pr2-primers: An 18S rRNA primer database for protists

Metabarcoding of microbial eukaryotes (collectively known as protists) has developed tremendously in the last decade, almost solely relying on the 18S rRNA gene. As microbial eukaryotes are extremely diverse, many primers and primer pairs have been developed. To cover a relevant and representative fraction of the protist community in a given study system, an informed primer choice is necessary, as no primer pair can target all protists equally well. As such, a smart primer choice is very difficult even for experts and there are very few online resources available to list existing primers. We built a database listing 285 primers and 83 unique primer pairs that have been used for eukaryotic 18S rRNA gene metabarcoding. In silico performance of primer pairs was tested against two sequence databases: PR² version 4.12.0 for eukaryotes and a subset of silva version 132 for bacteria and archaea. We developed an R -based web application enabling browsing of the database, visualization of the taxonomic distribution of the amplified sequences with the number of mismatches, and testing any user-defined primer or primer set ( https://app.pr2-primers.org ). Taxonomic specificity of primer pairs, amplicon size and location of mismatches can also be determined. We identified universal primer sets that matched the largest number of sequences and analysed the specificity of some primer sets designed to target certain groups. This tool enables guided primer choices that will help a wide range of researchers to include protists as part of their investigations.     

Automated work-flow for processing high-resolution direct infusion electrospray ionization mass spectral fingerprints

The use of mass spectrometry (MS) is pivotal in analyses of the metabolome and presents a major challenge for subsequent data processing. While the last few years have given new high performance instruments, there has not been a comparable development in data processing. In this paper we discuss an automated data processing pipeline to compare large numbers of fingerprint spectra from direct infusion experiments analyzed by high resolution MS. We describe some of the intriguing problems that have to be addressed, starting with the conversion and pre-processing of the raw data to the final data analysis. Illustrated on the direct infusion analysis (ESI-TOF-MS) of complex mixtures the method exploits the full quality of the high-resolution present in the mass spectra. Although the method is illustrated as a new library search method for high resolution MS, we demonstrate that the output of the preprocessing is applicable to cluster-, discriminant analysis, and related multivariate methods applied directly to mass spectra from direct infusion analysis of crude extracts. This is done to find the relationship between several terverticillate Penicillium species and identify the ions responsible for the segregation.     

肠道噬菌体组生物信息学分析方法的研究进展

噬菌体是感染细菌的病毒,广泛存在于各类环境中。由于传统实验研究的局限性及噬菌体基因的特异性,导致对肠道噬菌体的研究很少。随着宏基因组测序技术的发展和各种生物信息分析软件的开发,可以通过噬菌体组学,加深对肠道噬菌体的认识。噬菌体组分析流程主要包括原始数据质量控制和预处理,病毒基因组序列的拼接组装,类病毒颗粒的筛选和系统分类注释以及进化分析和预测相应宿主细菌。本文对噬菌体组分析流程和其中所需要的常用生物信息分析工具和数据库进行详细的介绍,可以为肠道噬菌体研究以及相关的研究人员提供参考。     

中国植物标本馆数字化发展的缩影——江苏省中国科学院植物研究所标本馆(NAS)

江苏省中国科学院植物研究所标本馆(NAS)是中国最早的植物标本馆之一,也是国内最早开展植物标本数字化的标本馆,其标本数字化发展经历了4个阶段: 20世纪80年代后期尝试的标本文字信息数字化的起步阶段; 20世纪90年代末的标本图像数字化和文字信息数字化规范阶段; 2004年以后的标本批量数字化与信息网络共享快速发展阶段; 2018年后的标本数字化信息维护与优化阶段。这一过程集中代表和反映了中国植物标本数字化的发展历程。此外,近年来开始了发掘和利用江苏植物标本的数字化信息工作,包括建设江苏省级数字植物标本馆、开发江苏省维管植物标本时空分布可视化系统、开展标本采集-入库过程数字化等。今后,将不断深化标本数字化的工作,以期形成有NAS特色的数字化植物标本馆。     

To mate or not to mate,and subsequent host search by a haplodiploid female parasitoid wasp

Mated females of haplodiploid species can vary the sex ratio of their offspring, but virgin or sperm‐depleted females can produce only males. Depending on the costs and benefits, the theory of constrained sex allocation states that female haplodiploids may vary in their propensity to mate, with important implications for the populations’ sex ratio. Unmated female parasitoid wasps Alabagrus texanus (Braconidae) have been observed to reject matings with males, even under highly confined spatial conditions. We performed field trials to determine whether unmated female A. texanus would mate. We then compared the preferences of the resulting unmated (constrained) and mated (unconstrained) female wasps for shelters constructed and occupied by their hosts, fern moth caterpillars Herpetogramma theseusalis (Crambidae) on fern fronds. We presented the wasps with pairs of shelters collected from the field that differed in size, as well as freshness, fern species, and presence or absence of caterpillars. Unconstrained females searched small shelters more frequently than did constrained females and tended to favor senesced (old) shelters over fresher ones. They did not differ in choice between shelters on marsh and sensitive ferns or between shelters containing caterpillars and empty shelters. The preference for small shelters by the unconstrained wasps may enhance their rate of contacting favorable hosts, but the foraging regime of the constrained females should expose them to caterpillars at sites infrequently searched by the unconstrained females.     

Efficient clustering in collaborative filtering recommender system: Hybrid method based on genetic algorithm and gravitational emulation local search algorithm

The ultimate goal of the Recommender System (RS) is to offer a proposal that is very close to the user's real opinion. Data clustering can be effective in increasing the accuracy of production proposals by the RS. In this paper, single-objective hybrid evolutionary approach is proposed for clustering items in the offline collaborative filtering RS. This method, after generating a population of randomized solutions, at each iteration, improves the population of solutions first by Genetic Algorithm (GA) and then by using the Gravitational Emulation Local Search (GELS) algorithm. Simulation results on standard datasets indicate that although the proposed hybrid meta-heuristic algorithm requires a relatively high run time, it can lead to more appropriate clustering of existing data and thus improvement of the Mean Absolute Error (MAE), Root Mean Square Error (RMSE) and Coverage criteria.     

MolMod – an open access database of force fields for molecular simulations of fluids

The MolMod database is presented, which is openly accessible at http://molmod.boltzmann-zuse.de and contains intermolecular force fields for over 150 pure fluids at present. It was developed and is maintained by the Boltzmann-Zuse Society for Computational Molecular Engineering (BZS). The set of molecular models in the MolMod database provides a coherent framework for molecular simulations of fluids. The molecular models in the MolMod database consist of Lennard-Jones interaction sites, point charges, and point dipoles and quadrupoles, which can be equivalently represented by multiple point charges. The force fields can be exported as input files for the simulation programmes ms2 and ls1 mardyn, GROMACS, and LAMMPS. To characterise the semantics associated with the numerical database content, a force field nomenclature is introduced that can also be used in other contexts in materials modelling at the atomistic and mesoscopic levels. The models of the pure substances that are included in the database were generally optimised such as to yield good representations of experimental data of the vapour–liquid equilibrium with a focus on the vapour pressure and the saturated liquid density. In many cases, the models also yield good predictions of caloric, transport, and interfacial properties of the pure fluids. For all models, references to the original works in which they were developed are provided. The models can be used straightforwardly for predictions of properties of fluid mixtures using established combination rules. Input errors are a major source of errors in simulations. The MolMod database contributes to reducing such errors.     

基于PDB数据库的三个RNA二级结构预测软件评估

随着21世纪分子生物学研究的蓬勃发展,RNA二级结构预测成为其中一项重要内容。由于RNA二级结构预测的准确性最为关键,因此寻找高精度且易操作的二级结构预测工具显得非常重要。本文选取三种简单且易操作的二级结构预测软件,先基于PDB数据库收录的318个RNA发夹序列进行二级结构预测,进而通过比较预测结果与实验测定结果进行软件预测性能评估。比较结果显示,RNAstructure为三个软件中性能最优的RNA二级结构预测软件。     

生物信息学数据库研究文献引文与热点分析

以Web of Science为数据源,简要概括生物信息学数据库研究的发展趋势。利用Cite Space可视化工具展现生物信息学数据库研究的知识基础和研究热点图谱,为开展生物信息学数据库领域相关的理论研究和实践活动提供借鉴,以便推动生物信息学数据库研究的发展。研究表明：1990年Altschul SF发表的＂局部比对搜索工具——BLAST＂是生物信息学数据库研究的重要知识来源文献;热点主题集中在序列库、基因组数据库、分类数据库、蛋白质数据库、数据库更新、集成系统等。