Metabolic network analysis revealed distinct routes of deletion effects between essential and non-essential genes

Interest in essential genes has arisen recently given their importance in antimicrobial drug development. Although knockouts of essential genes are commonly known to cause lethal phenotypes, there is insufficient understanding on the intermediate changes followed by genetic perturbation and to what extent essential genes correlate to other genes. Here, we characterized the gene knockout effects by using a list of affected genes, termed as 'damage lists'. These damage lists were identified through a refined cascading failure approach that was based on a previous topological flux balance analysis. Using an Escherichia coli metabolic network, we incorporated essentiality information into damage lists and revealed that the knockout of an essential gene mainly affects a large range of other essential genes whereas knockout of a non-essential gene only interrupts other non-essential genes. Also, genes sharing common damage lists tend to have the same essentiality. We extracted 72 core functional modules from the common damage lists of essential genes and demonstrated their ability to halt essential metabolites production. Overall, our network analysis revealed that essential and non-essential genes propagated their deletion effects via distinct routes, conferring mechanistic explanation to the observed lethality phenotypes of essential genes.     

大亚湾核电站邻近水域马氏珠母贝的种群生态

１９９３年７月－１９９４年１２月,在大亚湾东山珍珠养殖场进行马氏珠母贝的生长和死亡率研究,结果表明：中、小贝种群个体大小组成呈正态分布,进入中贝以后,正态分布不明显。小贝生长快,壳高增幅大,死亡率较低,中贝以后,生长较慢,死亡率较高。     

Definition of fibronectin-mediated uptake of gelatinized latex by liver slices and macrophages

These studies show that both liver slices and macrophages carried out fibronectin concentration-dependent uptake of ¹²⁵I-labeled gelatin-coated latex (test latex). Lack of phagocytosis of test latex by liver slices was shown directly by electron microscopy and indirectly by trypsin treatment, which caused the release of all test latex taken up in response to fibronectin. Inhibitors of phagocytosis did not alter this uptake. On the other hand, trypsin released only a portion of test latex from macrophages. Inhibitors of phagocytosis did not effect the released radioactive particles from macrophages but greatly reduced the trypsin-resistant radioactivity, taken as representing phagocytized particles. Opsonization of test latex with fibronectin did not require heparin but its association with liver slices occurred only in the presence of heparin. Macrophages, however, readily bound and internalized the opsonized test latex and heparin only potentiated these reactions. Gelatin competed with test latex for fibronectin for opsonization, but did not inhibit binding and phagocytosis of fibronectin-test latex complexes. Finally, soluble fibronectin-gelatin complexes did not compete for binding and phagocytosis of fibronectin-test latex complexes. Thus, fibronectin concentrated on the surface of latex is preferred for interaction with the fibronection receptor of macrophages. Gelatin, however, was not essential for this reaction, because fibronectin directly coupled to latex was also readily taken up.     

A study on the interaction between cadmium and α‐chymotrypsin and the underlying mechanisms

Because cadmium might interact with proteins and, thus, exert toxicity in organisms, it is vital to understand the molecular mechanism of the interaction between cadmium and biologically relevant proteins as well as the structural and functional changes in these proteins. In this study, the interaction between α‐chymotrypsin (α‐ChT) and cadmium chloride (CdCl₂) was investigated by performing enzyme activity determinations, multispectroscopic measurements, isothermal titration calorimetry, and molecular docking studies. It was demonstrated that CdCl ₂ binds to α‐ChT mainly via electrostatic forces with (21.0 ± 0.982) binding sites, leading to the increase of α‐helix and the decrease of β‐sheet. The interaction between CdCl ₂ and α‐ChT loosened the protein skeleton and increased the molecular volume of α‐ChT. CdCl ₂ first binds to the interface of α‐ChT and then interacts with the key residues His 57 or Asp 102 or both in the active sites, leading to the activity inhibition of α‐ChT under the exposure of high CdCl ₂ concentrations.     

HAP转录因子与DNA结合的活力受细胞内氧化还原系统的调节

ＨＡＰ 转录因子（ ＨＡＰ２／ＨＡＰ３／ＨＡＰ４／ＨＡＰ５） 是存在于酿酒酵母中的一种异源多聚蛋白,它能与酵母中许多启动子上游的ＣＣＡＡＴ盒（ 顺式作用元件） 专一性结合, 以增强基因的转录。在酵母ｈａｐ５ 突变株的细胞中,用酵母单杂交系统从水稻ｃＤＮＡＧＡＬ４ 表达文库中筛选出的阳性克隆是编码谷胱甘肽氧还蛋白的ｃＤＮＡ,提示细胞内的氧化还原系统可能作用于ＨＡＰ蛋白,从而对ＣＣＡＡＴ盒的结合活力起调节作用。对ＨＡＰ３ 亚基分子中半胱氨酸残基的突变实验结果支持上述推测     

重组猪乳铁蛋白N端的高效表达及抑菌活性检测

为获得表达猪乳铁蛋白基因的重组菌株,并检测其表达的重组猪乳铁蛋白抑菌活性,应用RT-PCR方法从泌乳3d后母猪乳腺组织中扩增了猪乳铁蛋白N端1077bp的PLF-N基因片段,与GenBank上发表的4株猪乳铁蛋白基因序列相比,核苷酸同源性均达到99%以上。为了得到高表达量的PLF-N基因,以扩增的PLF-N片段为参考模板,经过密码子优化,全基因合成了编码猪乳铁蛋白N端的基因PLF-NS。将其定向插入到原核表达载体pET-30b中,转化大肠杆菌BL21,获得了表达PLF-NS的重组菌pET-PLF-NS/BL21;经IPTG诱导,并对表达条件进行优化,以及通过SDS-PAGE和Western blotting分析均表明猪乳铁蛋白得到了正确表达,其产物分子量约为42kDa,最优表达条件下蛋白表达量占菌体总蛋白的32%,表达产物以包涵体形式存在。包涵体经裂解、纯化、复性处理后纯度达到98%。用琼脂孔穴扩散抑菌法检测表明重组猪乳铁蛋白具有明显的抑菌作用。表明通过基因优化对表达量低的基因进行改造使之高效表达,是一种提高表达效率的有效手段。     

口腔及肠道菌群与冠心病关系的研究进展

冠心病是由多种病理因素引起的复杂疾病,严重威胁人类健康,其机制尚未完全阐明。近年来,研究表明冠心病与口腔和肠道菌群密切相关。菌群失调导致的炎症反应、氧化应激反应、脂质代谢失调和氧化三甲胺累积是参与冠心病发生的主要风险因素。此外,口腔菌群与肠道菌群相关,参与冠心病的发生与发展。中医治疗疾病的优势在于辨证论治,而证型的判断缺乏客观标准。多项研究应用口腔菌群或肠道菌群分析了疾病的中医证型。本文系统地阐述了口腔菌群和肠道菌群在冠心病发病机制中的作用,阐述了不同中医证型冠心病菌群分析的研究进展,为临床开展此类研究提供参考。     

Enhanced stability of M1 protein mediated by a phospho-resistant mutation promotes the replication of prevailing avian influenza virus in mammals

Avian influenza virus (AIV) can evolve multiple strategies to combat host antiviral defenses and establish efficient infectivity in mammals, including humans. H9N2 AIV and its reassortants (such as H5N6 and H7N9 viruses) pose an increasing threat to human health; however, the mechanisms involved in their increased virulence remain poorly understood. We previously reported that the M1 mutation T37A has become predominant among chicken H9N2 isolates in China. Here, we report that, since 2010, this mutation has also been found in the majority of human isolates of H9N2 AIV and its emerging reassortants. The T37A mutation of M1 protein enhances the replication of H9N2 AIVs in mice and in human cells. Interestingly, having A37 instead of T37 increases the M1 protein stability and resistance to proteasomal degradation. Moreover, T37 of the H9N2 M1 protein is phosphorylated by protein kinase G (PKG), and this phosphorylation induces the rapid degradation of M1 and reduces viral replication. Similar effects are also observed in the novel H5N6 virus. Additionally, ubiquitination at K187 contributes to M1-37T degradation and decreased replication of the virus harboring T37 in the M1 protein. The prevailing AIVs thereby evolve a phospho-resistant mutation in the M1 protein to avoid viral protein degradation by host factors, which is advantageous in terms of replication in mammalian hosts.     

水稻蜡质基因第一内含子碱基突变引起其RNA二级结构的可能变化

通过体外转录得到籼稻品种232蜡质基因第一内含子5’端430 bp的ssRNA分子,以及在此区域发生了自然突变的粳稻品种寒丰蜡质基因第一内含子5’端同样长度的ssRNA分子。部分变性胶电泳结果表明两种ssRNA分子的迁移速率不同。将两种ssRNA分子的核酸序列用计算机分析,表明此两种ssRNA分子能形成不同的茎-环结构,自由能值也有差异。对突变引起的这些不同与两种水稻品种蜡质基因转录本剪接的差异进行了讨论。