快速，自动，平行定量免疫测定采用高度集成的微流控和AlphaLISA

Immunoassays represent one of the most popular analytical methods for detection and quantification of biomolecules. However, conventional immunoassays such as ELISA and flow cytometry, even though providing high sensitivity and specificity and multiplexing capability, can be labor-intensive and prone to human error, making them unsuitable for standardized clinical diagnoses. Using a commercialized no-wash, homogeneous immunoassay technology (‘AlphaLISA’) in conjunction with integrated microfluidics, herein we developed a microfluidic immunoassay chip capable of rapid, automated, parallel immunoassays of microliter quantities of samples. Operation of the microfluidic immunoassay chip entailed rapid mixing and conjugation of AlphaLISA components with target analytes before quantitative imaging for analyte detections in up to eight samples simultaneously. Aspects such as fluid handling and operation, surface passivation, imaging uniformity, and detection sensitivity of the microfluidic immunoassay chip using AlphaLISA were investigated. The microfluidic immunoassay chip could detect one target analyte simultaneously for up to eight samples in 45 min with a limit of detection down to 10 pg mL−1. The microfluidic immunoassay chip was further utilized for functional immunophenotyping to examine cytokine secretion from human immune cells stimulated ex vivo. Together, the microfluidic immunoassay chip provides a promising high-throughput, high-content platform for rapid, automated, parallel quantitative immunosensing applications.

• http://feeds.nature.com/~r/srep/rss/current/~3/C14LxDFSwqg/srep11339

[详细]

pedican：与文献证据儿科癌症在线基因资源

Pediatric cancer (PC), that is cancer occurring in children, is the leading cause of death among children worldwide, with an incidence of 175,000 per year. Elucidating the genetic abnormalities and underlying cellular mechanisms may provide less toxic curative treatments. Therefore, it is important to understand the pathology of pediatric cancer at the genetic, genomic and epigenetic level. To unveil the cellular complexity of PC, we have developed a database of pediatric cancers (Pedican), the first literature-based pediatric gene data resource by comprehensive literature curation and data integration. In the current release, Pedican contains 735 human genes, 88 gene fusion and 24 chromosome abnormal events curated from 2245 PubMed abstracts. Pedican provides detailed annotations for each gene, such as Entrez gene information, involved pathways, protein–protein interactions, mutations, gene expression, methylation sites, TF regulation, and post-translational modification. Additionally Pedican has a user-friendly web interface, which allows sophisticated text query, sequence searches, and browsing by highlighted literature evidence and hundreds of cancer types. Overall, our curated pediatric cancer-related gene list maps the genomic and cellular landscape for various pediatric cancers, providing a valuable resource for further experiment design. The Pedican is available at http://pedican.bioinfo-minzhao.org/.

• http://feeds.nature.com/~r/srep/rss/current/~3/OFgxgmxZiFA/srep11435

[详细]

水稻齿叶矮缩病毒诱导的细胞凋亡的影响及其媒介昆虫病毒的传播，对水稻褐飞虱

Most plant viruses that seriously damage agricultural crops are transmitted by insects. However, the mechanisms enabling virus transmission by insect vectors are poorly understood. The brown planthopper (Nilaparvata lugens) is one of the most serious rice pests, causing extensive damage to rice plants by sucking the phloem sap and transmitting viruses, including Rice ragged stunt virus (RRSV). In this study, we investigated the mechanisms of RRSV transmission from its insect vector to the rice plant in vivo using the terminal deoxynucleotidyl transferase dUTP nick-end labeling assay and RNA interference technology. RRSV induced apoptosis in the salivary gland cells of its insect vector, N. lugens. The RRSV-induced apoptosis was regulated through a caspase-dependent manner, and inhibition of the expression of N. lugens caspase-1 genes significantly interfered with virus transmission. Our findings establish a link between virus-associated apoptosis and virus transmission from the insect vector to the host plant.

• http://feeds.nature.com/~r/srep/rss/current/~3/6j83fSzct8U/srep11413

[详细]

洞察在蜜蜂行为的可塑性转录结构

Honey bee colonies exhibit an age-related division of labor, with worker bees performing discrete sets of behaviors throughout their lifespan. These behavioral states are associated with distinct brain transcriptomic states, yet little is known about the regulatory mechanisms governing them. We used CAGEscan (a variant of the Cap Analysis of Gene Expression technique) for the first time to characterize the promoter regions of differentially expressed brain genes during two behavioral states (brood care (aka “nursing”) and foraging) and identified transcription factors (TFs) that may govern their expression. More than half of the differentially expressed TFs were associated with motifs enriched in the promoter regions of differentially expressed genes (DEGs), suggesting they are regulators of behavioral state. Strikingly, five TFs (nf-kb, egr, pax6, hairy, and clockwork orange) were predicted to co-regulate nearly half of the genes that were upregulated in foragers. Finally, differences in alternative TSS usage between nurses and foragers were detected upstream of 646 genes, whose functional analysis revealed enrichment for Gene Ontology terms associated with neural function and plasticity. This demonstrates for the first time that alternative TSSs are associated with stable differences in behavior, suggesting they may play a role in organizing behavioral state.

• http://feeds.nature.com/~r/srep/rss/current/~3/sUbdWquKDvQ/srep11136

[详细]

对单分子定位显微镜软件定量评价

This Analysis reports a comparison of current software packages for single-molecule localization in localization-based super-resolution imaging. Performance of the participating software on synthetic, biologically inspired ground-truth data was assessed by multiple criteria.

• http://feeds.nature.com/~r/nmeth/rss/aop/~3/xazUSDzj_5Q/nmeth.3442

[详细]

有效集测试相关性状的遗传分析

The multi-trait set test (mtSet) is an efficient mixed-model method that enables genome-wide association tests for large cohorts and multiple quantitative traits using sets of variants to improve power and sensitivity, while addressing confounding due to population structure.

• http://feeds.nature.com/~r/nmeth/rss/aop/~3/S6fqsbUonJc/nmeth.3439

[详细]

一个完整的细菌基因组组装从头只使用纳米孔测序数据

By error-correcting long nanopore reads and calling a consensus sequence using nanopore signal data, an entire bacterial genome is assembled de novo.

• http://feeds.nature.com/~r/nmeth/rss/aop/~3/Qze6aRxOTZU/nmeth.3444

[详细]

大众宽容的数据库搜索确定蛋白质组修饰肽大比例分配的光谱

In shotgun proteomics experiments, modified peptides account for a large part of the unassigned spectra and can be identified using ultra-tolerant database searches.

• http://feeds.nature.com/~r/nbt/rss/aop/~3/Xj4y3YLa7W4/nbt.3267

[详细]

metapathways V2.5：定量的功能，分类，和可用性的改进

Summary: Next-generation sequencing is producing vast amounts of sequence information from natural and engineered ecosystems. While this data deluge has enormous potential to transform our lives, knowledge creation and translation need software applications that scale with increasing data processing and analysis requirements. Here, we present improvements to MetaPathways, an annotation and analysis pipeline for environmental sequence information that expedites this transformation. We specifically address pathway prediction hazards through integration of a weighted taxonomic distance and enable quantitative comparison of assembled annotations through a normalized read-mapping measure. Additionally, we improve LAST homology searches through BLAST-equivalent E-values and output formats that are natively compatible with prevailing software applications. Finally, an updated GUI allows for keyword annotation query and projection onto user defined functional gene hierarchies, including the Carbohydrate-Active Enzyme database.

Availability and Implementation: MetaPathways v2.5 is available on GitHub: http://github.com/hallamlab/metapathways2

Contact: shallam@mail.ubc.ca

Supplementary information: Supplementary data are available at Bioinformatics online.

• http://bioinformatics.oxfordjournals.org/cgi/content/short/btv361v1?rss=1

[详细]

细菌生理学：IV型菌毛的功能作为mechanosensors

Bacteria use a range of sensory systems to mount appropriate responses to their environment. A new study now shows that the opportunistic pathogen Pseudomonas aeruginosa uses its type IV pili (which are composed of pilin subunits and are mainly used for surface motility) to

• http://feeds.nature.com/~r/nrmicro/rss/current/~3/Zo35wxrcFjc/nrmicro3517

[详细]

全球流感病毒的进化：循环模式

Understanding the factors that influence the circulation of seasonal influenza viruses is a major public health challenge. By analysing 9,604 viral haemagglutinin (HA) sequences from the 2 influenza A subtypes H1N1 and H3N2, and the 2 influenza B viruses Yamagata and Victoria (all of which

• http://feeds.nature.com/~r/nrmicro/rss/current/~3/Per5g1ji6b4/nrmicro3518

[详细]

基因组表：适应：这是一个错误的比赛

This month's Genome Watch highlights studies that investigate links between Wolbachia genotypes and their phenotypes, and explore how Wolbachia adapts to new host environments.

• http://feeds.nature.com/~r/nrmicro/rss/current/~3/rjuLeydt7pQ/nrmicro3514

[详细]

广谱抗病毒药物对病毒融合

Effective antivirals have been developed against specific viruses, such as HIV, Hepatitis C virus and influenza virus. This 'one bug–one drug' approach to antiviral drug development can be successful, but it may be inadequate for responding to an increasing diversity of viruses that cause significant

• http://feeds.nature.com/~r/nrmicro/rss/current/~3/9RALc7WsW8Q/nrmicro3475

[详细]

在古细菌的基因导入和中温的适应

It is widely believed that the archaeal ancestor was hyperthermophilic, but during archaeal evolution, several lineages — including haloarchaea and their sister methanogens, the Thaumarchaeota, and the uncultured Marine Group II and Marine Group III Euryarchaeota (MGII/III) — independently adapted to lower temperatures. Recent phylogenomic

• http://feeds.nature.com/~r/nrmicro/rss/current/~3/vqmLwdVAr0Q/nrmicro3485

[详细]

PPU：Web服务器-网站具体预测脓

Motivation: Pseudouridine (), catalyzed by pseudouridine synthase (PUS), is the most abundant RNA modification and has important cellular functions. Developing an algorithm to identify sites is an important work. And it is better if the algorithm could assign which PUS modifies the sites. Here, we developed PPUS (http://lyh.pkmu.cn/ppus/), the first web server to predict PUS-specific sites. PPUS employed support vector machine as the classifier and used nucleotides around sites as the features. Currently, PPUS could accurately predict new sites for PUS1, PUS4 and PUS7 in yeast and PUS4 in human. PPUS is well designed and friendly to user.

• http://bioinformatics.oxfordjournals.org/cgi/content/short/btv366v1?rss=1

[详细]

救赎：降维集成建模与参数估计

Motivation: Here, we present REDEMPTION (Reduced Dimension Ensemble Modeling and Parameter estimation), a toolbox for parameter estimation and ensemble modeling of ordinary differential equations (ODEs) using time-series data. For models with more reactions than measured species, a common scenario in biological modeling, the parameter estimation is formulated as a nested optimization problem based on incremental parameter estimation strategy. REDEMPTION also includes a tool for the identification of an ensemble of parameter combinations that provide satisfactory goodness-of-fit to the data. The functionalities of REDEMPTION are accessible through a MATLAB user interface (UI), as well as through programming script. For computational speed-up, REDEMPTION provides a numerical parallelization option using MATLAB Parallel Computing toolbox.

Availability: REDEMPTION can be downloaded from http://www.cabsel.ethz.ch/tools/redemption.

Contact: rudi.gunawan@chem.ethz.ch

• http://bioinformatics.oxfordjournals.org/cgi/content/short/btv365v1?rss=1

[详细]

在蛋白组学的新的肽假发现率的一个注记

Motivation: Proteogenomics has been well accepted as a tool to discover novel genes. In most conventional proteogenomic studies, a global false discovery rate (FDR) is used to filter out false positives for identifying credible novel peptides. However, it has been found that the actual level of false positives in novel peptides is often out of control and behaves differently for different genomes. In order to quantitatively model this problem, we theoretically analyze the sub-group FDRs of annotated and novel peptides. Our analysis shows that the annotation completeness ratio of a genome is the dominant factor influencing the subgroup FDR of novel peptides. Experimental results on two real datasets of E. coli and M. tuberculosis support our conjecture.

Contact: yfu@amss.ac.cn, xupingghy@gmail.com, smhe@ict.ac.cn

• http://bioinformatics.oxfordjournals.org/cgi/content/short/btv340v1?rss=1

[详细]

hcsd：人类癌分泌蛋白质组数据库

The human cancer secretome database (HCSD) is a comprehensive database for human cancer secretome data. The cancer secretome describes proteins secreted by cancer cells and structuring information about the cancer secretome will enable further analysis of how this is related with tumor biology. The secreted proteins from cancer cells are believed to play a deterministic role in cancer progression and therefore may be the key to find novel therapeutic targets and biomarkers for many cancers. Consequently, huge data on cancer secretome have been generated in recent years and the lack of a coherent database is limiting the ability to query the increasing community knowledge. We therefore developed the Human Cancer Secretome Database (HCSD) to fulfil this gap. HCSD contains >80 000 measurements for about 7000 nonredundant human proteins collected from up to 35 high-throughput studies on 17 cancer types. It has a simple and user friendly query system for basic and advanced search based on gene name, cancer type and data type as the three main query options. The results are visualized in an explicit and interactive manner. An example of a result page includes annotations, cross references, cancer secretome data and secretory features for each identified protein.

Database URL: www.cancersecretome.org.

• http://database.oxfordjournals.org/cgi/content/short/2015/0/bav051?rss=1

[详细]

在红细胞膜蛋白质组分析的不一致：一种与诊断应用研究数据库的生成

Based on recent results, the determination of the easily accessible red blood cell (RBC) membrane proteins may provide new diagnostic possibilities for assessing mutations, polymorphisms or regulatory alterations in diseases. However, the analysis of the current mass spectrometry-based proteomics datasets and other major databases indicates inconsistencies—the results show large scattering and only a limited overlap for the identified RBC membrane proteins. Here, we applied membrane-specific proteomics studies in human RBC, compared these results with the data in the literature, and generated a comprehensive and expandable database using all available data sources. The integrated web database now refers to proteomic, genetic and medical databases as well, and contains an unexpected large number of validated membrane proteins previously thought to be specific for other tissues and/or related to major human diseases. Since the determination of protein expression in RBC provides a method to indicate pathological alterations, our database should facilitate the development of RBC membrane biomarker platforms and provide a unique resource to aid related further research and diagnostics.

Database URL: http://rbcc.hegelab.org

• http://database.oxfordjournals.org/cgi/content/short/2015/0/bav056?rss=1

[详细]

degps是检测RNA测序研究差异表达的有力工具

Background: The advent of the NGS technologies has permitted profiling of whole-genome transcriptomes (i.e., RNA-Seq) at unprecedented speed and very low cost. RNA-Seq provides a far more precise measurement of transcript levels and their isoforms compared to other methods such as microarrays. A fundamental goal of RNA-Seq is to better identify expression changes between different biological or disease conditions. However, existing methods for detecting differential expression from RNA-Seq count data have not been comprehensively evaluated in large-scale RNA-Seq datasets. Many of them suffer from inflation of type I error and failure in controlling false discovery rate especially in the presence of abnormal high sequence read counts in RNA-Seq experiments. Results: To address these challenges, we propose a powerful and robust tool, termed deGPS, for detecting differential expression in RNA-Seq data. This framework contains new normalization methods based on generalized Poisson distribution modeling sequence count data, followed by permutation-based differential expression tests. We systematically evaluated our new tool in simulated datasets from several large-scale TCGA RNA-Seq projects, unbiased benchmark data from compcodeR package, and real RNA-Seq data from the development transcriptome of Drosophila. deGPS can precisely control type I error and false discovery rate for the detection of differential expression and is robust in the presence of abnormal high sequence read counts in RNA-Seq experiments. Conclusions: Software implementing our deGPS was released within an R package with parallel computations (https://github.com/LL-LAB-MCW/deGPS). deGPS is a powerful and robust tool for data normalization and detecting different expression in RNA-Seq experiments. Beyond RNA-Seq, deGPS has the potential to significantly enhance future data analysis efforts from many other high-throughput platforms such as ChIP-Seq, MBD-Seq and RIP-Seq.

• http://www.biomedcentral.com/1471-2164/16/455

[详细]

单链特异性RNA测序在<它> <它>疟疾的恶性疟原虫发育调控的长非编码RNA识别和循环RNA

Background: The human malaria parasite Plasmodium falciparum has a complex and multi-stage life cycle that requires extensive and precise gene regulation to allow invasion and hijacking of host cells, transmission, and immune escape. To date, the regulatory elements orchestrating these critical parasite processes remain largely unknown. Yet it is becoming increasingly clear that long non-coding RNAs (lncRNAs) could represent a missing regulatory layer across a broad range of organisms. Results: To investigate the regulatory capacity of lncRNA in P. falciparum, we harvested fifteen samples from two time-courses. Our sample set profiled 56 h of P. falciparum blood stage development. We then developed and validated strand-specific, non-polyA-selected RNA sequencing methods, and pursued the first assembly of P. falciparum strand-specific transcript structures from RNA sequencing data. This approach enabled the annotation of over one thousand lncRNA transcript models and their comprehensive global analysis: coding prediction, periodicity, stage-specificity, correlation, GC content, length, location relative to annotated transcripts, and splicing. We validated the complete splicing structure of three lncRNAs with compelling properties. Non-polyA-selected deep sequencing also enabled the prediction of hundreds of intriguing P. falciparum circular RNAs, six of which we validated experimentally. Conclusions: We found that a subset of lncRNAs, including all subtelomeric lncRNAs, strongly peaked in expression during invasion. By contrast, antisense transcript levels significantly dropped during invasion. As compared to neighboring mRNAs, the expression of antisense-sense pairs was significantly anti-correlated during blood stage development, indicating transcriptional interference. We also validated that P. falciparum produces circRNAs, which is notable given the lack of RNA interference in the organism, and discovered that a highly expressed, five-exon antisense RNA is poised to regulate P. falciparum gametocyte development 1 (PfGDV1), a gene required for early sexual commitment events.

• http://www.biomedcentral.com/1471-2164/16/454

[详细]

小麦5DS实物图揭示了基因复制和小重排

Background: The substantially large bread wheat genome, organized into highly similar three sub-genomes, renders genomic research challenging. The construction of BAC-based physical maps of individual chromosomes reduces the complexity of this allohexaploid genome, enables elucidation of gene space and evolutionary relationships, provides tools for map-based cloning, and serves as a framework for reference sequencing efforts. In this study, we constructed the first comprehensive physical map of wheat chromosome arm 5DS, thereby exploring its gene space organization and evolution. Results: The physical map of 5DS was comprised of 164 contigs, of which 45 were organized into 21 supercontigs, covering 176 Mb with an N50 value of 2,173 kb. Fifty-eight of the contigs were larger than 1 Mb, with the largest contig spanning 6,649 kb. A total of 1,864 molecular markers were assigned to the map at a density of 10.5 markers/Mb, anchoring 100 of the 120 contigs (>5 clones) that constitute ~95 % of the cumulative length of the map. Ordering of 80 contigs along the deletion bins of chromosome arm 5DS revealed small-scale breaks in syntenic blocks. Analysis of the gene space of 5DS suggested an increasing gradient of genes organized in islands towards the telomere, with the highest gene density of 5.17 genes/Mb in the 0.67-0.78 deletion bin, 1.4 to 1.6 times that of all other bins. Conclusions: Here, we provide a chromosome-specific view into the organization and evolution of the D genome of bread wheat, in comparison to one of its ancestors, revealing recent genome rearrangements. The high-quality physical map constructed in this study paves the way for the assembly of a reference sequence, from which breeding efforts will greatly benefit.

• http://www.biomedcentral.com/1471-2164/16/453

[详细]

fdf-page：一个强大的技术，揭示了以前未被发现的小分子RNA被互补的成绩单

Small RNAs, between 18nt and 30nt in length, are a diverse class of non-coding RNAs that mediate a range of cellular processes, from gene regulation to pathogen defense. They guide ribonucleoprotein complexes to their target nucleic acids by Watson–Crick base pairing. We report here that current techniques for small RNA detection and library generation are biased by formation of RNA duplexes. To address this problem, we established FDF-PAGE (fully-denaturing formaldehyde polyacrylamide gel electrophoresis) to prevent annealing of sRNAs to their complement. By applying FDF-PAGE, we provide evidence that both strands of viral small RNA are present in near equimolar ratios, indicating that the predominant precursor is a long double-stranded RNA. Comparing non-denaturing conditions to FDF-PAGE uncovered extensive sequestration of miRNAs in model organisms and allowed us to identify candidate small RNAs under the control of competing endogenous RNAs (ceRNAs). By revealing the full repertoire of small RNAs, we can begin to create a better understanding of small RNA mediated interactions.

• http://nar.oxfordjournals.org/cgi/content/short/gkv604v1?rss=1

[详细]

基于DNA的纳米结构异型协同装配建模

DNA origami is a robust method for the fabrication of nanoscale 2D and 3D objects with complex features and geometries. The process of DNA origami folding has been recently studied, however quantitative understanding of it is still elusive. Here, we describe a systematic quantification of the assembly process of DNA nanostructures, focusing on the heterotypic DNA junction—in which arms are unequal—as their basic building block. Using bulk fluorescence studies we tracked this process and identified multiple levels of cooperativity from the arms in a single junction to neighboring junctions in a large DNA origami object, demonstrating that cooperativity is a central underlying mechanism in the process of DNA nanostructure assembly. We show that the assembly of junctions in which the arms are consecutively ordered is more efficient than junctions with randomly-ordered components, with the latter showing assembly through several alternative trajectories as a potential mechanism explaining the lower efficiency. This highlights consecutiveness as a new design consideration that could be implemented in DNA nanotechnology CAD tools to produce more efficient and high-yield designs. Altogether, our experimental findings allowed us to devise a quantitative, cooperativity-based heuristic model for the assembly of DNA nanostructures, which is highly consistent with experimental observations.

• http://nar.oxfordjournals.org/cgi/content/short/gkv602v1?rss=1

[详细]