Combining evolutionary and structural information for local protein structure prediction

We study the effects of various factors in representing and combining evolutionary and structural information for local protein structural prediction based on fragment selection. We prepare databases of fragments from a set of non-redundant protein domains. For each fragment, evolutionary information is derived from homologous sequences and represented as estimated effective counts and frequencies of amino acids (evolutionary frequencies) at each position. Position-specific amino acid preferences called structural frequencies are derived from statistical analysis of discrete local structural environments in database structures. Our method for local structure prediction is based on ranking and selecting database fragments that are most similar to a target fragment. Using secondary structure type as a local structural property, we test our method in a number of settings. The major findings are: (1) the COMPASS-type scoring function for fragment similarity comparison gives better prediction accuracy than three other tested scoring functions for profile-profile comparison. We show that the COMPASS-type scoring function can be derived both in the probabilistic framework and in the framework of statistical potentials. (2) Using the evolutionary frequencies of database fragments gives better prediction accuracy than using structural frequencies. (3) Finer definition of local environments, such as including more side-chain solvent accessibility classes and considering the backbone conformations of neighboring residues, gives increasingly better prediction accuracy using structural frequencies. (4) Combining evolutionary and structural frequencies of database fragments, either in a linear fashion or using a pseudocount mixture formula, results in improvement of prediction accuracy. Combination at the log-odds score level is not as effective as combination at the frequency level. This suggests that there might be better ways of combining sequence and structural information than the commonly used linear combination of log-odds scores. Our method of fragment selection and frequency combination gives reasonable results of secondary structure prediction tested on 56 CASP5 targets (average SOV score 0.77), suggesting that it is a valid method for local protein structure prediction. Mixture of predicted structural frequencies and evolutionary frequencies improve the quality of local profile-to-profile alignment by COMPASS.     

傅家边丘陵山地滨梅根围AM真菌与土壤酶活性的关系

为揭示AM真菌对宿主滨梅（Prunus maritima）的作用特点及对根部土壤酶活性的影响,于2009年4月、7月和10月分别从江苏傅家边丘陵山地滨梅根围分0～10、10～20、20～30、30～40、40～50 cm 5个土层采集土壤样品,观察滨梅AM菌根结构,测定了AM真菌侵染率、孢子密度、土壤磷酸酶、脲酶活性及有效磷、碱解氮含量,着重分析了AM真菌与土壤酶活性之间的关系。结果表明,滨梅能与AM真菌形成良好的共生关系,共生体为泡囊-丛枝结构;AM真菌侵染率和孢子密度分别在7月份和10月份最高,均出现在0～20 cm土层,并随土层加深而下降;AM真菌侵染率与土壤酸性磷酸酶、中性磷酸酶、碱磷酸酶活性显著正相关,而与脲酶活性无相关性;AM真菌孢子密度与碱性磷酸酶、脲酶活性呈极显著正相关关系;孢子密度与土壤有效磷、土壤碱解氮含量显著正相关,但AM真菌侵染率仅与土壤有效磷含量显著正相关;孢子密度与菌根侵染率之间无相关性。可见,滨梅AM真菌侵染率与孢子密度有明显的时空分布并与土壤因子尤其是某些土壤酶活性密切相关,且AM菌根的形成是滨梅适应丘陵山地干旱贫瘠环境的有效对策之一。     

Study of the Antifungal Ability of Bacillus subtilis Strain PY-1 in Vitro and Identification of its Antifungal Substance （Iturin A）

A Bacillus strain,denoted as PY-1,was isolated from the vascular bundle of cotton.Biochemical,physiological and 16S rDNA sequence analysis proved that it should belong to Bacillus subtilis.The PY-1strain showed strong ability against many common plant fungal pathogens in vitro.The antibiotics producedby this strain were stable in neutral and basic conditions,and not sensitive to high temperature.From theculture broth of PY-1 strain,five antifungal compounds were isolated by acidic precipitation,methanolextraction,gel filtration and reverse-phase HPLC.Advanced identification was performed by mass spec-trometry and nuclear magnetic resonance spectroscopy.These five antifungal compounds were proved to bethe isomers of iturin A:A2,A3,A4,A6 and A7.In fast atom bombardment mass spectrometry/mass spec-trometry collision-induced dissociation spectra,fragmentation ions from two prior linear acylium ions wereobserved,and the prior ion,Tyr-Asn-Gln-Pro-Asn-Ser-βAA-Asn-CO~ ,was first reported.     

有机磷降解菌的筛选及其促生特性

【目的】从环境中筛选高效有机磷降解菌及研究其促生机制。【方法】利用蒙金娜有机磷培养基筛选有机磷降解菌,用生化实验对其促生特性进行研究,且通过盆栽实验筛选对黄瓜苗有促生作用的高效有机磷降解菌。【结果】从草坪根周筛选到35株有机磷降解菌,选择5株代表性菌进行黄瓜盆栽实验。结果表明G3-6有机磷降解能力最强,溶磷圈直径(HD)与菌落直径(CD)比值为3.28,且对黄瓜苗的促生效果优于其他菌株。与CK相比,G3-6可提高黄瓜苗鲜重71.53%、干重69.78%和株高33.55%;与阳性对照枯草芽孢杆菌F-H-1相比,G3-6可提高黄瓜苗鲜重2.52%、干重21.14%和株高8.27%。相关分析结果表明降解有机磷能力在促进植物生长过程中可能发挥着比其他功能更重要的作用。16S r RNA序列分析初步鉴定G3-6为假单胞菌属。【结论】假单胞菌G3-6除具有较强的有机磷降解、分泌IAA和铁载体能力,对黄瓜苗也有较好的促生作用,是1株潜在的具有广阔市场应用价值的高效促生菌。     

高盐溶液预处理幽门螺杆菌对蒙古沙土鼠胃黏膜损伤作用

目的 探讨高盐预处理的幽门螺杆菌(H.pylori)对胃黏膜的损伤作用。 方法 将30%高盐预处理前后的胃癌来源的H.pylori菌株(4854)灌胃蒙古沙土鼠(MGs),在灌胃后13、26和73周解剖动物,通过组织病理学检查、免疫组化染色和黏膜厚度测量,探讨高盐预处理的H.pylori对胃黏膜的损伤作用。 结果 与未加盐预处理的相应菌株相比,高盐预处理组小鼠的慢性炎症、黏膜变性/坏死、腺体萎缩伴肠上皮化生的发生率较低,黏膜糜烂/溃疡和黏膜上皮增生的发生率较高,差异均有统计学意义(t=8.325 6,P=0.040 8)。第73周,高盐预处理4854菌株组胃体和胃窦黏膜增生显著高于未加盐预处理组(t=12.802 4,P=0.035 1;t=16.536 0,P=0.043 8)。 结论 高盐预处理改变了H.pylori的体内致病性,有助于阐明H.pylori感染与高盐饮食在胃病中的相互作用模式。     

补充益生菌对功能性腹泻患者焦虑抑郁状态的影响

目的 探讨益生菌对功能性腹泻患者临床症状和心理健康的影响。 方法 将2019年3月至2019年12月在广东省肇庆市高要区人民医院消化内科门诊收治的伴有焦虑抑郁状态的90例功能性腹泻住院病人随机分为试验组、对照组A、对照组B。三组受试者均口服匹维溴铵,试验组口服双歧杆菌四联活菌,对照组A服用氟西汀,对照组B未给其他药物治疗,疗程均为1个月。治疗前后,比较患者大便次数及性状、汉密尔顿焦虑量表(HAMA)和汉密尔顿抑郁量表(HAMD)评分。 结果 治疗前三组患者每周排便不同次数的人数比较,差异无统计学意义(P>0.05)。治疗第3周和第4周后,与对照组A相比,对照组B和试验组的排便不同次数的人数差异具有统计学意义(P0.05)。治疗第3和第4周后,与对照组A相比,对照组B和试验组的Bristol粪便性状评分比较,差异有统计学意义(P结论 通过补充益生菌可调节功能性腹泻患者腹泻次数,提高功能性腹泻患者生活质量,改善患者焦虑抑郁症状。     

Hyperosmolarity enhanced susceptibility to renal tubular fibrosis by modulating catabolism of type I transforming growth factor‐β receptors

Hyperosmolarity plays an essential role in the pathogenesis of diabetic tubular fibrosis. However, the mechanism of the involvement of hyperosmolarity remains unclear. In this study, mannitol was used to evaluate the effects of hyperosmolarity on a renal distal tubule cell line (MDCK). We investigated transforming growth factor‐β receptors and their downstream fibrogenic signal proteins. We show that hyperosmolarity significantly enhances the susceptibility to exogenous transforming growth factor (TGF)‐β1, as mannitol (27.5 mM) significantly enhanced the TGF‐β1‐induced increase in fibronectin levels compared with control experiments (5.5 mM). Specifically, hyperosmolarity induced tyrosine phosphorylation on TGF‐β RII at 336 residues in a time (0–24 h) and dose (5.5–38.5 mM) dependent manner. In addition, hyperosmolarity increased the level of TGF‐β RI in a dose‐ and time‐course dependent manner. These observations may be closely related to decreased catabolism of TGF‐β RI. Hyperosmolarity significantly downregulated the expression of an inhibitory Smad (Smad7), decreased the level of Smurf 1, and reduced ubiquitination of TGF‐β RI. In addition, through the use of cycloheximide and the proteasome inhibitor MG132, we showed that hyperosmolarity significantly increased the half‐life and inhibited the protein level of TGF‐β RI by polyubiquitination and proteasomal degradation. Taken together, our data suggest that hyperosmolarity enhances cellular susceptibility to renal tubular fibrosis by activating the Smad7 pathway and increasing the stability of type I TGF‐β receptors by retarding proteasomal degradation of TGF‐β RI. This study clarifies the mechanism underlying hyperosmotic‐induced renal fibrosis in renal distal tubule cells. J. Cell. Biochem. 109: 663–671, 2010. © 2010 Wiley‐Liss, Inc.     

Prohibitin is a cholesterol‐sensitive regulator of cell cycle transit

Cholesterol is essential in establishing most functional animal cell membranes; cells cannot grow or proliferate in the absence of sufficient cholesterol. Consequently, almost every cell, tissue, and animal tightly regulates cholesterol homeostasis, including complex mechanisms of synthesis, transport, uptake, and disposition of cholesterol molecules. We hypothesize that cellular recognition of cholesterol insufficiency causes cell cycle arrest in order to avoid a catastrophic failure in membrane synthesis. Here, we demonstrate using unbiased proteomics and standard biochemistry that cholesterol insufficiency causes upregulation of prohibitin, an inhibitor of cell cycle progression, through activation of a cholesterol‐responsive promoter element. We also demonstrate that prohibitin protects cells from apoptosis caused by cholesterol insufficiency. This is the first study tying cholesterol homeostasis to a specific cell cycle regulator that inhibits apoptosis. J. Cell. Biochem. 111: 1367–1374, 2010. © 2010 Wiley‐Liss, Inc.