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作者： Zhiming Li Chi-Meng Tzeng

miRNAs are involved in various biological processes and different diseases through interacting with their target mRNAs. Therefore, deciphering miRNA targets is important for diagnostics and therapeutics. However, it is still complex and expensive to do large scale screening for miRNA alterations and identify their downstream miRNA targets. Recently, integrating analysis of miRNA expression profiles and mRNA expression levels has been used to successfully identify the most prominent interactions. Here, we present a protocol that combines both expression data and computational prediction to refine the microarray result for identifying the miRNA targets. Many details are also provided to help researchers choose more appropriate tools and methods for a given type of application. Available web-based resources and experimental conditions for functional enrichment and validation of miRNA targets are also summarized. less

关键词： Microarray Western Blot Reverse Transcription PCR Plasmid Construction Transfection Luciferase Reporter Assay Functional Enrichment Cytoscape Gene Expression Profiling Real-time PCR Dual Luciferase Assay SDS-PAGE Molecular Cloning Cell And Tissue Culture Radioimmunoprecipitation Assay Data analysis programming language Homo sapiens HEK293 mRNA Enrichment miRNA target Integrated analysis Anti-β-tubulin

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Extraction of Plant Lipids for LC-MS-Based Untargeted Plant Lipidomics

Extraction of Plant Lipids for LC-MS-Based Untargeted Plant ...

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作者： Thusitha W. Rupasinghe Ute Roessner

Lipids are defined as hydrophobic or amphipathic small molecules which consist of a number of structurally and functionally distinct molecules that span from nonpolar to neutral to polar compounds. Lipidomics is the comprehensive analysis of all lipids in a biological system. Changes in lipid metabolism and composition, as well as of distinct lipid species have been linked with altered plant growth, development, and responses to environmental stresses including salinity. Recently, improved liquid chromatography mass spectrometry (LC-MS)-based techniques have provided the rapid expansion of lipidomics research. Sample preparation and lipid extraction are important steps in lipidomics, and this chapter describes important considerations in lipid monophasic and biphasic extractions from plant tissues prior to untargeted plant lipidomics approaches with LC-MS. less

关键词： Tissue Extraction Liquid Chromatography-mass Spectrometry Lipidomics Liquid Chromatography (LC) Positive Ion Mode Electrospray Ionization Mass Spectrometry Metabolomics Electrospray Ionization (ESI) HPLC Python programming language Lipids Cell extraction Monophasic lipid extraction Biphasic lipid extraction

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Polymorphic computation in locus coeruleus networks

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NATURE NEUROSCIENCE 2017年第11期20卷 1517-1519页

作者： Seo, Dong-oh Bruchas, Michael R. Washington Univ Sch Med Dept Anesthesiol Div Basic Res St Louis MO 63110 USA Washington Univ Sch Med Dept Neurosci Div Biol & Biomed Sci St Louis MO USA Washington Univ Sch Med Dept Psychiat Div Biol & Biomed Sci St Louis MO 63110 USA Washington Univ Sch Med Washington Univ Pain Ctr St Louis MO USA

Physiological and optogenetic dissection of discrete locus coeruleus neuronal populations reveals a functional disassociation, with heterogeneous engagement of locus coeruleus neurons in either fear learning or extinc... 详细信息

关键词： Fear conditioning Locus coeruleus Optogenetics programming language

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A Practical Guide for Comparative Genomics of Mobile Genetic Elements in Prokaryotic Genomes

A Practical Guide for Comparative Genomics of Mobile Genetic...

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作者： Danillo Oliveira Alvarenga Leandro M. Moreira Mick Chandler Alessandro M. Varani

Mobile genetic elements (MGEs) are an important feature of prokaryote genomes but are seldom well annotated and, consequently, are often underestimated. MGEs include transposons (Tn), insertion sequences (ISs), prophages, genomic islands (GEIs), integrons, and integrative and conjugative elements (ICEs). They are intimately involved in genome evolution and promote phenomena such as genomic expansion and rearrangement, emergence of virulence and pathogenicity, and symbiosis. In spite of the annotation bottleneck, there are so far at least 75 different programs and databases dedicated to prokaryotic MGE analysis and annotation, and this number is rapidly growing. Here, we present a practical guide to explore, compare, and visualize prokaryote MGEs using a combination of available software and databases tailored to small scale genome analyses. This protocol can be coupled with expert MGE annotation and exploited for evolutionary and comparative genomic analyses. less

关键词： CRISPR Genomics Rearrangement Genome Annotation Statistical Calculation NCBI BLAST Genome Visualization GenBank programming language Python Pull-down Assay Evolution Transposons Genomic islands Insertion sequences Prophages Integrons Integrative conjugative elements

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Proton Nuclear Magnetic Resonance (

Proton Nuclear Magnetic Resonance (

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作者： Niraj Kumar Srivastava

Proton nuclear magnetic resonance spectroscopy (1H NMR) is a useful tool for the analysis of lipid components in biofluids such as serum/plasma. Such tool is applied for the analysis of lipid components in serum/plasma of patients with Duchenne muscular dystrophy (DMD). The practical approach of sampling, storage, lipid extraction procedure, sample preparation before performing the 1H NMR spectroscopy experiments is presented. All the experimental parameters of NMR spectroscopy are also described. Details of the assignments of lipid components (qualitative analysis) and quantification of particular lipid components (quantitative analysis) are explained. less

关键词： NMR Metabolomics Proton NMR Sonication 1D NMR Spectroscopy Two dimensional correlation spectroscopy 1H--1H Correlation Spectroscopy High-field NMR programming language Data analysis Cholesterol Phospholipids Muscular dystrophy Triglycerides DMD

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The SQUAD Method for the Qualitative Modeling of Regulatory Networks

The SQUAD Method for the Qualitative Modeling of Regulatory ...

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作者： Akram Méndez Carlos Ramírez Mauricio Pérez Martínez Luis Mendoza

The wealth of molecular information provided by high-throughput technologies has enhanced the efforts dedicated to the reconstruction of regulatory networks in diverse biological systems. This information, however, has proven to be insufficient for the construction of quantitative models due to the absence of sufficiently accurate measurements of kinetic constants. As a result, there have been efforts to develop methodologies that permit the use of qualitative information about patterns of expression to infer the regulatory networks that generate such patterns. One of these approaches is the SQUAD method, which approximates a Boolean network with the use of a set of ordinary differential equations. The main benefit of the SQUAD method over purely Boolean approaches is the possibility of evaluating the effect of continuous external signals, which are pervasive in biological phenomena. A brief description and code on how to implement this method can be found at the following link: https://***/caramirezal/SQUADBookChapter . less

关键词： Fuzzy Logic programming language Cell fate Regulatory networks Expression pattern Network modeling

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Towards a language Framework for Thick Control Flows 31

Towards a Language Framework for Thick Control Flows

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31st IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPS)

作者： Makela, Jari-Matti Forsell, Martti Leppanen, Ville Univ Turku TUCS Turku Ctr Comp Sci Turku Finland VTT Oulu Finland Univ Turku Turku Finland

ISBN: (纸本)9780769561493

In the recent years the search for scalability in terms of computing power has led to very complex parallel computer architectures which require greater control of the storage and computation resources to utilize all the available hardware capacity for optimal performance. New solutions in the level of programming languages/models have increased the reliance and need for threads. A system with a huge number of threads can face problems with thread micro-management, smooth scaling between data and task parallelism, portability, and consistency. We present TCF++, a new concurrent C/C++ language extension generalizing on the idea of threads with so called thick control flows. Opposed to threading, thick control flows provide a way to orchestrate computation using lower number of independent actors, dynamically adapting to problem size. The language extension approach is chosen to support mixing with legacy code. We qualitatively analyze the new language's eligibility and explain its idiomatic use with a selection of core parallel algorithm kernels.

关键词： Parallel programming thread programming language control structures programming examples parallel architecture

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Genome-Wide Quantitative Fitness Analysis (QFA) of Yeast Cultures

Genome-Wide Quantitative Fitness Analysis (QFA) of Yeast Cul...

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作者： Eva-Maria Holstein Conor Lawless Peter Banks David Lydall

We provide a detailed protocol for robot-assisted, genome-wide measurement of fitness in the model yeast Saccharomyces cerevisiae using Quantitative Fitness Analysis (QFA). We first describe how we construct thousands of double or triple mutant yeast strains in parallel using Synthetic Genetic Array (SGA) procedures. Strains are inoculated onto solid agar surfaces by liquid spotting followed by repeated photography of agar plates. Growth curves are constructed and the fitness of each strain is estimated. Robot-assisted QFA, can be used to identify genetic interactions and chemical sensitivity/resistance in genome-wide experiments, but QFA can also be used in smaller scale, manual workflows. less

关键词： Image Analysis Sterilization Microscopy Statistical Modeling Data analysis Python programming language Saccharomyces cerevisiae Genetic interaction High-throughput SGA Quantitative Fitness Genome-wide Growth curve QFA Robotic Population model

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Let's Go: a Data-Driven Multi-Threading Support 17

Let's Go: a Data-Driven Multi-Threading Support

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14th ACM International Conference on Computing Frontiers

作者： Scionti, Alberto Mazumdar, Somnath Ist Super Mario Boella Turin Italy Univ Siena Siena Italy

ISBN: (纸本)9781450344876

Increasing performance of computing systems necessitates providing solutions for improving scalability and productivity. In recent times, data-driven Program eXecution Models (PXMs) are gaining popularity due to their superior support compared to traditional von Neumann execution models. However, exposing the benefits of such PXMs within a high-level programming language remains a challenge. Although many high-level programming languages and APIs support concurrency and multi-threading (e.g., C++11, Java, OpenMP, MPI, etc.), their synchronisation models make large use of mutex and locks, generally leading to poor system performance. Conversely, one major appeal of Go programming language is the way it supports concurrency: goroutines (tagged functions) are mapped on OS threads and communicate each other through data structures buffering input data (channels). By forcing goroutines to exchange data only through channels, it is possible to enable a data-driven execution. This paper proposes a first attempt to map goroutines on a data-driven based PXM. Go compilation procedure and the run-time library are modified to exploit the execution of fine-grain threads on an abstracted parallel machine model.

关键词： Data-driven programming language Multi-threading

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Modular and Flexible Coordination for Web-based Applications 2

Modular and Flexible Coordination for Web-based Applications

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2nd International Conference on Computer and Communication Systems (ICCCS)

作者： Li, Peng Beijing Inst Technol Sch Software Beijing Peoples R China

ISBN: (纸本)9781538605394

In this research, I want to investigate programming language and middleware abstractions which offer an alternative approach in client/server Web application development, for dealing specifically with coordination between client and server components that has flexibility in mapping components to physical locations. I work on a middleware and JavaScript interpreter that provides support for modular coordination that avoid problems with both of the patterns presented in this Introduction. In my approach, developers would write a separate coordination specification which mediated client and server workflow. To evaluate the performance of my framework and prove the low-performance overhead, I have modified a well-known open source Web application, Java Pet Store by using my framework and then I have evaluated the modified Web application provides low-performance overhead.

关键词： web-based application cloud-based application program partitioning AJAX programming language

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