Identification of suitable reference genes for real-time quantitative PCR analysis of hydrogen peroxide-treated human umbilical vein endothelial cells

Background

Oxidative stress can induce cell injury in vascular endothelial cells, which is the initial event in the development of atherosclerosis. Although quantitative real-time polymerase chain reaction (qRT-PCR) has been widely used in gene expression studies in oxidative stress injuries, using carefully validated reference genes has not received sufficient attention in related studies. The objective of this study, therefore, was to select a set of stably expressed reference genes for use in qRT-PCR normalization in oxidative stress injuries in human umbilical vein endothelial cells (HUVECs) induced by hydrogen peroxide (H₂O₂).

Results

Using geNorm analysis, we found that five stably expressed reference genes were sufficient for normalization in qRT-PCR analysis in HUVECs treated with H₂O₂. Genes with the most stable expression according to geNorm were U6, TFRC, RPLP0, GAPDH, and ACTB, and according to NormFinder were ALAS1, TFRC, U6, GAPDH, and ACTB.

Conclusion

Taken together, our study demonstrated that the expression stability of reference genes may differ according to the statistical program used. U6, TFRC, RPLP0, GAPDH, and ACTB was the optimal set of reference genes for studies on gene expression performed by qRT-PCR assays in HUVECs under oxidative stress study.

     

Synthesis and application of thiol‐functionalized magnetic nanoparticles for studying interactions of epirubicin hydrochloride with bovine serum albumin by fluorescence spectrometry

A novel method was developed for studying the interaction between epirubicin hydrochloride (EPI) and bovine serum albumin (BSA) by fluorescence spectrometry. Fe₃O₄ magnetic nanoparticles (MNPs) synthesized and functionalized with thiol group were employed for the immobilization and separation of target BSA in reaction solutions. The concentrations of the non‐immobilized BSA and unbound EPI were obtained separately by fluorescence spectrometry. The binding constants (K _a ) and number of binding sites (n ) of EPI with BSA were calculated. In this study, the K _a value was 5.05 × 10⁵ L mol^?1, suggesting a strong binding of EPI to BSA, and the n value was 1.15. The effects of common metal ions on K _a of EPI with BSA were also investigated, and the results showed there was clearly bindings between the metal ions and BSA. The precise binding sites of EPI on BSA were determined as being in site I from the competitive displacement experiments. Copyright © 2016 John Wiley & Sons, Ltd.     

LysGH15B,the SH3b Domain of Staphylococcal Phage Endolysin LysGH15, Retains High Affinity to Staphylococci

LysGH15, a phage endolysin, exhibits a particularly broad lytic spectrum against Staphylococcus aureus, especially methicillin-resistant S. aureus (MRSA). Sequence analysis reveals that this endolysin contains a C-terminal cell wall binding domain (SH3b), which causes the endolysin to bind to host strains. In this study, the substrate binding affinity of the SH3b domain (LysGH15B) was evaluated. A fusion protein of LysGH15B and green fluorescent protein (LysGH15B–GFP) were cloned and expressed in Escherichia coli. Laser scanning confocal microscopy was used to detect the fluorescence of the treated cells irradiated at different excitation wavelengths and to determine the binding activity of LysGH15B–GFP and GFP. We found that LysGH15B–GFP not only generated green fluorescence, but, more importantly, also displayed specific affinity to staphylococcal isolates, especially MRSA. In contrast, the single GFP did not display any binding activity. The high affinity was attributed to the portion of LysGH15B and the binding activity of the fusion protein was specific to staphylococci. This study provides an insight into the SH3b domain of LysGH15. The specific binding activity may cause LysGH15B to serve as an anchoring device, and offer an alternative approach for cell surface attachment onto staphylococci.     

Modeling of chromosome intermingling by partially overlapping uniform random polygons

During the early phase of the cell cycle the eukaryotic genome is organized into chromosome territories. The geometry of the interface between any two chromosomes remains a matter of debate and may have important functional consequences. The Interchromosomal Network model (introduced by Branco and Pombo) proposes that territories intermingle along their periphery. In order to partially quantify this concept we here investigate the probability that two chromosomes form an unsplittable link. We use the uniform random polygon as a crude model for chromosome territories and we model the interchromosomal network as the common spatial region of two overlapping uniform random polygons. This simple model allows us to derive some rigorous mathematical results as well as to perform computer simulations easily. We find that the probability that one uniform random polygon of length n that partially overlaps a fixed polygon is bounded below by \({1-O(\frac{1}{\sqrt n})}\). We use numerical simulations to estimate the dependence of the linking probability of two uniform random polygons (of lengths n and m, respectively) on the amount of overlapping. The degree of overlapping is parametrized by a parameter \({\epsilon\in [0,1]}\) such that \({\epsilon=0}\) indicates no overlapping and \({\epsilon=1}\) indicates total overlapping. We propose that this dependence relation may be modeled as \({f(\varepsilon, m, n) =1-{\frac{a(\epsilon)}{b(\epsilon)\sqrt{mn}+c(\epsilon)}}}\). Numerical evidence shows that this model works well when \({\epsilon}\) is relatively large \({(\varepsilon \ge 0.5)}\). We then use these results to model the data published by Branco and Pombo and observe that for the amount of overlapping observed experimentally the URPs have a non-zero probability of forming an unsplittable link.     

The development of a high-yield recombinant protein bioreactor through RNAi induced knockdown of ATP/ADP transporter in Solanum tuberosum

There is an increased need for high-yield protein production platforms to meet growing demand. Tuber-based production in Solanum tuberosum offers several advantages, including high biomass yield, although protein concentration is typically low. In this work, we investigated the question whether minor interruption of starch biosynthesis can have a positive effect on tuber protein content and/or tuber biomass, as previous work suggested that partial obstruction of starch synthesis had variable effects on tuber yield. To this end, we used a RNAi approach to knock down ATP/ADP transporter and obtained a large number of transgenic lines for screening of lines with improved tuber protein content and/or tuber biomass. The initial screening was based on tuber biomass because of its relative simplicity. We identified a line, riAATP1-10, with minor (less than 15%) reduction in starch, that had a nearly 30% increase in biomass compared to wild-type, producing both more and larger tubers with altered morphological features compared to wild-type. riAATP1-10 tubers have a higher concentration of soluble protein compared to wild-type tubers, with nearly 50% more soluble protein. We assessed the suitability of this line as a new bioreactor by expressing a human scFv, reaching over 0.5% of total soluble protein, a 2-fold increase over the highest accumulating line in a wild-type background. Together with increased biomass and increased levels in total protein content, foreign protein expression in riAATP1-10 line would translate into a nearly 4-fold increase in recombinant protein yield per plant. Our results indicate that riAATP1-10 line provides an improved expression system for production of foreign proteins.     

RELN基因启动子区SNP位点与精神分裂症的相关性分析

目前有很多证据证明RELN基因在世界人群中是一个精神分裂症的致病基因.基于之前报道过的RELN基因在精神分裂症患者中表达下降的事实,可以推测在RELN基因启动子区可能包含影响精神分裂症发生的多态位点.该研究分析了中国西南地区病例——对照人群中(940位患者和1369位正常人)RELN基因启动子区的3个单核苷酸多态性位点与精神分裂症的相关性.研究结果显示,这些多态位点都不与精神分裂症相关,表明RELN基因的致病位点并不在其启动子区.将前人研究结果与该研究结果进行综合分析(共2843个样本),结果仍不显著.因此,该研究表明,RELN基因启动子区的单核苷酸多态性位点在中国人群中并不与精神分裂症相关.     

TRAF4 participates in Wnt/β-catenin signaling in breast cancer by upregulating β-catenin and mediating its translocation to the nucleus

Tumor necrosis factor receptor-associated factor 4 (TRAF4) is upregulated in various subtypes of breast cancers and cell lines; however, the precise functions of TRAF4 are poorly understood. Our objective was to investigate its relationship with β-catenin. TRAF4 participates in several signaling pathways, such as NF-κB and JNK signaling pathways. In this study, we identified β-catenin as a TRAF4-binding protein, have shown that TRAF4 enhanced expression of β-catenin, and found that TRAF4 mediated the translocation of β-catenin from the cytoplasm to the nucleus, thereby facilitating activation of the Wnt signaling pathway in breast cancer.