Accurate prediction of the burial status of transmembrane residues of α-helix membrane protein by incorporating the structural and physicochemical features

Predicting the burial status (the residue exposure to the lipid bilayer or buried within the protein core) of transmembrane (TM) residues of α-helix membrane protein (αHMP) is of great importance for genome-wide annotation and for experimental researchers to elucidate diverse physiological processes. In this work, we developed a new computational model that can be used for predicting the burial status of TM residues of αHMP. By incorporating physicochemical scales and conservation index, an efficient prediction model using least squares support vector machine (LS-SVM) was developed. The model was developed from 43 protein chains and its prediction ability was evaluated by an independent test set of other non-redundant ten protein chains. The prediction accuracy of our method was much better than the results of the reported works. Our results demonstrate that the LS-SVM prediction model incorporating structural and physicochemical features derived from sequence information could greatly improve the prediction accuracy.     

NaCl和Na2SO4胁迫下两种刺槐叶肉细胞叶绿体超微结构

二倍体刺槐(diploid Robinia pseudoacacia)是我国水土保持林的先锋树种,具有较强的适应性和抗逆性,对改善生态环境、防治水土流失、调节水文状况有重要作用。四倍体刺槐(tetraploid Robinia pseudoacacia)是二倍体刺槐的加倍品种,也称多倍体刺槐,由韩国引进,具有速生、耐盐碱、耐干旱和耐烟尘等特点。目前,关于四倍体刺槐的研究,主要集中于栽培技术和繁殖技术方面,而关于四倍体刺槐叶片超微结构与其耐盐性的关系尚缺乏报道。比较了二倍体刺槐和四倍体刺槐在NaCl和Na₂SO₄胁迫下,叶片叶绿体超微结构的变化特点,一方面可以对二者的耐盐性进行鉴定,同时也可以探讨不同盐分胁迫条件下的作用机制。利用NaCl和Na₂SO₄进行20d的盐胁迫处理,观察叶绿体超微结构的变化特点,发现:NaCl处理前,二者叶肉细胞叶绿体为梭形、形态饱满、结构完整,NaCl处理后10d时,二倍体刺槐的叶绿体出现变形、膜模糊、基粒片层松散、类囊体解体、脂质球增多等现象,NaCl处理后20d时,叶绿体肿胀、变形,基粒片层断裂,膜系统解体。Na₂SO₄处理后10d时,二倍体刺槐的叶绿体肿胀,膜模糊,基粒片层松散、类囊体解体,Na₂SO₄盐胁迫处理后20d时,膜系统全部解体,结构破坏更为严重。总体来说,四倍体刺槐在盐胁迫后叶绿体结构变化不明显,只是在Na₂SO₄处理20d时,四倍体刺槐的叶绿体出现中空、基粒片层松散、膜边缘模糊现象。在处理前,两种刺槐的叶绿体均紧贴细胞壁,分布于细胞壁边缘。在NaCl处理后10d时,二倍体刺槐的叶绿体仍呈有序排列,紧贴细胞壁,但在处理后20d时,大部分叶绿体脱离细胞壁,呈随机分布。在Na₂SO₄处理后10d时,二倍体刺槐部分叶绿体脱离细胞壁,位于细胞中央。在Na₂SO₄处理后20d时,二倍体刺槐叶绿体大部分与细胞壁脱离。四倍体刺槐在两种盐胁迫处理前后叶绿体的排列变化不明显,均分布于细胞壁边缘,紧贴细胞壁。所以在盐胁迫下,耐盐植物叶片的叶绿体表现为结构完整,基粒片层清晰,类囊体结构完整,而不耐盐植物则表现为叶绿体超微结构松散、变形,基粒片层模糊,破坏严重时基粒片层扭曲,叶绿体解体,失去完整结构。     

Study on the Promotion of Bacterial Biofilm Formation by a Salmonella Conjugative Plasmid and the Underlying Mechanism

To investigate the effect of the pR_ST98 plasmid, originally isolated from Salmonella enterica serovar Typhi (S. Typhi), on biofilm (BF) formation, we carried out in vitro experiments using S. Typhi, Salmonella enterica serovar Typhimurium (S. Typhimurium) and Escherichia coli (E. coli). We further explored the effects of pR_ST98 in vivo by establishing two animal models, a tumor-bearing mouse model and a mouse urethral catheter model. Moreover, we examined the relationship between the quorum-sensing (QS) system and pR_ST98-mediated BF formation. These studies showed that pR_ST98 enhanced BF formation in different bacteria in vitro. In both animal models, pR_ST98 promoted BF formation and caused more severe pathological changes. It was previously reported that Salmonella senses exogenous N-acylhomoserine lactones (AHLs) through the regulatory protein SdiA and regulates the expression of genes including the virulence gene rck, which is located on the virulence plasmid of some serotypes of Salmonella. In this study, we confirmed the locus of the rck gene on pR_ST98 and found that AHLs increased rck expression in pR_ST98-carrying strains, thereby enhancing bacterial adherence, serum resistance and bacterial BF formation. In conclusion, the Salmonella conjugative plasmid pR_ST98 promotes bacterial BF formation both in vitro and in vivo, and the mechanism may relate to the AHL-SdiA-Rck signaling pathway.     

Synthesis and evaluation of near-infrared (NIR) dye-herceptin conjugates as photoacoustic computed tomography (PCT) probes for HER2 expression in breast cancer

We are evaluating PCT imaging in conjunction with NIR dye labeled Herceptin antibody for noninvasive assessment of HER2 expression in tumors. Herceptin was labeled with Alexa Fluor-750 amine reactive dye for characterization of photoacoustic and fluorescence signals. Measurements were performed in solution and after incubation in cultured cell lines that were positive or negative in expression of HER2. The dye to antibody ratio was controlled to achieve a broad range of degree of labeling (DOL = 2 to 15). Photoacoustic signal intensity of Herceptin-dye conjugates in solution increased with increases over the entire DOL range studied. In contrast, fluorescence exhibited significant quenching for higher DOL. In vitro PCT imaging of the labeled HER2 (+) and HER2 (-) cells revealed the targeting specificity of the NIR dye labeled Herceptin. In HER2 (+) cells lines, photoacoustic signal intensity gradually increased with increasing DOL and with increasing number of cells. These results demonstrate that PCT-based measurement of HER2 receptor binding using NIR dye labeled Herceptin is feasible. The absence of a quenching effect with increased DOL advantages this method over traditional methods based on fluorescence measurement.     

几种野生植物提取物抑菌作用研究

本文以乙醇为溶剂,分别提取了瓦松、泽漆及一组中草药配方的有效成分;室内测定了三种提取液对5种植物病原菌(棉花枯萎病菌Fusarium oxysporum f.sp.vasinfectum;小麦赤霉病菌Fusarium graminearum Schw;西瓜枯萎病菌Fusarium oxysporum f.sp.niveum;仙人掌软腐病菌Erwinia chrysanthemi pv.chrysanthemi;魔芋软腐病菌Erwiniacarotovora pv.carotovora)的抑菌作用.结果表明:三种提取物对镰刀菌均有不同程度的抑制作用,且三种提取物的抑菌效果差异显著,其中瓦松的抑菌效果最强.当在50 mL培养基中加入5mL不同提取液时,瓦松对不同镰刀菌的相对抑制率为91.39%～100%;中草药配方提取液对不同镰刀菌的相对抑制率分别为41.11%～85.37%;而泽漆提取液对镰刀菌的相对抑制率仅为12.86%～21.23%;当在50 mL培养基中加入提取液体积降低为2 mL、1 mL、0.5mL时,三种提取液对三种镰刀菌的抑制效果骤然下降,但下降的梯度不一.对大白菜软腐病菌与魔芋软腐病菌而言也是瓦松的抑菌效果最强,中草药配方次之,泽漆的抑制效果最差.