Altered membrane proteins and permeability correlate with cardiac dysfunction in cardiomyopathic hamsters

A mutation in the delta-sarcoglycan (SG) gene with absence of delta-SG protein in the heart has been identified in the BIO14.6 cardiomyopathic (CM) hamster, but how the defective gene leads to myocardial degeneration and dysfunction is unknown. We correlated left ventricular (LV) function with increased sarcolemmal membrane permeability and investigated the LV distribution of the dystrophin-dystroglycan complex in BIO14.6 CM hamsters. On echocardiography at 5 wk of age, the CM hamsters showed a mildly enlarged diastolic dimension (LVDD) with decreased LV percent fractional shortening (%FS), and at 9 wk further enlargement of LVDD with reduction of %FS was observed. The percent area of myocardium exhibiting increased membrane permeability or membrane rupture, assessed by Evans blue dye (EBD) staining and wheat germ agglutinin, was greater at 9 than at 5 wk. In areas not stained by EBD, immunostaining of dystrophin was detected in CM hamsters at sarcolemma and T tubules, as expected, but it was also abnormally expressed at the intercalated discs; in addition, the expression of beta-dystroglycan was significantly reduced compared with control hearts. As previously described, alpha-SG was completely deficient in CM hearts compared with control hearts. In myocardial areas showing increased sarcolemmal permeability, neither dystrophin nor beta-dystroglycan could be identified by immunolabeling. Thus, together with the known loss of delta-SG and other SGs, abnormal distribution of dystrophin and reduction of beta-dystroglycan are associated with increased sarcolemmal permeability followed by cell rupture, which correlates with early progressive cardiac dysfunction in the BIO14.6 CM hamster.     

SASI-Seq: sample assurance Spike-Ins,and highly differentiating 384 barcoding for Illumina sequencing

Background

A minor but significant fraction of samples subjected to next-generation sequencing methods are either mixed-up or cross-contaminated. These events can lead to false or inconclusive results. We have therefore developed SASI-Seq; a process whereby a set of uniquely barcoded DNA fragments are added to samples destined for sequencing. From the final sequencing data, one can verify that all the reads derive from the original sample(s) and not from contaminants or other samples.

Results

By adding a mixture of three uniquely barcoded amplicons, of different sizes spanning the range of insert sizes one would normally use for Illumina sequencing, at a spike-in level of approximately 0.1%, we demonstrate that these fragments remain intimately associated with the sample. They can be detected following even the tightest size selection regimes or exome enrichment and can report the occurrence of sample mix-ups and cross-contamination.As a consequence of this work, we have designed a set of 384 eleven-base Illumina barcode sequences that are at least 5 changes apart from each other, allowing for single-error correction and very low levels of barcode misallocation due to sequencing error.

Conclusion

SASI-Seq is a simple, inexpensive and flexible tool that enables sample assurance, allows deconvolution of sample mix-ups and reports levels of cross-contamination between samples throughout NGS workflows.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-110) contains supplementary material, which is available to authorized users.     

The comparison of the confidence regions in phylogeny

In this paper, several different procedures for constructing confidence regions for the true evolutionary tree are evaluated both in terms of coverage and size without considering model misspecification. The regions are constructed on the basis of tests of hypothesis using six existing tests: Shimodaira Hasegawa (SH), SOWH, star form of SOWH (SSOWH), approximately unbiased (AU), likelihood weight (LW), generalized least squares, plus two new tests proposed in this paper: single distribution nonparametric bootstrap (SDNB) and single distribution parametric bootstrap (SDPB). The procedures are evaluated on simulated trees both with small and large number of taxa. Overall, the SH, SSOWH, AU, and LW tests led to regions with higher coverage than the nominal level at the price of including large numbers of trees. Under the specified model, the SOWH test gives accurate coverage and relatively small regions. The SDNB and SDPB tests led to the small regions with occasional undercoverage. These two procedures have a substantial computational advantage over the SOWH test. Finally, the cutoff levels for the SDNB test are shown to be more variable than those for the SDPB test.     

LBX2-AS1 promotes ovarian cancer progression by facilitating E2F2 gene expression via miR-455-5p and miR-491-5p sponging

LBX2-AS1 is a long non-coding RNA that facilitates the development of gastrointestinal cancers and lung cancer, but its participation in ovarian cancer development remained uninvestigated. Clinical data retrieved from TCGA ovarian cancer database and the clinography of 60 ovarian cancer patients who received anti-cancer treatment in our facility were analysed. The overall cell growth, colony formation, migration, invasion, apoptosis and tumour formation on nude mice of ovarian cancer cells were evaluated before and after lentiviral-based LBX2-AS1 knockdown. ENCORI platform was used to explore LBX2-AS1-interacting microRNAs and target genes of the candidate microRNAs. Luciferase reporter gene assay and RNA pulldown assay were used to verify the putative miRNA-RNA interactions. Ovarian cancer tissue specimens showed significant higher LBX2-AS1 expression levels that non-cancerous counterparts. High expression level of LBX2-AS1 was significantly associated with reduced overall survival of patients. LBX2-AS1 knockdown significantly down-regulated the cell growth, colony formation, migration, invasion and tumour formation capacity of ovarian cancer cells and increased their apoptosis in vitro. LBX2-AS1 interacts with and thus inhibits the function of miR-455-5p and miR-491-5p, both of which restrained the expression of E2F2 gene in ovarian cancer cells via mRNA targeting. Transfection of miRNA inhibitors of these two miRNAs or forced expression of E2F2 counteracted the effect of LBX2-AS1 knockdown on ovarian cancer cells. LBX2-AS1 was a novel cancer-promoting lncRNA in ovarian cancer. This lncRNA increased the cell growth, survival, migration, invasion and tumour formation of ovarian cancer cells by inhibiting miR-455-5p and miR-491-5p, thus liberating the expression of E2F2 cancer-promoting gene.     

Dynamic changes in the gonadotrope cell subpopulations during an estradiol-induced surge in the ewe

Whether estradiol targets a subpopulation of gonadotrope cells was investigated in this study. Ovariectomized ewes (OVX) or OVX ewes immunized against GnRH and treated with hourly pulses of GnRH analogue (OVX-IMG) were killed at 6, 12, 16, and 24 h after administration of 50 microg of 17beta-estradiol (E(2)). Control ewes received no E(2) treatment. In OVX or OVX-IMG ewes killed 6 h after E(2) injection, a decrease in gonadotropin plasma levels was observed compared with non-E(2)-treated ewes. In contrast, a surge in gonadotropin plasma concentrations occurred in ewes killed 16 h after injection. The percentage of total immunoreactive gonadotrope cells among the pituitary cells was lower in E(2)-treated ewes compared with nontreated animals. The proportion of monohormonal LH cells was constant throughout the experiment, except at the surge peak, where it was enhanced. In the OVX ewes, the proportion of bihormonal LH/FSH cells was lower in the E(2)-treated ewes compared to the nontreated ewes (P: < 0.001), with a more pronounced decrease 16 h after E(2) injection. A slight increase occurred 12 h after E(2) injection compared with 6 h after injection (P: < 0.05). A similar pattern was observed in the OVX-IMG ewes, except at 12 h after E(2) injection, when no increase occurred. In both OVX and OVX-IMG ewes, injection of E(2) decreased FSHbeta mRNA expression but did not alter the relative levels of LHbeta mRNA. These data suggest that the negative feedback of E(2) on LH and FSH secretion mainly targets the bihormonal cells and occurs, at least in part, directly at the pituitary level. During the gonadotropin surge, the sustained FSH release from the bihormonal cells would induce a switch from bihormonal cells to monohormonal LH cells by depleting these cells of FSH.     

用毛细管电泳-激光诱发荧光技术检测清醒吗啡戒断大鼠导水管周围灰质微透析液中谷氨酸和精氨酸的含量

清醒动物脑微透析技术能够用于动态观察某一特定核团中生物活性物质变化及其与行为的关系,结合高效毛细管电泳-激光诱发荧光对衍生后的透析样品进行检测,使这一技术更趋完善。本实验用荧光素异硫氰酸酯(FITC)与痕量氨基酸样品进行衍生,通过适当增加衍生温度,能明显缩短衍生时间,衍生效果与传统的室温下衍生16h无明显差别;进一步确定30℃水浴反应5h是较理想的FITC与痕量氨基酸的衍生条件。在此优化衍生条件下,成功检测了清醒吗啡戒断大鼠脑导水管周围灰质(periaqueductal gray matter,PAG)微透析液中谷氨酸(glutamate,Glu)和精氨酸(arginine,Arg)含量变化。结果表明,非吗啡依赖和吗啡依赖大鼠脑PAG中L-精氨酸(L-arginine,L-Arg)和L-谷氨酸(L-glutamate,L-Glu)含量无明显差别,纳洛酮催促戒断后的第一个10min内PAG中的L-Arg和L-Glu含量显著增加,分别比戒断前增加了63％和105％,10min后含量逐渐下降,这种变化趋势与同时观察的吗啡戒断评分变化相一致。     

Engineering the Thermoelectric Transport in Half‐Heusler Materials through a Bottom‐Up Nanostructure Synthesis

Half‐Heusler (HH) alloys are among the best promising thermoelectric (TE) materials applicable for the middle‐to‐high temperature power generation. Despite of the large thermoelectric power factor and decent figure‐of‐merit ZT (≈1), their broad applications and enhancement on TE performance are limited by the high intrinsic lattice thermal conductivity (κ_L) due to insufficiencies of phonon scattering mechanisms, and the fewer powerful strategies associated with the microstructural engineering for HH materials. This study reports a bottom‐up nanostructure synthesis approach for these HH materials based on the displacement reaction between metal chlorides/bromides and magnesium (or lithium), followed by vacuum‐assisted spark plasma sintering process. The samples are featured with dense dislocation arrays at the grain boundaries, leading to a minimum κ_L of ≈1 W m^?1 K^?1 at 900 K and one of the highest ZT (≈1) and predicted η (≈11%) for n‐type Hf_0.25Zr_0.75NiSn_0.97Sb_0.03. Further manipulation on the dislocation defects at the grain boundaries of p‐type Nb_0.8Ti_0.2FeSb leads to enhanced maximum power factor of 47 × 10^?4 W m^?1 K^?2 and the predicted η of ≈7.5%. Moreover, vanadium substitution in FeNb_0.56V_0.24Ti_0.2Sb significantly promotes the η to ≈11%. This strategy can be extended to a broad range of advanced alloys and compounds for improved properties.     

The limited photochemical activity of solid aggregated forms of bovine rhodopsin

The visual pigment rhodopsin has been purified and depleted of detergent. Under these conditions, the pigment strongly aggregates. When dried, a significant fraction of these aggregates appear insensitive to light. We have characterized them by means of absorption and photoacoustic spectroscopies and we find that their photochemical behavior is best explained by a limited activity that does not reach photointermediates beyond the lumirhodopsin step in the bleaching sequence of rhodopsin. We interpret this result as an indication of a significant conformational change of the protein during the transition from lumi- to meta-rhodopsin.     

DNA水平上的植物系统学研究方法

本文简要总结了近年来在ＤＮＡ水平上的植物系统学研究方法,着重介绍了限制性长度多态性分析,ＰＣＲ技术在植物系统学上的应用等这一领域最新的进展,并对分子数据的分析方法及系统树的构建进行了详细讨论。