Identification of the hot spot residues for pyridine derivative inhibitor CCT251455 and ATP substrate binding on monopolar spindle 1 (MPS1) kinase by molecular dynamic simulation

Protein kinase monopolar spindle 1 plays an important role in spindle assembly checkpoint at the onset of mitosis. Over expression of MPS1 correlated with a wide range of human tumors makes it an attractive target for finding an effective and specific inhibitor. In this work, we performed molecular dynamics simulations of protein MPS1 itself as well as protein bound systems with the inhibitor and natural substrate based on crystal structures. The reported orally bioavailable 1 h-pyrrolo [3,2-c] pyridine inhibitors of MPS1 maintained stable binding in the catalytic site, while natural substrate ATP could not stay. Comparative study of stability and flexibility of three systems reveals position shifting of β-sheet region within the catalytic site, which indicates inhibition mechanism was through stabilizing the β-sheet region. Binding free energies calculated with MM-GB/PBSA method shows different binding affinity for inhibitor and ATP. Finally, interactions between protein and inhibitor during molecular dynamic simulations were measured and counted. Residue Gly605 and Leu654 were suggested as important hot spots for stable binding of inhibitor by molecular dynamic simulation. Our results reveal an important position shifting within catalytic site for non-inhibited proteins. Together with hot spots found by molecular dynamic simulation, the results provide important information of inhibition mechanism and will be referenced for designing novel inhibitors.     

Ensifer fredii symbiovar vachelliae nodulates endemic Vachellia gummifera in semiarid Moroccan areas

The purpose of this work was to study the genetic diversity of the nodule-forming bacteria associated with native populations of Vachellia gummifera growing wild in Morocco. The nearly complete 16S rRNA gene sequences from three selected strains, following ARDRA and REP-PCR results, revealed they were members of the genus Ensifer and the sequencing of the housekeeping genes recA, gyrB, dnaK and rpoB, and their concatenated phylogenetic analysis, showed that the 3 strains belong to the species E. fredii. Based on the nodC and nodA phylogenies, the 3 strains clearly diverged from the type and other reference strains of E. fredii and formed a clearly separated cluster. The strains AGA1, AGA2 and AGB23 did not form nodules on Glycine max, Phaseolus vulgaris and Medicago truncatula, and effectively nodulated V. gummifera, Acacia cyanophylla, Prosopis chilensis and Leucaena leucocephala. Based on similarities of the nodC and nodA symbiotic genes and differences in the host range, the strains isolated from Moroccan endemic V. gummifera may form a different symbiovar within Ensifer species, for which the name “vachelliae” is proposed.     

Prediction of quaternary structure by analysis of hot spot residues in protein-protein interfaces: the case of anthranilate phosphoribosyltransferases

It is an important goal of computational biology to correctly predict the association state of a protein based on its amino acid sequence and the structures of known homologues. We have pursued this goal on the example of anthranilate phosphoribosyltransferase (AnPRT), an enzyme that is involved in the biosynthesis of the amino acid tryptophan. Firstly, known crystal structures of naturally occurring homodimeric AnPRTs were analyzed using the Protein Interfaces, Surfaces, and Assemblies (PISA) service of the European Bioinformatics Institute (EBI). This led to the identification of two hydrophobic “hot spot” amino acids in the protein-protein interface that were predicted to be essential for self-association. Next, in a comprehensive multiple sequence alignment (MSA), naturally occurring AnPRT variants with hydrophilic or charged amino acids in place of hydrophobic residues in the two hot spot positions were identified. Representative variants were characterized in terms of thermal stability, enzymatic activity, and quaternary structure. We found that AnPRT variants with charged residues in both hot spot positions exist exclusively as monomers in solution. Variants with hydrophilic amino acids in one hot spot position occur in both forms, monomer and dimer. The results of the present study provide a detailed characterization of the determinants of the AnPRT monomer-dimer equilibrium and show that analysis of hot spots in combination with MSAs can be a valuable tool in prediction of protein quaternary structures.     

Phyllachora species infecting maize and other grass species in the Americas represents a complex of closely related species

The genus Phyllachora contains numerous obligate fungal parasites that produce raised, melanized structures called stromata on their plant hosts referred to as tar spot. Members of this genus are known to infect many grass species but generally do not cause significant damage or defoliation, with the exception of P. maydis which has emerged as an important pathogen of maize throughout the Americas, but the origin of this pathogen remains unknown. To date, species designations for Phyllachora have been based on host associations and morphology, and most species are assumed to be host specific. We assessed the sequence diversity of 186 single stroma isolates collected from 16 hosts representing 15 countries. Samples included both herbarium and contemporary strains that covered a temporal range from 1905 to 2019. These 186 isolates were grouped into five distinct species with strong bootstrap support. We found three closely related, but genetically distinct groups of Phyllachora are capable of infecting maize in the United States, we refer to these as the P. maydis species complex. Based on herbarium specimens, we hypothesize that these three groups in the P. maydis species complex originated from Central America, Mexico, and the Caribbean. Although two of these groups were only found on maize, the third and largest group contained contemporary strains found on maize and other grass hosts, as well as herbarium specimens from maize and other grasses that include 10 species of Phyllachora. The herbarium specimens were previously identified based on morphology and host association. This work represents the first attempt at molecular characterization of Phyllachora species infecting grass hosts and indicates some Phyllachora species can infect a broad range of host species and there may be significant synonymy in the Phyllachora genus.     

Diagnosis of light leaf spot (Pyrenopeziza brassicae) on winter oilseed rape (Brassica napus) in the UK

Light leaf spot lesions were generally first observed as light green areas on leaves of UK winter oilseed rape crops in January or February and later became brittle and bleached. Elongated lesions, which were brown with indistinct edges, developed on stems in the spring and summer, when lesions were also observed on flower buds, pedicels and pods. Development of diagnostic white pustules (spore masses of Pyrenopeziza brassicae, which erupt through surfaces of infected tissues) for confirmation of light leaf spot infection on symptomless plants or plants with indistinct or ambiguous symptoms in the autumn, winter or spring was enhanced by incubating plants in polyethylene bags. In experiments with artificially inoculated plants, glasshouse-grown plants exposed in infected crops and plants sampled from crops, white pustules developed at all incubation temperatures from 2^oC to 20^oC on infected leaves of different cultivars. The period of incubation required before the appearance of pustules decreased as the time that had already elapsed since the initial infection increased. The longest periods of incubation were required at the lowest temperatures (2^oC or 5^oC) but leaves senesced and abscised from plants most quickly at the highest temperatures (15^oC or 20^oC), suggesting that the optimal incubation temperature was between 10^oC and 15^oC.     

The effect of treating seed potato tubers with benzimidazole, imidazole and phenylpyrrole fungicides on the control of rot and skin blemish diseases

Over 6 yr the effectiveness of imazalil, prochloraz and fenpiclonil, applied either alone or in a mixture, in controlling gangrene, dry rot, skin spot and silver scurf on potato tubers in store was compared with that of 2-aminobutane and thiabendazole. An assessment was also made of their efficiency in controlling the development of these diseases on the daughter tubers of seed tubers treated at harvest or before planting. Overall, 2-aminobutane was more effective in controlling gangrene (Phoma foveata) in store than the spray-applied fungicides. Deposits of imazalil, thiabendazole and fenpiclonil were greater when sprays were applied with an electrostatic sprayer than with a hydraulic sprayer. The opposite was found with the mixture of prochloraz Mn and tolclofos-methyl. More effective gangrene control was associated with the highest deposits. Fenpiclonil and the mixture of thiabendazole and imazalil were more effective in controlling dry rot (Fusarium solani var. coeruleum) than imazalil alone. The development of dry rot was, however, increased by 2-aminobutane treatment on eight out of 14 stocks. 2-aminobutane gave the greatest reduction (83%) in the severity of skin spot during storage whereas thiabendazole alone, and the mixture of thiabendazole and imazalil, gave mean reductions of 70% and 65% respectively. This mixture and fenpiclonil gave the greatest reduction in the severity of silver scurf although, in general, reductions in silver scurf with fungicide treatment were less than with skin spot. The type of sprayer used to apply a fungicide did not affect the effectiveness of the fungicides in controlling either skin spot or silver scurf on tubers in store, or on the daughter tubers. The incidence of gangrene and dry rot on daughter tubers was not reduced consistently by fungicide treatment of seed tubers of the six stocks tested. However, the severity of skin spot and silver scurf was reduced by fungicide treatments of all eight stocks but the reduction in disease was greater for skin spot than for silver scurf. All fungicides gave reductions in the severity of skin spot, and fenpiclonil and the mixture of thiabendazole and imazalil were the most effective for silver scurf. The effectiveness of the fungicides in controlling these diseases was similar for seed treated at harvest and that treated before planting.     

湖北四湖泊营养类型与轮虫群落的关系

对湖北梁子湖水系不同营养类型(中营养型、富营养型)4个湖泊中轮虫的群落结构和物种多样性进行了周年研究,分析比较了不同营养类型湖泊的轮虫种类组成、分布、优势种组成、密度、生物量和多样性指数。结果表明：轮虫的种类数、物种多样性与营养水平呈负相关关系,轮虫密度大体上随营养水平提高而增大,富营养化引起轮虫空间异质性降低,受污染湖泊与非污染湖泊轮虫种类数、寡污性种类数及分布差异尤为明显。用多样性指数评价湖泊营养状态与TLIc方法一致。     

山东省冬小麦干热风灾害预警模型研究

以30年的气象和产量数据为研究对象,对冬小麦成熟收获前16天的23个温度指标、23个空气相对湿度指标和16个风速指标与相对气象产量进行统计分析.通过相关分析确定不同生态区的干热风灾害风险因子,对不同生态区的风险因子和相对气象产量进行回归分析,构建冬小麦干热风灾害风险预警模型.结果表明:同类气象因子在不同生态区中的作用表现不同,模型因素构成以因子的互作为主,单因子的直接影响作用不突出.鲁西北和鲁中是干热风灾害的高危险区,鲁西南干热风灾害的危险最小.     

生物入侵的危害与防治对策

生物入侵是一个世界范围的生态学现象。入侵种通过竞争、捕食、改变生境和传播疾病等方式对本地种及其系统产生影响。生物入侵的危害表现为：造成巨大的经济损失,仅美国每年因外来种入侵造成的经济损失近1370亿美元;威胁到人类的健康和生存。成千上万的人被外来种传染疾病以致死亡;引起严重的社会恐慌和动荡,人们寝食不安;改变了生态系统的结构和功能,全球自然灾害频频爆发;导致生物多样性的急剧下降,威胁到子孙后代的生存和发展。防治生物入侵有3条途径：实行全面检疫,阻止外来种的偶然入侵;采取全面的生态评估和监测,防范引进品种的入侵灾难;对已入侵的外来种采用机械法、化学法和生物防治法进行根除和控制,应用生物防治法、筛选天敌和对其进行危害评估时要特别慎重。     

长江口潮沟大型底栖动物群落的初步研究

通过对长江口崇明东滩潮沟系统与大型底栖无脊椎动物进行取样调查 ,研究了潮沟不同生境的底栖动物群落及其多样性 ,分析了潮沟生境异质性与底栖动物群落的关系。研究发现 :①潮沟剖面中出现明显的动物群落分带现象 ,从潮沟底、潮沟边滩到草滩 ,底栖动物种类、生活型组成和生活类群比例反映了河口潮滩潮沟底栖动物生态系列 ;②密度和生物量的分布皆为潮沟边滩 >草滩 >潮沟底 ,但密度与生物量的面上群 /面下群值格局却有不同 ,说明了密度和生物量的优势生活型和生活类群随潮沟生境的差异而变化 ;③潮沟系统 3种生境的多样性指数D ,H′和J值均为草滩 >潮沟边滩 >潮沟底 ,是潮沟系统生境结构分化的结果。潮沟底和潮沟边滩等特殊生境的存在 ,提高了淤泥质河口潮滩的生境异质性 ,说明了潮沟系统在维持河口生态系统底栖动物物种多样性中的重要作用。