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  • 1.

    【2hr】Genome-Wide Search for Tyrosine Phosphatases in the Human GenomeThrough Computational Approaches Leads to the Discovery of Few New DomainArchitectures

    包量

    机译 人类基因组中酪氨酸磷酸酶的全基因组搜索通过计算方法可发现很少的新领域建筑学
    摘要：Reversible phosphorylation maintained by protein kinases and phosphatases is an integral part of intracellular signalling, and phosphorylation on tyrosine is extensively utilised in higher eukaryotes. Tyrosine phosphatases are enzymes that not only scavenge phosphotyrosine but are also involved in wide range of signalling pathways. As a result, mutations in these enzymes have been implicated in the pathogenesis of several diseases like cancer, autoimmune disorders, and muscle-related diseases. The genes that harbour phosphatase domain also display diversity in co-existing domains suggesting the recruitment of the catalytic machinery in diverse pathways. We have examined the current draft of the human genome, using a combination of 3 sequence search methods and validations, and identified 101 genes encoding tyrosine phosphatase-containing gene products, agreeing with previous reports. Such gene products adopt 37 unique domain architectures (DAs), including few new ones and harbouring few co-existing domains that have not been reported before. This semi-automated computational approach for detection of gene products belonging to a particular superfamily can now be easily applied at whole genome level on other mammalian genomes and for other protein domains as well.
  • 2.

    【2hr】Genome-Wide Identification of Long Non-coding RNAs Responsive toLasiodiplodia theobromae Infection inGrapevine

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    机译 全基因组识别长非编码RNA响应。Lasiodiplodia theobromae感染于葡萄藤
    摘要：Long non-coding RNAs (lncRNAs) refer to a class of RNA molecules that are longer than 200 nucleotides and do not encode proteins. Numerous lncRNAs have recently emerged as important regulators of many biological processes in animals and plants, including responses to environmental stress and pathogens. Botryosphaeria dieback is one of the more severe grapevine trunk diseases worldwide. However, how lncRNAs function during Botryosphaeriaceae infection is largely unknown. We performed high-throughput RNA-sequencing (RNA-seq) of susceptible and more tolerant grapevine cultivars infected with Lasiodiplodia theobromae. Overall, we predicted 1826 novel candidate lncRNAs, including long intergenic non-coding RNAs (lincRNAs) and natural antisense transcripts (lncNATs). The data reveal the functions of a set of lncRNAs that were differentially expressed between the resistant cultivar Merlot and the susceptible cultivar Cabernet Franc. Several lncRNAs were predicted to be precursors for grape microRNAs involved in the L theobromae infection. These results provide new insight into the lncRNAs of grapevine that are involved in the response to L theobromae infection.
  • 3.

    【2hr】OSTRFPD: Multifunctional Tool for Genome-Wide Short Tandem Repeat Analysis for DNA, Transcripts, and Amino Acid Sequences with Integrated Primer Designer

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    机译 OSTRFPD：使用集成的引物设计器进行基因组范围的短基因组短串联重复序列分析的多功能工具，用于DNA，转录本和氨基酸序列
    摘要：Microsatellite mining is a common outcome of the in silico approach to genomic studies. The resulting short tandemly repeated DNA could be used as molecular markers for studying polymorphism, genotyping and forensics. The omni short tandem repeat finder and primer designer (OSTRFPD) is among the few versatile, platform-independent open-source tools written in Python that enables researchers to identify and analyse genome-wide short tandem repeats in both nucleic acids and protein sequences. OSTRFPD is designed to run either in a user-friendly fully featured graphical interface or in a command line interface mode for advanced users. OSTRFPD can detect both perfect and imperfect repeats of low complexity with customisable scores. Moreover, the software has built-in architecture to simultaneously filter selection of flanking regions in DNA and generate microsatellite-targeted primers implementing the Primer3 platform. The software has built-in motif-sequence generator engines and an additional option to use the dictionary mode for custom motif searches. The software generates search results including general statistics containing motif categorisation, repeat frequencies, densities, coverage, guanine–cytosine (GC) content, and simple text-based imperfect alignment visualisation. Thus, OSTRFPD presents users with a quick single-step solution package to assist development of microsatellite markers and categorise tandemly repeated amino acids in proteome databases. Practical implementation of OSTRFPD was demonstrated using publicly available whole-genome sequences of selected Plasmodium species. OSTRFPD is freely available and open-sourced for improvement and user-specific adaptation.
  • 4.

    【2hr】A Commentary on Diversity Measures UniFrac in Very Small Sample Size

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    机译 在非常小的样本量中对多样性衡量UniFrac的评论
    摘要：In phylogenetic, the diversity measures as UniFrac, weighted UniFrac, and normalized weighted UniFrac are used to estimate the closeness between two samples of genetic material sequences. These measures are widely used in microbiology to compare microbial communities. Furthermore, when the sample size is large enough, very good results have been obtained experimentally. However, some authors do not suggest using them when the sample size is very small. Recently, it has been mentioned that the weighted UniFrac measure can be seen as the Kantorovich-Rubinstein metric between the corresponding empirical distributions of samples of genetic material. Also, it is well known that the Kantorovich-Rubinstein metric complies the metric definition. However, one of the main reasons to establish it is that the sample size is large enough. The goal of this article is to prove that the diversity measures UniFrac are not metrics when the sample size is very small, which justifies why it must not be used in that case, but yes the Kantorovich-Rubinstein metric.
  • 5.

    【2hr】Isolation, Characterization, and Genomic Analysis ofPseudomonas sp. Strain SMT-1, an EfficientFluorene-Degrading Bacterium

    包量

    机译 的分离，表征和基因组分析假单胞菌应变SMT-1，高效芴降解细菌
    摘要：Comprehensive study of novel microbial organisms capable of degrading fluorene is crucial to develop essential strategies for further application on enhanced bioremediation technologies. Many fluorene-degrading bacteria have been studied; however, little information about the genome sequences of these organisms, which would facilitate investigation of the molecular mechanisms of fluorene degradation, is available. In this study, a bacterial strain designated SMT-1, which uses fluorene as its sole carbon source, was isolated from Laogang landfill in Shanghai, People’s Republic of China, and identified as a Pseudomonas sp., based on 16S rRNA gene sequence analysis. Maximum growth and degrading activity of strain SMT-1 were observed at 30°C, pH 7.0 and 200 r/min in mineral salt medium containing 0.4 mm fluorene. We obtained a draft genome sequence of strain SMT-1 to gain insight into the genetic mechanisms for the degradation of aromatic compounds. Sequences greater than 1 kb in length were obtained by Illumina sequencing; strain SMT-1 was found to contain 5542 predicted genes. This working draft genome comprises 68 contigs and DNA scaffolds and has a total size of 6 108 237 bp and a calculated G + C content of 61.59%. Amino acid metabolism clusters were enriched inSMT-1 genes annotation, with the highest abundant observedfor the “ABC transporters” subcategories, followed by transcription, energyproduction and conversion, and inorganic ion transport and metabolism. Thegenomic information for SMT-1 provides a useful resource for elucidating themolecular mechanism of fluorene catabolism.
  • 6.

    【2hr】Sequence-based Prediction of Protein-Protein Interactions Using Gray Wolf Optimizer–Based Relevance Vector Machine

    包量

    机译 基于灰狼优化器的相关向量机基于序列的蛋白质-蛋白质相互作用预测
    摘要：Protein-protein interactions (PPIs) are essential to a number of biological processes. The PPIs generated by biological experiment are both time-consuming and expensive. Therefore, many computational methods have been proposed to identify PPIs. However, most of these methods are limited as they are difficult to compute and rely on a large number of homologous proteins. Accordingly, it is urgent to develop effective computational methods to detect PPIs using only protein sequence information. The kernel parameter of relevance vector machine (RVM) is set by experience, which may not obtain the optimal solution, affecting the prediction performance of RVM. In this work, we presented a novel computational approach called GWORVM-BIG, which used Bi-gram (BIG) to represent protein sequences on a position-specific scoring matrix (PSSM) and GWORVM classifier to perform classification for predicting PPIs. More specifically, the proposed GWORVM model can obtain the optimum solution of kernel parameters using gray wolf optimizer approach, which has the advantages of less control parameters, strong global optimization ability, and ease of implementation compared with other optimization algorithms. The experimental results on yeast and human data sets demonstrated the good accuracy and efficiency of the proposed GWORVM-BIG method. The results showed that the proposed GWORVM classifier can significantly improve the prediction performance compared with the RVM model using other optimizer algorithms including grid search (GS), genetic algorithm (GA), and particle swarm optimization (PSO). In addition, the proposed method is also compared with other existing algorithms, and the experimental results further indicated that the proposed GWORVM-BIG model yields excellent prediction performance. For facilitating extensive studies for future proteomics research, the GWORVMBIG server is freely available for academic use at .
  • 7.

    【2hr】Evaluation of the Function of Wild Animal Gut Microbiomes Using Next-Generation Sequencing and Bioinformatics and its Relevance to Animal Conservation

    包量

    机译 利用下一代测序和生物信息学评估野生动物肠道微生物组的功能及其与动物保护的关系
    摘要：The relationship between animal conservation and the animal gut microbiome is a hot topic in current microbial ecology research. Our group has recently revealed that the occurrence of diverse combinations of gut microbial compositions and functions (metagenomics) in Père David’s deer (Elaphurus davidianus) populations is likely to lead to increased evolutionary potential and resilience in response to environmental changes. Thus, considering the effects of diet on the gut microbiome and the importance of a stable gut microbial community to host health, we suggest that a transitional buffer period (with feeding on a regular diet and a diet from the translocation habitat) is needed before animal translocation. When the gut microbiome enters into relatively stable stages and adapts to the new diet from the translocation site, the time is suitable for translocation. Long-term monitoring of the gut microbiomes of translocated animals (by collecting fresh feces and carrying out next-generation sequencing) is still necessary after their translocation.
  • 8.

    【2hr】SWSPM: A Novel Alignment-Free DNA Comparison Method Based on Signal Processing Approaches

    包量

    机译 SWSPM：一种基于信号处理方法的新型无比对DNA比较方法
    摘要：Computing similarity between 2 nucleotide sequences is one of the fundamental problems in bioinformatics. Current methods are based mainly on 2 major approaches: (1) sequence alignment, which is computationally expensive, and (2) faster, but less accurate, alignment-free methods based on various statistical summaries, for example, short word counts. We propose a new distance measure based on mathematical transforms from the domain of signal processing. To tolerate large-scale rearrangements in the sequences, the transform is computed across sliding windows. We compare our method on several data sets with current state-of-art alignment-free methods. Our method compares favorably in terms of accuracy and outperforms other methods in running time and memory requirements. In addition, it is massively scalable up to dozens of processing units without the loss of performance due to communication overhead. Source files and sample data are available at
  • 9.

    【2hr】Are Gaming-Enabled Graphic Processing Unit Cards Convenient for Molecular Dynamics Simulation?

    包量

    机译 具有游戏功能的图形处理单元卡是否方便进行分子动力学模拟？
    摘要：In several fields of research, molecular dynamics simulation techniques are exploited to evaluate the temporal motion of particles constituting water, ions, small molecules, macromolecules, or more complex systems over time. These techniques are considered difficult to setup, computationally demanding and require high specialization and scientific skills. Moreover, they need specialized computing infrastructures to run faster and make the simulation of big systems feasible. Here, we have simulated 3 systems of increasing sizes on scientific- and gaming-enabled graphic processing unit (GPU) cards with Amber, GROMACS, and NAMD and measured their performance accounting also for the market prices of the GPU cards where they were run on.
  • 10.

    【2hr】Molecular Characterization of Microbiota Associated With Sperm ofMalaysian Mahseer Tor tambroides

    包量

    机译 与精子有关的微生物的分子表征。马来西亚Mahseer Tor tambroides
    摘要：Malaysian Mahseer (Tor tambroides) is considered as a good prospect for aquaculture in Malaysia. However, knowledge about Malaysian Mahseer-associated sperm microbiota is still limited, although some studies reported that sperm-related bacteria are a factor in the decline of sperm quality, as sperm may become the carrier of pathogenic bacteria to the egg. The goal of this study was to evaluate the sperm microbiota associated with Malaysian Mahseer from 3 different locations (Universiti Malaysia Terengganu [UMT], Ajil, and Pahang) using polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) fingerprinting and to compare location differences by cluster analysis. Our results showed that the UMT sample had different sperm microbiota composition and a different trend in its relationship with sperm quality. Correlation analysis showed a relationship between bacterial diversity and sperm quality. Phylogenetic analysis indicated that sperm microbiota was composed of diverse phyla, including Proteobacteria, Firmicutes, and Actinobacteria. Interestingly, bacteria such as Salinisphaera sp., Pelomonas sp., and Staphylococcus spp. were detected in all the locations, suggesting that these bacteria areindigenous bacterial members of the Malaysian Mahseer sperm microbiota, althoughtheir function is still unclear.
  • 11.

    【2hr】Molecular Characterization and Gene Expression of Glutathione Peroxidase 1 in Tor tambroides Exposed to Temperature Stress

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    机译 暴露于温度胁迫的Tor tambroides中谷胱甘肽过氧化物酶1的分子表征和基因表达
    摘要：Temperature is an abiotic factor that affects various biological and physiological processes in fish. Temperature stress is known to increase the production of reactive oxygen species (ROS) that subsequently cause oxidative stress. Fish is known to evolve a system of antioxidant enzymes to reduce ROS toxicology. Glutathione peroxidase (GPx) family consists of key enzymes that protect fish from oxidative stress. In this study, full-length GPx1 cDNA (GenBank accession no. ) of Tor tambroides was cloned and characterized by rapid amplification of cDNA ends (RACE). The 899-base-pair (bp) GPx1 cDNA includes a 576-bp open reading frame encoding for 191 amino acids, plus 28 bp of 5′-untranslated region (UTR) and 295 bp of 3′-UTR. Homology analysis revealed that GPx1 of T tambroides (Tor-GPx1) shared high similarity with GPx1 sequences of other fish species. The phylogenetic construction based on the amino acid sequence showed that Tor-GPx1 formed a clade with GPx1 sequences of various fish species. Real-time polymerase chain reaction (PCR) was performed to assess the levels of GPx1 gene expression in the liver and muscle of T tambroides under thermal stress. The results indicated that GPx1 gene expression was down-regulated under decreased temperature. However, there was no significant difference between GPx1 gene expression in fish exposed to high temperature and control. Our study provides the first data regarding GPx gene expression in T tambroides under thermal stress.
  • 12.

    【2hr】Using Pseudoenzymes to Probe Evolutionary Design Principles of Enzymes

    包量

    机译 使用伪酶探索酶的进化设计原理
    摘要：Enzymes are governed by unique evolutionary design principles as their catalytic sites were shown to induce long-range evolutionary conservation gradients. We have recently used a comparative bioinformatics approach to disentangle structural determinants from other possible determinants of the evolutionary conservation gradients. The approach is based on comparing the evolutionary patterns of enzymes to those of pseudoenzymes with the same tertiary structure where the catalytic functionality is turned off. This approach provides a way to evaluate several hypotheses regarding the origin of the observed evolutionary conservation gradient in enzymes. The conclusions from such comparative analyses are important for a better understanding of the unique evolutionary design principles of enzymes, which can in turn potentially guide the design of new and improved enzymes.
  • 13.

    【2hr】The Estimated Pacemaker for Great Apes Supports the Hominoid Slowdown Hypothesis

    包量

    机译 估计的大猿起搏器支持类人动物减慢假说
    摘要：The recent surge of genomic data has prompted the investigation of substitution rate variation across the genome, as well as among lineages. Evolutionary trees inferred from distinct genomic regions may display branch lengths that differ between loci by simple proportionality constants, indicating that rate variation follows a pacemaker model, which may be attributed to lineage effects. Analyses of genes from diverse biological clades produced contrasting results, supporting either this model or alternative scenarios where multiple pacemakers exist. So far, an evaluation of the pacemaker hypothesis for all great apes has never been carried out. In this work, we tested whether the evolutionary rates of hominids conform to pacemakers, which were inferred accounting for gene tree/species tree discordance. For higher precision, substitution rates in branches were estimated with a calibration-free approach, the relative rate framework. A predominant evolutionary trend in great apes was evidenced by the recovery of a large pacemaker, encompassing most hominid genomic regions. In addition, the majority of genes followed a pace of evolution that was closely related to the strict molecular clock. However, slight rate decreases were recovered in the internal branches leading to humans, corroborating the hominoid slowdown hypothesis. Our findings suggest that in great apes, life history traits were the major drivers of substitution rate variation across the genome.
  • 14.

    【2hr】Variations in the Structure and Evolution of Rice WRKY Genes in Indica and Japonica Genotypes and their Co-expression Network in Mediating Disease Resistance

    包量

    机译 Rice稻和粳稻基因型水稻WRKY基因结构和进化的变异及其在抗病性中的共表达网络
    摘要：WRKY transcription factor (TF) family regulates many functions in plant growth and development and also during biotic and abiotic stress. In this study, 101 WRKY TF gene models in indica and japonica rice were used to conduct evolutionary analysis, gene structure analysis, and motif composition. Co-expression analysis was carried out first by selecting the differentially expressing genes that showed a significant change in response to the pathogens from Rice Oligonucleotide Array Database (ROAD). About 82 genes showed responses to infection by Magnaporthe oryzae or Xanthomonas oryzae pv. oryzae. Co-expression gene network was constructed using direct neighborhood and context associated inbuilt mode in RiceNetv2 tool. Only 41 genes showed interaction with 2299 non-WRKY genes. Variations exist in the structure and evolution of WRKY genes among indica and japonica genotypes which have important implications in their differential roles including disease resistance. WRKY genes mediate a complex networking and co-express along with other WRKY and non-WRKY genes to mediate resistance against fungal and bacterial pathogens in rice.
  • 15.

    【2hr】Addressing the Missing Heritability Problem With the Help of RegulatoryFeatures

    包量

    机译 借助法规解决遗漏的遗传性问题特征
    摘要：Genome-wide association studies (GWASs) have successfully identified thousands of susceptibility loci for human complex diseases. However, missing heritability is still a challenging problem. Considering most GWAS loci are located in regulatory elements, we recently developed a pipeline named functional disease-associated single-nucleotide polymorphisms (SNPs) prediction (FDSP), to predict novel susceptibility loci for complex diseases based on the interpretation of regulatory features and published GWAS results with machine learning. When applied to type 2 diabetes and hypertension, the predicted susceptibility loci by FDSP were proved to be capable of explaining additional heritability. In addition, potential target genes of the predicted positive SNPs were significantly enriched in disease-related pathways. Our results suggested that taking regulatory features into consideration might be a useful way to address the missing heritability problem. We hope FDSP could offer help for the identification of novel susceptibility loci for complex diseases.
  • 16.

    【2hr】Genome-Wide Comprehensive Analysis of the SABATH Gene Family inArabidopsis and Rice

    包量

    机译 SABATH基因家族的全基因组综合分析拟南芥和水稻
    摘要：Low molecular weight metabolites are important plant hormones and signaling molecules, and play an important part among the processes of plant development. Their activities may also be affected by the chemical modifications of methylation performed by SABATH. In this study, a total of 24 and 21 SABATH genes in Arabidopsis and rice, respectively, were identified and taken a comprehensive study. Phylogenetic analysis showed that AtSABATH and OsSABATH genes could be classified into 4 major groups and 6 subgroups. Gene expansion analysis showed that the main expansion mechanism of SABATH gene family in Arabidopsis and rice was tandem duplication and segmental duplication. The ratios of nonsynonymous (Ka) and synonymous (Ks) substitution rates of 12 pairs paralogous of AtSABATH and OsSABATH genes indicated that the SABATH gene family in Arabidopsis and rice had gone through purifying selection. Positive selection analysis with site models and branch-site models revealed that AtSABATH and OsSABATH genes had undergone selective pressure for adaptive evolution. Motif analysis showed that certainmotifs only existed in specific subgroups or species, which indicated that theSABATH proteins of Arabidopsis and rice appear divergence indifferent species and subgroups. Functional divergence analysis also suggestedthat the AtSABATH and OsSABATH subgroup geneshad functional differences, and the positive selection sites which contributedto functional divergence among subgroups were detected. These results provideinsights into functional conservation and diversification of SABATH gene family,and are useful information for further elucidating SABATH gene familyfunctions.
  • 17.

    【2hr】In Silico Analysis of Hepatitis B Virus Genotype D Subgenotype D1Circulating in Pakistan, China, and India

    包量

    机译 乙型肝炎病毒基因型D亚型D1的计算机分析在巴基斯坦，中国和印度流通
    摘要：The focus of this study was the computational analysis of hepatitis B virus (HBV) genotype D subgenotype D1 in Pakistan, China, and India. In total, 54 complete genome sequences of HBV genotype D subgenotype D1 were downloaded from National Center for Biotechnology Information (NCBI). Of these, 6 complete genome sequences were from Pakistan, 14 were from China, and 34 were from India. Sequence alignment showed less than 4% divergence in these sequences. C and X genes showed divergence of less than 3%. Comparison over the S gene showed more than 97% similarity among the nucleotide sequences of genotype D subgenotype D1. The identity and similarity matrix of 54 nucleotide sequences of HBV genotype D subgenotype D1 from Pakistan, China, and India revealed more than 93% identity and 93% similarity. Phylogenetic analysis highlighted that complete genome isolates of HBV circulating in Pakistan had the closest evolutionary relationship with its neighboring countries China and India. China’s () and Pakistan’s () isolates shared the same ancestor. Gene structure analysis showed that “P” gene exons were the longest, about three-fourth of the genome size, whereas gene “S” had the second longest coding regions with 2 exons and 1 intron. However, “C” and “X” genes had 1 smallest exon. X proteins hadproven role in spreading of the HBV infection diseases. For HBx analysis, 1 Xprotein sequence of HBV genotype D subgenotype D1 belonging to each country wasobtained. Homology models of the 3 X proteins generated using SWISS-MODELrevealed GMQE (Global Model Quality Estimation) = 0.1. Global and local qualityestimate scores including Z-scores for Qualitative Model EnergyAnalysis (QMEAN) C-beta, all-atom, solvation, and torsion energy scores weresimilar indicating good quality, accuracy, and reliability of the predictedmodels. Three-dimensional (3D) visualization showed similar structures andRamachandran plots showed a high percentage of protein residues into thefavorable region for X protein models.
  • 18.

    【2hr】Applications and Considerations of GToTree: A User-Friendly Workflowfor Phylogenomics

    包量

    机译 GToTree的应用和注意事项：用户友好的工作流程药理学
    • 作者：Michael D Lee
    • 刊名：Evolutionary Bioinformatics Online
    • 2019年第期
    摘要：Phylogenomics is the practice of attempting to infer evolutionary relationships at a genome-level. This is becoming a standard step in the characterization of newly recovered genomes and to direct/constrain further research; yet the process from start to finish of building a de novo phylogenomic tree that is specific to the organisms of interest can still be computationally intractable for many biologists. GToTree is a recently published user-friendly workflow for phylogenomics intended to give more researchers the capability to generate phylogenomic trees to help guide their work. This commentary describes two common applications where GToTree can be helpful and then discusses some things to consider when using the program.
  • 19.

    【2hr】A Stress Response Program at the Origin of Evolutionary Innovation inthe Skin

    包量

    机译 进化创新起源的压力响应程序皮
    摘要：The skin epithelium, ie, the epidermis, of dolphins and whales (cetaceans) is up to 50 times thicker than that of humans and other mammals living on land. Recently, comparative genomics revealed further striking differences in the cytoskeleton of the outer layers of the epidermis in aquatic and terrestrial mammals. Cetaceans lack the cytoskeletal keratins, which make up more than half of the total protein mass in the cornified epidermal layer of terrestrial mammals under homeostatic conditions. By contrast, orthologs of stress-inducible epithelial keratins are conserved in cetaceans and these keratins are constitutively expressed in their skin. Thus, the epidermal stress response program of a terrestrial common ancestor of modern mammals has become the default program of epidermal differentiation and a central component of the unique cutaneous organization of cetaceans. We propose that phenotypic plasticity during stress responses plays important roles in the evolution of the skin.
  • 20.

    【2hr】Versatile Quality Control Methods for Nanopore Sequencing

    包量

    机译 纳米孔测序的多功能质量控制方法
    摘要：Third-generation sequencing using nanopores as biosensors has recently emerged as a strategy capable to overcome next-generation sequencing drawbacks and pitfalls. Assessing the quality of the data produced by nanopore sequencing platforms is essential to decide how useful these may be in making biological discoveries. Here, we briefly contextualized NanoR, a quality control method for nanopore sequencing data we developed, in the scenario of preexistent similar tools. We also illustrated 2 quality control pipelines, readily applicable to nanopore sequencing data, respectively, based on NanoR and PyPore, a second quality control method published by our group.
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