Primary structure effects on peptide group hydrogen exchange

The rate of exchange of peptide group NH hydrogens with the hydrogens of aqueous solvent is sensitive to neighboring side chains. To evaluate the effects of protein side chains, all 20 naturally occurring amino acids were studied using dipeptide models. Both inductive and steric blocking effects are apparent. The additivity of nearest-neighbor blocking and inductive effects was tested in oligo-and polypeptides and, suprisingly, confirmed. Reference rates for alanine-containing peptides were determined and effects of temperature considered. These results provide the information necessary to evaluate measured protein NH to ND exchange rates by comparing them with rates to be expected for the same amino acid sequence is unstructured aligo- and polypeptides. The application of this approach to protein studies is discussed. © 1993 Wiley-Liss, Inc.     

两株聚球藻伴生细菌分离纯化与促生功能鉴定

【背景】蓝藻周围存在伴生细菌,伴生细菌与蓝藻具有复杂的作用关系。【目的】研究淡水聚球藻伴生细菌对聚球藻生长的影响。【方法】采用高通量测序分析聚球藻伴生细菌多样性;平板划线法纯化聚球藻伴生细菌,通过形态观察结合16S rRNA基因序列同源性比对,对其种属关系进行确定;通过聚球藻和不同浓度伴生细菌共培养测定其叶绿素a浓度,分析伴生细菌对聚球藻生长的影响;采用种子发芽试验验证伴生细菌促生功能。【结果】淡水聚球藻伴生细菌优势菌属为产卟啉杆菌属(Porphyrobacter)、根瘤菌属(Rhizobium)、水单胞菌属(Aquimonas)和中慢生根瘤菌属(Mesorhizobium),从聚球藻分离获得了两株伴生细菌JQ1和JQ2,基于16S rRNA基因序列鉴定其分别属于Rhizobium和Peribacillus,通过在聚球藻与不同浓度伴生细菌共培养及水稻发芽试验验证,证明伴生细菌JQ1和JQ2在菌藻比例分别为5:1和15:1时具有促生作用,都对增强秧苗素质和根系发育有一定影响但JQ2与JQ1相比能显著提高水稻种子的发芽率。【结论】淡水聚球藻伴生细菌JQ1和JQ2在适宜的浓度均可显著促进聚球...     

Interactive Effects of Iron and Photoperiods on Tomato Plant Growth and Fruit Quality

Journal of Plant Growth Regulation - Photoperiod and micronutrient iron (Fe) are critical for plant growth and development. However, the interactive effects of Fe nutrition and photoperiod on...     

三角帆蚌Hc-GSK3β基因鉴定及内壳色性状相关SNP筛选

为了探究三角帆蚌(Hyriopsis cumingii)糖原合成激酶-3β(GSK3β)基因对壳色的影响,研究采用RACE技术获得Hc-GSK3β基因cDNA全长1867 bp,其中包含1261 bp的ORF区编码420个氨基酸, ORF中含有一个S＿TKc结构域,该结构域序列高度保守。组织差异表达分析发现Hc-GSK3β基因在紫色蚌鳃、斧足、内脏团和边缘膜组织中表达量高于白色蚌的表达量(P<0.05),且在斧足和边缘膜表达差异水平达到极显著(P<0.01),而在紫色蚌闭壳肌组织中表达量显著低于白色蚌(P<0.05)。原位杂交(ISH)实验结果显示在三角帆蚌外套膜的外褶、中褶、內褶、背膜区和腹膜区均有阳性信号产生,且在外褶的信号表达较强烈。该基因经重测序比较,共鉴定出6个SNP位点,其中在C+185A位点的CA基因型在紫色蚌的分布频率显著高于白色三角帆蚌(P<0.05);在紫色蚌中, T+341G位点TT基因型三角帆蚌内壳颜色参数b值显著低于TG基因型(P<0.05)。研究表明, Hc-GSK3β基因参与了三角帆蚌壳色形成,筛选的SNP标记可用于三角帆蚌壳...     

硕叶杜英,中国杜英科一新记录种

文章报道了产自中国云南杜英科杜英属一新记录种,硕叶杜英(Elaeocarpus grandifolius Kurz),并对硕叶杜英叶绿体基因组进行了测序和系统发育分析。该种与近缘种毛果杜英(Elaeocarpus rugosus)的区别是叶基部渐狭或下延,花瓣外部被锈色短柔毛,核果被锈色短柔毛,该种与水石榕(Elaeocarpus hainanensis)的区别是叶片长圆形或卵圆形,核果椭球形。     

越南槐根的抗HIV活性成分研究

为研究越南槐(Sophora tonkinensis)根的抗HIV蛋白酶活性成分及其分子对接机制,采用硅胶、MCI、Sephadex LH-20等多种色谱分离方法,对越南槐根的化学成分进行分离,采用HIV蛋白酶对化合物进行体外抗HIV活性筛选,运用分子对接手段初步探究活性化合物与HIV-1蛋白酶的结合机制。结果表明,从越南槐中共分离得到8个化合物,根据波谱数据分别鉴定为三叶豆紫檀苷(1)、苦参碱(2)、N-acetylnicotinamide (3)、2′-O-甲基腺苷(4)、毛蕊异黄酮苷(5)、玫瑰花苷(6)、环广豆根素(7)、芒柄花苷(8),此外还分离得到塑化剂衍生物邻苯二甲酸二(2-乙基)己酯(9)和邻苯二甲酸二异丁酯(10)。抗HIV蛋白酶活性测试显示化合物1和2的IC50分别为13.2和38.6μg/m L,分子对接表明其与HIV蛋白酶有一定的结合作用。化合物3～5为首次从该植物中分离得到,化合物1和2显示中等的抗HIV蛋白酶活性。     

ploidyfrost: Reference-free estimation of ploidy level from whole genome sequencing data based on de Bruijn graphs

Polyploidy is ubiquitous and its consequences are complex and variable. A change of ploidy level generally influences genetic diversity and results in morphological, physiological and ecological differences between cells or organisms with different ploidy levels. To avoid cumbersome experiments and take advantage of the less biased information provided by the vast amounts of genome sequencing data, computational tools for ploidy estimation are urgently needed. Until now, although a few such tools have been developed, many aspects of this estimation, such as the requirement of a reference genome, the lack of informative results and objective inferences, and the influence of false positives from errors and repeats, need further improvement. We have developed ploidyfrost , a de Bruijn graph-based method, to estimate ploidy levels from whole genome sequencing data sets without a reference genome. ploidyfrost provides a visual representation of allele frequency distribution generated using the ggplot2 package as well as quantitative results using the Gaussian mixture model. In addition, it takes advantage of colouring information encoded in coloured de Bruijn graphs to analyse multiple samples simultaneously and to flexibly filter putative false positives. We evaluated the performance of ploidyfrost by analysing highly heterozygous or repetitive samples of Cyclocarya paliurus and a complex allooctoploid sample of Fragaria × ananassa. Moreover, we demonstrated that the accuracy of analysis results can be improved by constraining a threshold such as Cramér's V coefficient on variant features, which may significantly reduce the side effects of sequencing errors and annoying repeats on the graphical structure constructed.     

Peptide MSI-1 inhibited MCR-1 and regulated outer membrane vesicles to combat immune evasion of Escherichia coli

Polymyxin resistance is conferred by MCR-1 (mobile colistin resistance 1)-induced lipopolysaccharide (LPS) modification of G⁻ bacteria. However, the peptide MSI-1 exerts potent antimicrobial activity against mcr-1-carrying bacteria. To further investigate the potential role of MCR-1 in improving bacterial virulence and facilitating immune evasion, and the immunomodulatory effect of peptide MSI-1, we first explored outer membrane vesicle (OMV) alterations of mcr-1-carrying bacteria in the presence and absence of sub-MIC MSI-1, and host immune activation during bacterial infection and OMV stimulation. Our results demonstrated that LPS remodelling induced by MCR-1 negatively affected OMV formation and protein cargo by E. coli. In addition, MCR-1 diminished LPS-stimulated pyroptosis but facilitated mitochondrial dysfunction, further aggravating apoptosis in macrophages induced by OMVs of E. coli. Similarly, TLR4-mediated NF-κB activation was markedly alleviated once LPS was modified by MCR-1. However, peptide MSI-1 at the sub-MIC level inhibited the expression of MCR-1, further partly rescuing OMV alteration and attenuation of immune responses in the presence of MCR-1 during both infection and OMV stimulation, which can be exploited for anti-infective therapy.     

High-resolution mapping of the S and Z loci of Phalaris coerulescens.

Self incompatibility (SI) in Phalaris coerulescens is gametophytically determined by two unlinked multi allelic loci (S and Z). Neither the S nor Z genes have yet been cloned. As part of a map-based cloning strategy, high-resolution maps of the S and Z regions were generated from distorted segregating populations using RFLP probes from wheat, barley, oat, and Phalaris. The S locus was delimited to 0.26 cM with two boundary markers (Xwg811 and Xpsr168) and cosegregated with Xbm2 and Xbcd762. Xbcd266 was the closest marker linked to Z (0.9 cM). A high level of colinearity in the S and Z regions was found in both self-incompatible and -compatible species. The S locus was localized to the subcentromere region of chromosome 1 and the Z locus to the long arm end of chromosome 2. Several rice BAC clones orthologous to the S and Z locus regions were identified. This opens the possibility of using the rice genome sequence data to generate more closely linked markers and identify SI candidate genes. These results add further support to the conservation of gene order in the S and Z regions of the grass genomes.