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Comprehensive comparison of three commercial human whole-exome capture platforms

Background Exome sequencing, which allows the global analysis of protein coding sequences in the human genome, has become an effective and affordable approach to detecting causative genetic mutations in diseases. Currently, there are several commercial human exome capture platforms; however, the relative performances of these have not been characterized sufficiently to know which...

Characterization and comparative analysis of HMW glutenin 1Ay alleles with differential expressions

Background High-molecular-weight glutenin subunits (HMW-GSs) have been considered as most important seed storage proteins for wheat flour quality. 1Ay subunits are of great interest because they are always silent in common wheat. The presence of expressed 1Ay subunits in diploid and tetraploid wheat genotypes makes it possible to investigate molecular information of active 1Ay...

Rational Design of a Live Attenuated Dengue Vaccine: 2′-O-Methyltransferase Mutants Are Highly Attenuated and Immunogenic in Mice and Macaques

Dengue virus is transmitted by Aedes mosquitoes and infects at least 100 million people every year. Progressive urbanization in Asia and South-Central America and the geographic expansion of Aedes mosquito habitats have accelerated the global spread of dengue, resulting in a continuously increasing number of cases. A cost-effective, safe vaccine conferring protection with ideally...

Computational prediction of novel non-coding RNAs in Arabidopsis thaliana

Background Non-coding RNA (ncRNA) genes do not encode proteins but produce functional RNA molecules that play crucial roles in many key biological processes. Recent genome-wide transcriptional profiling studies using tiling arrays in organisms such as human and Arabidopsis have revealed a great number of transcripts, a large portion of which have little or no capability to encode...

Excess of Rare Variants in Genes that are Key Epigenetic Regulators of Spermatogenesis in the Patients with Non-Obstructive Azoospermia

430030, ChinaHonggang Li & Chengliang XiongBGI-Shenzhen, Shenzhen 518083, ChinaJingchu Hu, Xiao Liu, Tao Jiang, Guangqing Sun, Wei Zhao, Yu Xu, Tingting He, Chengliang Dong, Shengjie Gao, Guangwu Guo ... journals • PubMed • Google ScholarSearch for Xiao Liu in:Nature Research journals • PubMed • Google ScholarSearch for Tao Jiang in:Nature Research journals • PubMed • Google ScholarSearch for Guangqing Sun

Early Second-Trimester Serum MiRNA Profiling Predicts Gestational Diabetes Mellitus

Background Gestational diabetes mellitus (GDM) is one type of diabetes that presents during pregnancy and significantly increases the risk of a number of adverse consequences for the fetus and mother. The microRNAs (miRNA) have recently been demonstrated to abundantly and stably exist in serum and to be potentially disease-specific. However, no reported study investigates the...

Profiling the DNA-binding specificities of engineered Cys2His2 zinc finger domains using a rapid cell-based method

The C2H2 zinc finger is the most commonly utilized framework for engineering DNA-binding domains with novel specificities. Many different selection strategies have been developed to identify individual fingers that possess a particular DNA-binding specificity from a randomized library. In these experiments, each finger is selected in the context of a constant finger framework...

High β-catenin/Tcf-4 activity confers glioma progression via direct regulation of AKT2 gene expression

Recent data suggest that the β-catenin/Tcf-4 signaling pathway plays an important role in human cancer tumorigenesis. However, the mechanism of β-catenin/Tcf-4 signaling in tumorigenesis is poorly understood. In this study, we show that Tcf-4 protein levels were significantly elevated in high-grade gliomas in comparison with low-grade gliomas and that Tcf-4 levels correlated with...

Regulation of Renal Fatty Acid and Cholesterol Metabolism, Inflammation, and Fibrosis in Akita and OVE26 Mice With Type 1 Diabetes

In Akita and OVE26 mice, two genetic models of type 1 diabetes, diabetic nephropathy is characterized by mesangial expansion and loss of podocytes, resulting in glomerulosclerosis and proteinuria, and is associated with increased expression of profibrotic growth factors, proinflammatory cytokines, and increased oxidative stress. We have also found significant increases in renal...

Plasma IGFBP-2 levels predict clinical outcomes of patients with high-grade gliomas

Insulin-like growth factor binding protein 2 (IGFBP-2) is a malignancy-associated protein measurable in tumors and blood. Increased IGFBP-2 is associated with shortened survival of advanced glioma patients. Thus, we examined plasma IGFBP-2 levels in glioma patients and healthy controls to evaluate its value as a plasma biomarker for glioma. Plasma IGFBP-2 levels in 196 patients...

Development and validation of a prokaryotically expressed foot-and-mouth disease virus non-structural protein 2C'3AB-based immunochromatographic strip to differentiate between infected and vaccinated animals

Background Foot-and-mouth disease (FMD) is an extremely contagious viral disease of cattle, pigs, sheep, goats, and many cloven-hoofed wild animals. FMDV serotypes O and Asia 1 have circulated separately in China during the last fifty years, and eliminating infected animals and vaccination are the main policies to prevent and control FMD. Antibodies to NSPs exist in infected...

Seizure characteristics and outcomes in 508 Chinese adult patients undergoing primary resection of low-grade gliomas: a clinicopathological study

Seizure is a common presenting manifestation and plays an important role in the clinical presentation and quality of life for patients with low-grade gliomas (LGGs). The authors set out to identify factors that influence preoperative seizure characteristics and postoperative seizure control. Cases involving adult patients who had undergone initial surgery for LGGs in a single...

Translational Regulation by the 3′ Untranslated Region of the Dengue Type 2 Virus Genome

, Beijing Institute of Microbiology and Epidemiology , Beijing , People's Republic of China 2 Authors' address:Yan Wei , Chengfeng Qin,Tao Jiang, Xiaofeng Li, Hui Zhao, Zhongyu Liu, Yongqiang Deng, Ran Liu

Efficient selection of unique and popular oligos for large EST databases†

Motivation: Expressed sequence tag (EST) databases have grown exponentially in recent years and now represent the largest collection of genetic sequences. An important application of these databases is that they contain information useful for the design of gene-specific oligonucleotides (or simply, oligos) that can be used in PCR primer design, microarray experiments and genomic...

A New Instrument for Testing Wind Erosion by Soil Surface Shape Change

Wind erosion, a primary cause of soil degeneration, is a problem in arid and semiarid areas throughout the world. Many methods are available to study soil erosion, but there is no an effective method for making quantitative measurements in the field. To solve this problem, we have developed a new instrument that can measure the change in the shape of the soil surface, allowing...

A Systems Biology-Based Gene Expression Classifier of Glioblastoma Predicts Survival with Solid Tumors

Accurate prediction of survival of cancer patients is still a key open problem in clinical research. Recently, many large-scale gene expression clusterings have identified sets of genes reportedly predictive of prognosis; however, those gene sets shared few genes in common and were poorly validated using independent data. We have developed a systems biology-based approach by...

Estimation of allele frequency and association mapping using next-generation sequencing data

Geng Tian Niels Grarup Tao Jiang Gitte Andersen Daniel Witte Torben Jorgensen Torben Hansen Oluf Pedersen Jun Wang Rasmus Nielsen 0 0 Departments of Integrative Biology and Statistics, UC Berkeley

A duplex real-time RT-PCR assay for detecting H5N1 avian influenza virus and pandemic H1N1 influenza virus

A duplex real-time reverse transcriptase polymerase chain reaction (RT-PCR) assay was improved for simultaneous detection of highly pathogenic H5N1 avian influenza virus and pandemic H1N1 (2009) influenza virus, which is suitable for early diagnosis of influenza-like patients and for epidemiological surveillance. The sensitivity of this duplex real-time RT-PCR assay was 0.02...

Study of gene function based on spatial co-expression in a high-resolution mouse brain atlas

Background The Allen Brain Atlas (ABA) project systematically profiles three-dimensional high-resolution gene expression in postnatal mouse brains for thousands of genes. By unveiling gene behaviors at both the cellular and molecular levels, ABA is becoming a unique and comprehensive neuroscience data source for decoding enigmatic biological processes in the brain. Given the...