Experimental conditions improving in‐solution target enrichment for ancient DNA

High‐throughput sequencing has dramatically fostered ancient DNA research in recent years. Shotgun sequencing, however, does not necessarily appear as the best‐suited approach due to the extensive contamination of samples with exogenous environmental microbial DNA. DNA capture‐enrichment methods represent cost‐effective alternatives that increase the sequencing focus on the endogenous fraction, whether it is from mitochondrial or nuclear genomes, or parts thereof. Here, we explored experimental parameters that could impact the efficacy of MYbaits in‐solution capture assays of ~5000 nuclear loci or the whole genome. We found that varying quantities of the starting probes had only moderate effect on capture outcomes. Starting DNA, probe tiling, the hybridization temperature and the proportion of endogenous DNA all affected the assay, however. Additionally, probe features such as their GC content, number of CpG dinucleotides, sequence complexity and entropy and self‐annealing properties need to be carefully addressed during the design stage of the capture assay. The experimental conditions and probe molecular features identified in this study will improve the recovery of genetic information extracted from degraded and ancient remains.     

Interplay between HTRA1 and classical signalling pathways in organogenesis and diseases

The high temperature requirement factor A1 (HTRA1) is a serine protease which modulates an array of signalling pathways driving basal biological processes. HTRA1 plays a significant role in cell proliferation, migration and fate determination, in addition to controlling protein aggregates through refolding, translocation or degradation. The mutation of HTRA1 has been implicated in a plethora of disorders and this has also led to its growing interest as drug therapy target. This review details the involvement of HTRA1 in certain signalling pathways, namely the transforming growth factor beta (TGF-β), canonical Wingless/Integrated (WNT) and NOTCH signalling pathways during organogenesis and various disease pathogenesis such as preeclampsia, age-related macular degeneration (AMD), small vessel disease and cancer. We have also explored possible avenues of exploiting the serine proteases for therapeutic management of these disorders.     

四个脂肪酸合成酶基因在哺乳动物细胞中的超表达提高长链多不饱和脂肪酸生物合成效率

DHA(22:6n-3)、EPA(20:5n-3)和ARA(20:4n-6)三种长链多不饱和脂肪酸在生物体内活性最强,它们在促进大脑发育和功能维持以及在预防和治疗心血管疾病、炎症、癌症等多种疾病方面有着重要作用。然而,尽管哺乳动物体内有完整的长链多不饱和脂肪酸合成酶系,但哺乳动物合成这些长链多不饱和脂肪酸的效率很低而主要依赖于食物获取。本研究应用转基因方法,将哺乳动物来源的Δ6和Δ5脂肪酸去饱和酶以及Δ6和Δ5脂肪酸延长酶这4种酶的编码基因构建成为一个多基因表达载体,然后转染哺乳动物细胞HEK293T,实现了4个目的基因的超表达,再通过气质联用(GC-MS)分析证实了DHA、EPA和ARA等长链多不饱和脂肪酸的合成效率及水平显著增加,DHA的水平更是提高了2.5倍。由此可见,哺乳动物具有某种抑制长链多不饱和脂肪酸高水平合成的机制,但通过Δ6和Δ5脂肪酸去饱和酶以及Δ6和Δ5脂肪酸延长酶的超表达,能够打破哺乳动物这种抑制机制,从而显著提高DHA、EPA、ARA等的合成水平。同时,本研究的思路也为在转基因动物中生产长链多不饱和脂肪酸提供了重要的启示。     

Fully automated protein complex prediction based on topological similarity and community structure

To understand the function of protein complexes and their association with biological processes, a lot of studies have been done towards analyzing the protein-protein interaction (PPI) networks. However, the advancement in high-throughput technology has resulted in a humongous amount of data for analysis. Moreover, high level of noise, sparseness, and skewness in degree distribution of PPI networks limits the performance of many clustering algorithms and further analysis of their interactions.In addressing and solving these problems we present a novel random walk based algorithm that converts the incomplete and binary PPI network into a protein-protein topological similarity matrix (PP-TS matrix). We believe that if two proteins share some high-order topological similarities they are likely to be interacting with each other. Using the obtained PP-TS matrix, we constructed and used weighted networks to further study and analyze the interaction among proteins. Specifically, we applied a fully automated community structure finding algorithm (Auto-HQcut) on the obtained weighted network to cluster protein complexes. We then analyzed the protein complexes for significance in biological processes. To help visualize and analyze these protein complexes we also developed an interface that displays the resulting complexes as well as the characteristics associated with each complex.Applying our approach to a yeast protein-protein interaction network, we found that the predicted protein-protein interaction pairs with high topological similarities have more significant biological relevance than the original protein-protein interactions pairs. When we compared our PPI network reconstruction algorithm with other existing algorithms using gene ontology and gene co-expression, our algorithm produced the highest similarity scores. Also, our predicted protein complexes showed higher accuracy measure compared to the other protein complex predictions.     

Controlling the sugar beet fly Pegomyia mixta Vill. with entomopathogenic nematodes

Sugar beet, Beta vulgaris L. is a strategic crop of sugar industry in Egypt. It is threatened by several insect pests among most important of them is the beet fly Pegomyia mixta. This work deals with the biological control of this insect using four entomopathogenic nematodes (EPNs). The nematodes included Steinernema carpocapsae S2, Steinernema feltiae, Heterorhabditis bacteriophora (HB1-3) and Heterorhabditis bacteriophora S1. Daily mortality of larvae and pupae of P. mixta were recorded after treatment with serial concentrations (500, 1000, 2000 and 4000 infective juveniles (IJs)/ml) of each of four studied EPNs. In the laboratory all tested nematodes killed the larvae inside their mines in the sugar beet leaves and developed in their bodies in different extends. They also killed the insect pupae in the soil and developed in their bodies. Young larvae were more susceptible than old ones. New pupae were more susceptible than old ones. In the field a single spray of S. feltiae or H. bacteriophora caused 81.3 or 75.9% reduction in the larval population of the in sugar beet leaves.     

MicroRNAs 33, 122, and 208: a potential novel targets in the treatment of obesity,diabetes, and heart-related diseases

Despite decades of research, obesity and diabetes remain major health problems in the USA and worldwide. Among the many complications associated with diabetes is an increased risk of cardiovascular diseases, including myocardial infarction and heart failure. Recently, microRNAs have emerged as important players in heart disease and energy regulation. However, little work has investigated the role of microRNAs in cardiac energy regulation. Both human and animal studies have reported a significant increase in circulating free fatty acids and triacylglycerol, increased cardiac reliance on fatty acid oxidation, and subsequent decrease in glucose oxidation which all contributes to insulin resistance and lipotoxicity seen in obesity and diabetes. Importantly, MED13 was initially identified as a negative regulator of lipid accumulation in Drosophilia. Various metabolic genes were downregulated in MED13 transgenic heart, including sterol regulatory element-binding protein. Moreover, miR-33 and miR-122 have recently revealed as key regulators of lipid metabolism. In this review, we will focus on the role of microRNAs in regulation of cardiac and total body energy metabolism. We will also discuss the pharmacological and non-pharmacological interventions that target microRNAs for the treatment of obesity and diabetes.     

人端粒酶逆转录酶(hTERT)基因第3内含子的克隆和分析

从端粒酶活性呈阳性的永生细胞株人肺腺癌细胞SPC A 1中分离了总RNA ,以此为模板 ,结合RT PCR技术和长模板PCR技术 ,用hTERT基因特异性引物扩增到一长约 2 .2kb的cDNA片段。将该片段纯化后克隆到通用测序载体T easyvector上得到重组质粒。用测序引物SP6和T7对该片段进行部分双向测序。经序列分析和同源比较推测该片段包含了hTERT基因的第 3内含子。该结果提示了RT PCR技术和长模板PCR技术用于真核生物基因内含子克隆的可行性。进一步的分析表明 ,该片段在不同细胞的RT PCR产物中的产量不同 ,提示hTERT基因前体mRNA中的第 3内含子可能在不同细胞中有不同的剪接效率。     

哺乳动物细胞多不饱和脂肪酸合成酶系的重建将亚油酸代谢转变为二十二碳六烯酸

二十二碳六烯酸(DHA,22:6n-3)是一种长度为22个碳原子且含有6个双键的ω-3系多不饱和脂肪酸,在人体中具有重要生物学功能。人体及其他哺乳动物体内只能合成少量的DHA,更多的需求必须从食物中获取。然而,DHA的天然资源(主要是深海鱼类等海洋产品)日趋枯竭,开发新型资源以满足不断扩大的市场需求势在必行。本研究利用转基因技术,在哺乳动物细胞中使Δ6和Δ5脂肪酸去饱和酶以及Δ6和Δ5脂肪酸延长酶超表达,同时表达来源于秀丽隐杆线虫Caenorhabditis elegans的Δ15去饱和酶和小眼虫Euglena gracilis的Δ4去饱和酶,结果表明,这6种酶的表达或超表达能将ω-6系的亚油酸(LA,18:2n-6)有效地转化为DHA(22:6n-3),后者的含量从对照组的16.74%提高到实验组的25.3%。本研究的策略及技术路线为将来利用遗传改造的哺乳动物生产珍稀的DHA(22:6n-3)等长链多不饱和脂肪酸产品提供了重要的启示。