Selective antibacterial activity of the cationic peptide PaDBS1R6 against Gram-negative bacteria

Infections caused by Gram-negative bacteria, Escherichia coli and Pseudomonas aeruginosa foremost among them, constitute a major worldwide health problem. Bioinformatics methodologies are being used to rationally design new antimicrobial peptides, a potential alternative for treating these infections. One of the algorithms used to develop antimicrobial peptides is the Joker, which was used to design the peptide PaDBS1R6. This study evaluates the antibacterial activities of PaDBS1R6 in vitro and in vivo, characterizes the peptide interaction to target membranes, and investigates the PaDBS1R6 structure in contact with mimetic vesicles. Moreover, we demonstrate that PaDBS1R6 exhibits selective antimicrobial activity against Gram-negative bacteria. In the presence of negatively charged and zwitterionic lipids the structural arrangement of PaDBS1R6 transits from random coil to α-helix, as characterized by circular dichroism. The tertiary structure of PaDBS1R6 was determined by NMR in zwitterionic dodecylphosphocholine (DPC) micelles. In conclusion, PaDBS1R6 is a candidate for the treatment of nosocomial infections caused by Gram-negative bacteria, as template for producing other antimicrobial agents.     

基于多组学数据的肿瘤药物敏感性预测北大核心CSCD

肿瘤药物敏感性预测在指导患者临床用药方面具有重要意义。本文基于癌症药物敏感性基因组学数据库(genomics of drug sensitivity in cancer, GDSC) 198种药物的细胞系敏感性IC50数据,通过Stacking集成学习构建了包含基因表达、基因突变、拷贝数变异数据的多组学癌症药物敏感性预测模型。采用多种特征选择方法对基因特征进行降维,使用Stacking方法集成6种初级学习器和1种次级学习器进行建模,采用5折交叉进行模型验证。预测结果中AUC大于0.9的占比为36.4%,在0.8–0.9之间的占比为49.0%,最低AUC为0.682。基于Stacking构建的多组学预测模型较已有单组学和多组学模型的准确性和稳定性具有优势。多组学整合预测药物敏感性优于单一组学。特征基因功能注释和富集分析解析了肿瘤对sorafenib潜在的耐药机制,从生物学角度提供了模型可解释性及其应用于临床用药指导的价值。     

基于人工神经网络的农业病虫害预测模型及其效果检验

选取与病虫害有关的因子作为样本的输入特征,建立了农业病虫害年分类预测的Ｂ－Ｐ人工神经网络模型。该方法应用于稻瘟病的预测建模结果的拟合率为１００％,预留样本检验报率为８３％。     

近江牡蛎共附生耐热真菌C051的鉴定、生理学特性及抗菌活性研究

为进一步开发利用耐热海洋真菌,以1株近江牡蛎共附生耐热真菌C051为出发菌株,对其进行系统鉴定、生理学特性及抗菌活性研究。采用形态学鉴定并结合18S rRNA序列分析,确定菌株C051为烟曲霉(Aspergillus fumigatus)。3种培养基比较,适合基础培养基为PDA;生长温度范围为15～50℃,最适生长温度45℃,具有明显的耐热真菌特性;生长pH范围3～9,最适生长pH 6;生长盐浓度0%～16%,最适生长盐浓度3.5%,具兼性海洋真菌的特点。其发酵产物对铜绿假单胞菌(Pseudomons aeruginosa)、金黄色葡萄球菌(Staphylococcus aureus)、交替假单胞菌属SL-1(Pseudoalteromonas sp.)、金黄杆菌属SL-4(Chryseobacterium sp.)均有良好的抑菌效果,最大抑菌圈直径达22.15 mm,为耐热海洋真菌的开发与研究提供参考。     

The influence of temperature on chromosome elimination during embryo development in crosses involving Hordeum spp., wheat (Triticum aestivum L.) and rye (Secale cereale L.)

Summary Several interspecific and intergeneric crosses involving five Hordeum species, Triticum aestivum and Secale cereale were carried out to investigate the influence of two contrasting temperatures on chromosome elimination during embryo development. In four of the interspecific Hordeum crosses, chromosome elimination was significantly increased at the higher of the two temperatures, resulting in greater proportions of haploid plant progenies. However, there was no significant effect of temperature in the other interspecific cross between H. lechleri x H. bulbosum nor in the two intergeneric crosses between H. vulgare x S. cereale and T. aestivum x H. bulbosum whose progeny were exclusively hybrid and haploid, respectively.     

缺失数据下蛋白质多结构叠加的迭代方法

蛋白质三维结构叠加面临的主要问题是,参与叠加的目标蛋白质的氨基酸残基存在某些缺失,但是多结构叠加方法却大多数需要完整的氨基酸序列,而目前通用的方法是直接删去缺失的氨基酸序列,导致叠加结果不准确。由于同源蛋白质间结构的相似性,因此,一个蛋白质结构中缺失的某个区域,可能存在于另一个同源蛋白质结构中。基于此,本文提出一种新的、简单、有效的缺失数据下的蛋白质结构叠加方法（ITEMDM）。该方法采用缺失数据的迭代思想计算蛋白质的结构叠加,采用优化的最小二乘算法结合矩阵SVD分解方法,求旋转矩阵和平移向量。用该方法成功叠加了细胞色素C家族的蛋白质和标准Fischer’s 数据库的蛋白质（67对蛋白质）,并且与其他方法进行了比较。数值实验表明,本算法有如下优点：①与THESEUS算法相比较,运行时间快,迭代次数少;②与PSSM算法相比较,结果准确,运算时间少。结果表明,该方法可以更好地叠加缺失数据的蛋白质三维结构。     

A CLIQUE algorithm using DNA computing techniques based on closed-circle DNA sequences

DNA computing has been applied in broad fields such as graph theory, finite state problems, and combinatorial problem. DNA computing approaches are more suitable used to solve many combinatorial problems because of the vast parallelism and high-density storage. The CLIQUE algorithm is one of the gird-based clustering techniques for spatial data. It is the combinatorial problem of the density cells. Therefore we utilize DNA computing using the closed-circle DNA sequences to execute the CLIQUE algorithm for the two-dimensional data. In our study, the process of clustering becomes a parallel bio-chemical reaction and the DNA sequences representing the marked cells can be combined to form a closed-circle DNA sequences. This strategy is a new application of DNA computing. Although the strategy is only for the two-dimensional data, it provides a new idea to consider the grids to be vertexes in a graph and transform the search problem into a combinatorial problem.     

Stepwise prediction of conformational discontinuous B-cell epitopes using the Mapitope algorithm

Mapping the epitope of an antibody is of great interest, since it contributes much to our understanding of the mechanisms of molecular recognition and provides the basis for rational vaccine design. Here we present Mapitope, a computer algorithm for epitope mapping. The algorithm input is a set of affinity isolated peptides obtained by screening phage display peptide-libraries with the antibody of interest. The output is usually 1-3 epitope candidates on the surface of the atomic structure of the antigen. We have systematically tested the performance of Mapitope by assessing the effect of the algorithm parameters on the final prediction. Thus, we have examined the effect of the statistical threshold (ST) parameter, relating to the frequency distribution and enrichment of amino acid pairs from the isolated peptides and the D (distance) and E (exposure) parameters which relate to the physical parameters of the antigen. Two model systems were analyzed in which the antibody of interest had previously been co-crystallized with the antigen and thus the epitope is a given. The Mapitope algorithm successfully predicted the epitopes in both models. Accordingly, we formulated a stepwise paradigm for the prediction of discontinuous conformational epitopes using peptides obtained from screening phage display libraries. We applied this paradigm to successfully predict the epitope of the Trastuzumab antibody on the surface of the Her-2/neu receptor in a third model system.     

外周血NETs、TP53、STAT3表达与弥漫性大B细胞淋巴瘤临床病理及预后的关系分析

摘要 目的：探究外周血中性粒细胞胞外诱捕网（NETs）、TP53、信号转导与转录因子3（STAT3）表达与弥漫性大B细胞淋巴瘤（DLBCL）临床病理及预后的关系。方法：选取2020年3月-2021年12月收治的71例DLBCL患者作为研究对象,抽取患者外周静脉血,采用R-CHOP方案进行治疗,记录患者外周血NETs、TP53、STAT3表达情况并分析DLBCL患者外周血NETs、TP53、STAT3表达与其临床病理及预后的关系。结果：髓细胞组织增生蛋白（MYC）阳性在TP53阳性中的占比显著高于TP53阴性,差异有统计学意义（x²=28.844,P＜0.001）;Hans分型生发中心B细胞（GCB）在STAT3阳性中的占比显著高于STAT3阴性（x²=4.331,P=0.037）,其余差异无统计学意义（P>0.05）;随访截止至2022年6月,随访时长8~28个月,71例患者中共53例缓解DLBCL患者,其余18例为R/R DLBCL患者;NETs阳性、TP53阳性、STAT3阳性患者无进展生存期（PFS）显著低于NETs阴性、TP53阴性、STAT3阴性患者,差异有统计学意义（P<0.05）且NETs阳性、TP53阳性、STAT3阳性患者存活率均低于NETs阴性、TP53阴性、STAT3阴性患者（P<0.05）;单因素分析结果显示Ann Arbor分期、NETs、TP53、STAT3为DLBCL患者的影响因素（P<0.05）;以患者预后情况（R/R DLBCL=1,缓解DLBCL=0）为因变量,将Ann Arbor分期、NETs、TP53、STAT3单因素分析有统计学意义的因素纳入COX回归模型中,结果显示：NETs、TP53、STAT3为DLBCL患者预后的危险因素（P<0.05）。结论：TP53、STAT3表达与DLBCL临床病理存在一定相关性,临床应对DLBCL患者TP53、STAT3表达情况引起重视;NETs、TP53、STAT3表达为DLBCL预后的危险因素,可作为DLBCL患者不良预后的预测指标。     

穿透雨减少下锐齿栎叶片光合色素季节动态及其反射光谱响应

通过林地穿透雨排除的方法模拟降雨减少,测定河南宝天曼自然保护区锐齿栎叶片光合色素含量与反射光谱的季节变化,对减雨处理造成的光合色素变化及其反射光谱的变化进行了定量分析,并探讨了水分控制条件下反射光谱对叶片光合色素变化的响应机制.结果表明: 锐齿栎叶片的光合色素含量和色素比率均呈现明显的季节变化.减雨样地与对照样地叶片的光合色素含量和比率在生长季的各个时期存在差异,其中,叶片叶绿素b(Chl b)含量的差异显著,说明Chl b对减雨处理的敏感性最高,叶片类胡萝卜素(Car)含量的差异较小,说明Car对减雨处理的敏感性相对较弱.550 nm处的光谱反射率对色素季节变化的响应最敏感,以其构造的简单比值指数(SR_750,550)与叶片Chl a、Chl b、总Chl和Car含量的正相关关系显著,光化学反射指数(PRI)与叶片Car/Chl的负相关关系显著.550 nm处的光谱反射率对减雨处理造成的色素变化响应最为敏感.SR_750,550对减雨处理造成的叶片Chl a、Chl b和总Chl的含量变化表现敏感(P<0.01),对Chl a/b的变化不敏感.PRI对减雨处理造成的叶片Car/Chl变化表现敏感(P<0.01).