Predicting protein-protein interactions by combing various sequence- derived features into the general form of Chou's Pseudo amino acid composition

Knowledge of protein-protein interactions (PPIs) plays an important role in constructing protein interaction networks and understanding the general machineries of biological systems. In this study, a new method is proposed to predict PPIs using a comprehensive set of 930 features based only on sequence information, these features measure the interactions between residues a certain distant apart in the protein sequences from different aspects. To achieve better performance, the principal component analysis (PCA) is first employed to obtain an optimized feature subset. Then, the resulting 67-dimensional feature vectors are fed to Support Vector Machine (SVM). Experimental results on Drosophila melanogaster and Helicobater pylori datasets show that our method is very promising to predict PPIs and may at least be a useful supplement tool to existing methods.     

Comparisons of developmental and reproductive biology between parthenogenetic and sexual Echinothrips americanus (Thysanoptera: Thripidae)

Echinothrips americanus Morgan, an invasive pest on various ornamentals and greenhouse crops, was introduced into mainland China recently, posing a potential threat to ornamentals and greenhouse crops. It exhibits two different reproductive modes: arrhenotokous parthenogenesis and sexual reproduction. Laboratory studies were conducted to compare the developmental and reproductive biology of E. americanus in these two reproductive modes. Results showed that the oviposition period, and longevity of female adults using sexual reproduction were longer than those using parthenogenesis. Furthermore, sexual female adults had higher fecundity and survival rates. However, no significant differences were found among immature stages in the durations of first and second instars, prepupae, and pupae between the two reproductive modes, with the exception of the duration of the egg stadium. The survival rates for eggs and first and second instars were higher in sexual E. americanus whereas there were no survival differences for prepupae and pupae. These results provide valuable insights into the mechanisms of parthenogenesis and sex determination in Thysanoptera.     

Enhanced thermostability of a Rhizopus chinensis lipase by in vivo recombination in Pichia pastoris

ABSTRACT: BACKGROUND: Lipase from Rhizopus chinensis is a versatile biocatalyst for various bioconversions and has been expressed at high-level in Pichia pastoris. However, the use of R. chinensis lipase in industrial applications is restricted by its low thermostability. Directed evolution has been proven to be a powerful and efficient protein engineering tool for improvement of biocatalysts. The present work describes improvement of the thermostability of R. chinensis lipase by directed evolution using P. pastoris as the host. RESULTS: An efficient, fast and highly simplified method was developed to create a mutant gene library in P. pastoris based on in vivo recombination, whose recombination efficiency could reach 2.3 x 105 /mug DNA. The thermostability of r27RCL was improved significantly by two rounds of error-prone PCR and two rounds of DNA shuffling in P. pastoris. The S4-3 variant was found to be the most thermostable lipase, under the conditions tested. Compared with the parent, the optimum temperature of S4-3 was two degrees higher, Tm was 22 degrees higher and half-lives at 60degreesC and 65degreesC were 46- and 23- times longer. Moreover, the catalytic efficiency kcat/Km of S4-3 was comparable to the parent. Stabilizing mutations probably increased thermostability by increasing the hydrophilicity and polarity of the protein surface and creating hydrophobic contacts inside the protein. CONCLUSIONS: P. pastoris was shown to be a valuable cell factory to improve thermostability of enzymes by directed evolution and it also could be used for improving other properties of enzymes. In this study, by using P. pastoris as a host to build mutant pool, we succeeded in obtaining a thermostable variant S4-3 without compromising enzyme activity and making it a highly promising candidate for future applications at high temperatures.     

DTNBP1, a schizophrenia susceptibility gene, affects kinetics of transmitter release

Schizophrenia is one of the most debilitating neuropsychiatric disorders, affecting 0.5-1.0% of the population worldwide. Its pathology, attributed to defects in synaptic transmission, remains elusive. The dystrobrevin-binding protein 1 (DTNBP1) gene, which encodes a coiled-coil protein, dysbindin, is a major susceptibility gene for schizophrenia. Our previous results have demonstrated that the sandy (sdy) mouse harbors a spontaneously occurring deletion in the DTNBP1 gene and expresses no dysbindin protein (Li, W., Q. Zhang, N. Oiso, E.K. Novak, R. Gautam, E.P. O'Brien, C.L. Tinsley, D.J. Blake, R.A. Spritz, N.G. Copeland, et al. 2003. Nat. Genet. 35:84-89). Here, using amperometry, whole-cell patch clamping, and electron microscopy techniques, we discovered specific defects in neurosecretion and vesicular morphology in neuroendocrine cells and hippocampal synapses at the single vesicle level in sdy mice. These defects include larger vesicle size, slower quantal vesicle release, lower release probability, and smaller total population of the readily releasable vesicle pool. These findings suggest that dysbindin functions to regulate exocytosis and vesicle biogenesis in endocrine cells and neurons. Our work also suggests a possible mechanism in the pathogenesis of schizophrenia at the synaptic level.     

中国红豆杉内生细菌的分离鉴定及活性研究

从中国红豆杉的茎中分离得到两株内生细菌G18、F19,通过生物学特性和16S rDNA序列分析,初步鉴定这两株菌分别为假单胞菌属(Psudomonas)和寡养单胞菌属(Stenotrophomonas)细菌.活性研究表明,G18、F19发酵液均对3种病原细菌有抑制作用,分剐对棉花黄萎病菌(Verticillium dahliae)和柑橘炭疽病菌(Colletotrichum gloeosporioides)有较强的抑制作用.G18和F19分别能降解水杨酸和敌敌畏.     

The Timing of Calling and Mating in <Emphasis Type="Italic">Heterolocha jinyinhuaphaga</Emphasis> and the Influence of Environmental Determinants

We investigated the periodicities of calling and mating of Heterolocha jinyinhuaphaga (Lepidoptera: Geometridae) and the effects of temperature, relative humidity, and photoperiod on the timing of these behaviors. Females called on the first night after emergence, mainly during the second half of scotophase. The calling percentage increased on the second night and peaked on the third night, before decreasing. Mating had similar rhythms but peaked 1 h later than calling. As the moth aged, the mean onset times of calling and mating were advanced. Temperature, relative humidity, and photoperiod all affected the calling and mating. We found that 25°C was the most suitable temperature for calling and mating, whereas at higher or lower temperatures, the total calling percentage and the total mating percentage decreased, the onset time of calling was delayed, and mating duration decreased. Increased the relative humidity facilitated calling and mating. However, lengthened photoperiods inhibited the calling and mating.     

巨噬细胞免疫调变信号——Raf-1,MAPK,cPLA2的激活和IL-12分泌的研究

LPS介导的小鼠腹腔巨噬细胞免疫调变的信号和机理是不清楚的.应用LPS和PMA处理抑制性巨噬细胞后,发现Ras下游信号分子Raf-1,MAPK和cPLA₂均被活化,包括Raf-1的磷酸化,MAPK p44和p42磷酸化以及cPLA_2的活化,使花生四烯酸的释放显著增加,结合新近发现的LPS、PMA能诱导抑制性巨噬细胞PKC-α和PKC-ε同工酶的激活与转位,认为在LPS介导的免疫调变中,PKC信号通路的活化及其与Raf-1/MAPK通路的“连接”是主要信号传导通路.同时调变巨噬细胞也能分泌IL-12.     

Gelsolin rs1078305 and rs10818524 polymorphisms were associated with risk of oral squamous cell carcinoma in a Chinese Han population

Background: Gelsolin (GSN) is one of the most abundant actin-binding proteins, and is involved in cancer development and progression.

Patients and methods: A hospital-based case-control study including 201 patients with OSCC and 199 healthy controls was conducted. Seventeen single-nucleotide polymorphisms (SNPs) of GSN were investigated by Sequenom Mass ARRAY and iPLEX-MALDI-TOF technology.

Results: Through comparison of the 17 SNPs on GSN gene between the two groups, SNP rs1078305 and rs10818524 were verified to be significantly associated with an increased risk of OSCC. For GSN rs1078305, the TT genotype was associated with increased risk for OSCC (OR?=?1.92, 95% CI?=?1.11–3.32, p?=?0.028). CT/TT variants were also associated with increased risk for OSCC compared to the CC genotype (OR?=?1.83, 95% CI?=?1.25–3.84, p?=?0.032).

Conclusion: The rs1078305 and rs10818524 SNPs of GSN were associated with increased risk for OSCC development in a Chinese Han population.     

盐胁迫下棉花基因组基于毛细管电泳的MSAP分析

以棉花杂交种中棉所29为材料,用甲基化敏感扩增多态性(methylation sensitive amplification polymorphism,MSAP) 分析法结合毛细管电泳检测技术进行甲基化鉴定,以初步探讨棉花耐盐的分子机理．应用24个引物组合,中棉所29在0.4%盐水胁迫及清水对照下,平均每引物组合检测甲基化位点数分别为69.2和56.7,差异达显著水平．盐胁迫下的DNA甲基化水平与清水对照下相比,52.6%位点表现出甲基化水平提高,即发生了超甲基化;19.7%位点甲基化水平降低,即表现为次甲基化;二者差异达极显著水平．研究结果表明,中棉所29盐胁迫后发生了广泛的DNA甲基化变化,包括超甲基化和次甲基化,以及其它甲基化类型的转变|发生超甲基化位点极显著地多于发生次甲基化位点．盐胁迫下的中棉所29与对照相比,DNA总体甲基化水平显著提高,暗示中棉所29有提高基因组甲基化水平以应对盐胁迫的潜在机制,棉花基因组整体甲基化水平的提高可能与棉花对盐胁迫的耐受性起重要作用．本研究中,甲基化序列的初步克隆及比对分析表明,盐胁迫前后多个ATP合成相关基因甲基化程度维持在同一水平,其表达不受甲基化影响,这也可能是中棉所29耐盐性较强,在一定时间盐处理后能维持正常生长的原因之一．