Compressed variance component mixed model reveals epistasis associated with flowering in .

Introduction: Epistasis is currently a topic of great interest in molecular and quantitative genetics. , as a model organism, plays a crucial role in studying the fundamental biology of diverse plant species. However, there have been limited reports about identification of epistasis related to flowering in genome-wide association studies (GWAS).

Identification of QTN-by-environment interactions for yield related traits in maize under multiple abiotic stresses.

Introduction: Quantitative trait nucleotide (QTN)-by-environment interactions (QEIs) play an increasingly essential role in the genetic dissection of complex traits in crops as global climate change accelerates. The abiotic stresses, such as drought and heat, are the major constraints on maize yields. Multi-environment joint analysis can improve statistical power in QTN and QEI detection, and further help us to understand the genetic basis and provide implications for maize improvement.

mrMLM v4.0.2: An R Platform for Multi-locus Genome-wide Association Studies.

Previous studies have reported that some important loci are missed in single-locus genome-wide association studies (GWAS), especially because of the large phenotypic error in field experiments. To solve this issue, multi-locus GWAS methods have been recommended. However, only a few software packages for multi-locus GWAS are available.

QTL.gCIMapping.GUI v2.0: An R software for detecting small-effect and linked QTLs for quantitative traits in bi-parental segregation populations.

The methodologies and software packages for mapping quantitative trait loci (QTLs) in bi-parental segregation populations are well established. However, it is still difficult to detect small-effect and linked QTLs. To address this issue, we proposed a genome-wide composite interval mapping (GCIM) in bi-parental segregation populations.

An efficient multi-locus mixed model framework for the detection of small and linked QTLs in F2.

In the genetic system that regulates complex traits, metabolites, gene expression levels, RNA editing levels and DNA methylation, a series of small and linked genes exist. To date, however, little is known about how to design an efficient framework for the detection of these kinds of genes. In this article, we propose a genome-wide composite interval mapping (GCIM) in F2.

Rapid Increase in Prevalence of Carbapenem-Resistant Enterobacteriaceae (CRE) and Emergence of Colistin Resistance Gene in CRE in a Hospital in Henan, China.

The global spread of carbapenem-resistant (CRE) is one of the most severe threats to human health in a clinical setting. The recent emergence of plasmid-mediated colistin resistance gene among CRE strains greatly compromises the use of colistin as a last resort for the treatment of infections caused by CRE. This study aimed to understand the current epidemiological trends and characteristics of CRE from a large hospital in Henan, the most populous province in China.

pKWmEB: integration of Kruskal-Wallis test with empirical Bayes under polygenic background control for multi-locus genome-wide association study.

Although nonparametric methods in genome-wide association studies (GWAS) are robust in quantitative trait nucleotide (QTN) detection, the absence of polygenic background control in single-marker association in genome-wide scans results in a high false positive rate. To overcome this issue, we proposed an integrated nonparametric method for multi-locus GWAS. First, a new model transformation was used to whiten the covariance matrix of polygenic matrix K and environmental noise.

Mapping small-effect and linked quantitative trait loci for complex traits in backcross or DH populations via a multi-locus GWAS methodology.

Composite interval mapping (CIM) is the most widely-used method in linkage analysis. Its main feature is the ability to control genomic background effects via inclusion of co-factors in its genetic model. However, the result often depends on how the co-factors are selected, especially for small-effect and linked quantitative trait loci (QTL).

Improving power and accuracy of genome-wide association studies via a multi-locus mixed linear model methodology.

Genome-wide association studies (GWAS) have been widely used in genetic dissection of complex traits. However, common methods are all based on a fixed-SNP-effect mixed linear model (MLM) and single marker analysis, such as efficient mixed model analysis (EMMA). These methods require Bonferroni correction for multiple tests, which often is too conservative when the number of markers is extremely large.

Lactobacillus species shift in distal esophagus of high-fat-diet-fed rats.

Aim: To analyze the microbiota shift in the distal esophagus of Sprague-Dawley rats fed a high-fat diet.

Methods: Twenty Sprague-Dawley rats were divided into high-fat diet and normal control groups of 10 rats each. The composition of microbiota in the mucosa from the distal esophagus was analyzed based on selective culture.

Effects of two Lactobacillus strains on lipid metabolism and intestinal microflora in rats fed a high-cholesterol diet.

Background: The hypocholesterolemic effects of lactic acid bacteria (LAB) have now become an area of great interest and controversy for many scientists. In this study, we evaluated the effects of Lactobacillus plantarum 9-41-A and Lactobacillus fermentum M1-16 on body weight, lipid metabolism and intestinal microflora of rats fed a high-cholesterol diet.

Methods: Forty rats were assigned to four groups and fed either a normal or a high-cholesterol diet.

GPC3 fused to an alpha epitope of HBsAg acts as an immune target against hepatocellular carcinoma associated with hepatitis B virus.

Background: The incidence of hepatocellular carcinoma (HCC) in China is closely related to the population infected with hepatitis B virus (HBV). HCC cells with HBV secrete soluble HBsAg into blood but do not express it on the cell membrane. This study aimed to construct and investigate a new glycosyl-phosphatidylinositol (GPI)-anchored protein (GPC3+alpha+EGFP) as a DNA vaccine against HCC associated with HBV.