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.     

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...     

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.     

单甲脒农药对模型池塘生态系统群落结构的影响

在３ｍ×１ｍ×１ｍ（Ｖ＝３ｍ３）含有底泥的模型池塘生态系统中研究单脒农药对水生生物群落结构的影晌。规定实验浓度力０、１．５、３．０、６．０和１２．０ｍｇ／Ｌ,每１５ｄ加入１次２５％单甲脒农药水剂,连续加入４次,实验进行２个多月。在实验浓度范围内,童甲脒农药对水生生物群落产生不同程度的影响。浮游生物比较敏感：加药后头几天内,种类、数量及多样性指数下降,浓度越大,影响越明显;大约１周以后,各处理组浮游生物群落逐步得到恢复,实验后期其数量甚至可超过对照水平,但群落结构发生改变,敏感种类少或消失,耐污种类增加,生物多样性降低。底栖生物比较耐污：处理槽大型水生植物的叶绿素含量有所减少,但其种类和生物量未见明显差异;底栖动物种类、数量也未见明显变化。微生物最耐污,在处理槽水层及沉积物中好氧异养菌数量有所增加,沉积物中厌气菌数量也有增加的趋势。青鱼对单甲脒农药较敏感,在１．５ｍｇ／Ｌ以下浓度尚能正常存活和繁殖。单甲脒农药水剂明显增加水体氮、磷含量,尤其磷酸盐含量高,使水体氮、磷比例失调,可能导致水体富营养化。根据综合指标分析,在规定单甲脒盆酸盐浓度＜１．５ｍｇ／Ｌ的实验条件下,水生生物群落结构未见明显改变．     

高原适应过程中大鼠脑内β－内啡肽含量变化的研究

选用成年雄性Ｗｉｓｔａｒ大鼠,由平原（海拔５ｍ,上海）直接运送到高原（２２６１ｍ,西宁和３４６０ｍ,天峻）。以放射免疫分折法研究了大鼠在高原２４ｈ．急性缺氧期和３０ｄ慢性缺氧期中枢脑内β－内啡肽样免疫活性物质（β－ＥＰ）的含量变化。结果表明：１．大鼠在两个不同海拔（２２６１ｍ,３４６０ｍ）环境２４ｈ急性缺氧期与平原对照组相比,脑垂体内β－ＥＰ含量降低非常显著（Ｐ＜０．０１）,纹状体、丘脑、下丘脑、桥－延脑、海马内β－ＥＰ含量均增加非常显著（Ｐ＜０．０１）。２．大鼠在３４６０ｍ高原３０ｄ慢性习服期,垂体及各脑区内β－ＥＰ的含量变化呈时相性：即１—３ｄ均呈进行性增加（Ｐ＜０．０１）：３－１５ｄ呈持续性减少,除中脑、纹状体、丘脑外,均为Ｐ＜０．０１。１５－３０ｄ垂体、丘脑、皮层、纹状体内β－ＥＰ含量仍持续减少（毒体、皮层Ｐ＜０．０１）,桥－延脑、下丘脑、海马趋于回升（Ｐ＜０．０１）,中脑亦趋于回升（Ｐ＞０．０５）。脑内β－ＥＰ的这种变化可能具有十分重要的生物学意义。