that the latency period of the infected cells is constant, the corresponding model is a delay differential system. The model with delay of latency and two types of...