eQTL Viewer: visualizing how sequence variation affects genome-wide transcription

Background  

Expression Quantitative Trait Locus (eQTL) mapping methods have been used to identify the genetic basis of gene expression variations. To map eQTL, thousands of expression profiles are related with sequence polymorphisms across the genome through their correlated variations. These eQTL distribute in many chromosomal regions, each of which can include many genes. The large number of mapping results produced makes it difficult to consider simultaneously the relationships between multiple genomic regions and multiple expressional profiles. There is a need for informative bioinformatics tools to assist the visualization and interpretation of these mapping results.     

Alterations in the biorheological features of some soft tissues after limb lengthening.

The aim of this study was to investigate the effects of a surgical limb lengthening procedure on the biorheological features of some lengthened soft tissues. In this procedure external fixators were applied to goats' right radius to stretch the tissues. The right forelegs of goats were lengthened by 2, 4 cm, respectively. After lengthening ceased, the goats were examined after different periods of time. The lengthened median nerves, arteries and veins were harvested and used to study their biorheological features. Tensile strength of lengthened and control specimens were measured and their stress relaxation features and stress-strain relationships were studied. Results showed that at the beginning of recovery, the stress-strain curves, relaxation curves and tensile strengths of the lengthened specimens began to deviate from those of their controls. However, with increasing recovery time, the curves and tensile strength of the lengthened specimens reverted to those of their controls. All the tissues studied exhibited the same behavior.     

Microbial Reduction of Cr (VI)-loaded Schwertmannite by Shewanella oneidensis MR-1

Microbial transformation of sulfate minerals plays an important role in controlling the behavior of heavy metals in mining areas. Here, the anaerobic reduction of Cr (VI)-loaded schwertmannite by Shewanella oneidensis MR-1 (S. oneidensis MR-1) was investigated. The release of ferrous iron (Fe(II)) to the solution demonstrated the microbial reduction of structural Fe(III) from the schwertmannite to Fe(II). The concentration of Cr in solution decreased in all treatments, indicating that no Cr was released to the solution during this bio-reduction process of schwertmannite. The incorporation of chromate into the mineral structure of schwertmannite increased the microbial stability of the mineral, retarding the formation of secondary phases during bio-reduction process. Analysis of the XRD, SEM and fourier transform infrared spectroscopy (FT-IR) results further showed that goethite formed after 3 or 7 days with a lower content (0.22% or 0.37%) of Cr in schwertmannite, while no secondary mineral was observed with a higher concentration of Cr (0.6 wt%) incorporated in schwertmannite until 22 days. These results imply that microbial reduction of Cr(VI)-loaded schwertmannite does not lead to the release of Cr to the solution, and the microbial stability of schwertmannite will be increased by the incorporation of chromate.     

Genome-wide analysis of the Chinese sturgeon sox gene family: identification,characterisation and expression profiles of different tissues

The sox family is assumed to be responsible for a number of developmental systems. Genome sequencing technology makes it possible to scan sox genes and conduct characteristic analyses of different species. In fish, full characterisation of sox genes at the genome-wide level has been reported for pufferfish Takifugu rubripes, medaka Oryzias latipes, tilapia Oreochromis niloticus and channel catfish Ictalurus punctatus. However, no systematic investigation of the sox family in sturgeons (Acipenseridae) has been reported to date. This study conducted genome-wide identification of the sox genes in the Chinese sturgeon Acipenser sinensis and profiled their tissue distribution between male and female individuals. In total, 19 sox genes were identified, including soxb1, b2, c, d, e, f and h, in the Chinese sturgeon. Genomic structure analysis indicated relatively conserved exon–intron structures in each sox group and phylogenetic analysis supported the previous classification of the sox family. Most of the sox genes showed a tissue-specific expression pattern, indicating the possible involvement of Chinese sturgeon sox genes at different developmental processes such as cardiac and gonadal development. This study provides a comprehensive resource of Chinese sturgeon sox genes and enables a better understanding of the evolution and function of the sox family.     

Oxalate production at different initial Pb²+ concentrations and the influence of oxalate during solid-state fermentation of straw with Phanerochaete chrysosporium

The production of oxalate at different initial Pb²⁺ concentrations during solid-state fermentation of straw with Phanerochaete chrysosporium was investigated. It was found that the maximal peak value of oxalate concentration (22.84 mM) was detected at the initial Pb²⁺ concentration of 200 mg kg⁻¹ dry straw, while the minimum (15.89 mM) at the concentration of 600 mg Pb²⁺ kg⁻¹ dry straw, and at moderate concentration of Pb²⁺ the capability of oxalic acid secretion was enhanced. In addition, it was also found that more oxalic acid accumulation went together with better Pb²⁺ passivation effect and higher manganese peroxidase (MnP) activity. The present findings will improve the understandings of the interactions of heavy metals with white-rot fungi and the role of oxalate in lignin degradation system, which could provide useful references for more efficient treatment of Pb-contaminated lignocellulosic waste.     

Proteome analysis of sorbitol fermentation specific protein in Vibrio cholerae by 2-DE and MS

Vibrio cholerae can be differentiated into epidemic and non-epidemic strains by sorbitol fermentation speed, but little research has been done on its mechanisms. In this study, we investigated differential protein expression of the two strains in response to sorbitol metabolism. V. cholerae strains were cultured in media with and without sorbitol, respectively. Proteins were separated by 2-DE, and those that showed different expression in the two media were identified by MALDI-TOF MS. Fifteen proteins in epidemic strains and 11 proteins in non-epidemic strains showed a different expression in sorbitol medium. Among them, 4 proteins were common to epidemic and non-epidemic strains. Gene sequence analysis showed that some mutations occurred in these proteins between the two strains. Potential functions of these proteins included sugar uptake, amino acid uptake, electron transport, sulfate and thiosulfate transport.     

低能铁离子束对原卟啉IX二钠盐的辐照效应研究

110ke V Fe^ 离子注入原卟啉IX二钠盐薄膜亲品后的一些谱学分析结果表明,低能铁离子束辐照可以导致生物分子的损伤和化学改性,并且初步证实注入铁离子在样品分子中慢化沉积后形成含铁的金属络合物,即注入铁离子的质量沉积。     

吡哆胺对糖尿病大鼠视皮质AGE-RAGE系统的影响

目的观察吡哆胺对糖尿病大鼠视皮质高级糖基化终末产物(AGE)及其受体(RAGE)表达的影响,探讨吡哆胺对视皮质的保护作用。方法健康SD大鼠随机分为正常对照组(NC组)、糖尿病未治疗组(DM组)、糖尿病吡哆胺治疗组(PM组)和氨基胍治疗对照组(AG组)各20只,用链脲佐菌素(STZ)建立糖尿病模型,PM组和AG组分别于造模成功后第二天开始予吡哆胺和氨基胍灌胃。各组于治疗4w和12w后取材,用酶联免疫吸附(ELISA)法定量检测大鼠视皮质中AGEs含量,荧光免疫组化及图像分析半定量检测各组视皮质RAGE的表达。结果糖尿病治疗组和未治疗组血糖无显著性差异。4w时各组AGEs含量无明显差异,12w时PM组视皮质中AGEs含量与AG组、NC组比较差异无统计学意义,与DM组相比显著降低,差异具有统计学意义(P0.05)。PM组视皮质中RAGE表达比DM组显著减少,差异具有统计学意义(P0.05),但高于NC组(P0.05)。结论糖尿病大鼠12w后视皮质中AGEs含量和RAGE的表达高于正常对照组,吡哆胺类似氨基胍可减少AGEs的堆积,还能抑制RAGE的表达,减轻AGEs-RAGE通路作用导致的组织损伤,对视皮质具有一定的保护作用。     

SNP-based pool genotyping and haplotype analysis accelerate fine-mapping of the wheat genomic region containing stripe rust resistance gene <Emphasis Type="Italic">Yr26</Emphasis>

Key message

NGS-assisted super pooling emerging as powerful tool to accelerate gene mapping and haplotype association analysis within target region uncovering specific linkage SNPs or alleles for marker-assisted gene pyramiding.

Abstract

Conventional gene mapping methods to identify genes associated with important agronomic traits require significant amounts of financial support and time. Here, a single nucleotide polymorphism (SNP)-based mapping approach, RNA-Seq and SNP array assisted super pooling analysis, was used for rapid mining of a candidate genomic region for stripe rust resistance gene Yr26 that has been widely used in wheat breeding programs in China. Large DNA and RNA super-pools were genotyped by Wheat SNP Array and sequenced by Illumina HiSeq, respectively. Hundreds of thousands of SNPs were identified and then filtered by multiple filtering criteria. Among selected SNPs, over 900 were found within an overlapping interval of less than 30 Mb as the Yr26 candidate genomic region in the centromeric region of chromosome arm 1BL. The 235 chromosome-specific SNPs were converted into KASP assays to validate the Yr26 interval in different genetic populations. Using a high-resolution mapping population (>?30,000 gametes), we confined Yr26 to a 0.003-cM interval. The Yr26 target region was anchored to the common wheat IWGSC RefSeq v1.0 and wild emmer WEWSeq v.1.0 sequences, from which 488 and 454 kb fragments were obtained. Several candidate genes were identified in the target genomic region, but there was no typical resistance gene in either genome region. Haplotype analysis identified specific SNPs linked to Yr26 and developed robust and breeder-friendly KASP markers. This integration strategy can be applied to accelerate generating many markers closely linked to target genes/QTL for a trait of interest in wheat and other polyploid species.