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检索条件"主题词=Programming Language"

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Searching Sequence Databases via

Searching Sequence Databases via

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作者： Richard S. Johnson J. Alex Taylor

The initial stages of tandem mass spectral data interpretation for a pro-teomics project usually involve looking for exact matches between the query spectrum and theoretical fragmentation data derived from database sequences (1–3). A number of programs are available that use the observed peptide mass as a filter for identifying portions of database sequences with the same calculated mass prior to evaluating the congruency between the database sequence candidates and the tandem mass spectrum (4–7). These programs generally fall short when analyzing peptides whose sequences differ in a manner that alters its mass compared with the database sequence (seeNote 1 ). For example, a single conservative substitution of isoleucine for valine is sufficient to thwart algorithms that rely on peptide mass prefilters. We commonly obtain high-quality tandem mass spectral data of peptides for which no exact database match can be made, and the question remains whether these nonmatching spectra are due to novel sequences, or are a result of less interesting possibilities such as interspecies variation, database sequence errors, or unexpected pro-teolytic cleavages. less

关键词： Tandem Mass Spectrometry Electrospray Ionization (ESI) Database Search Collision-induced Dissociation Protein Purification De Novo Sequencing Expasy TrEMBL programming language Malus domestica

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EnzymeML: seamless data flow and modeling of enzymatic data

EnzymeML: seamless data flow and modeling of enzymatic data

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作者： Simone Lauterbach Hannah Dienhart Jan Range Stephan Malzacher Jan-Dirk Spöring Dörte Rother Maria Filipa Pinto Pedro Martins Colton E. Lagerman Andreas S. Bommarius Amalie Vang Høst John M. Woodley Sandile Ngubane Tukayi Kudanga Frank T. Bergmann Johann M. Rohwer Dorothea Iglezakis Andreas Weidemann Ulrike Wittig Carsten Kettner Neil Swainston Santiago Schnell Jürgen Pleiss

The design of biocatalytic reaction systems is highly complex owing to the dependency of the estimated kinetic parameters on the enzyme, the reaction conditions, and the modeling method. Consequently, reproducibility of enzymatic experiments and reusability of enzymatic data are challenging. We developed the XML-based markup language EnzymeML to enable storage and exchange of enzymatic data such as reaction conditions, the time course of the substrate and the product, kinetic parameters and the kinetic model, thus making enzymatic data findable, accessible, interoperable and reusable (FAIR). The feasibility and usefulness of the EnzymeML toolbox is demonstrated in six scenarios, for which data and metadata of different enzymatic reactions are collected and analyzed. EnzymeML serves as a seamless communication channel between experimental platforms, electronic lab notebooks, tools for modeling of enzyme kinetics, publication platforms and enzymatic reaction databases. EnzymeML is open and transparent, and invites the community to contribute. All documents and codes are freely available at https://*** . less

关键词： programming language Python Statistical Calculation Enzymatic Assay Data integration Biocatalysis Enzymes

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Development of a Computational Approach/Model to Explore NMDA Receptors Functions

Development of a Computational Approach/Model to Explore NMD...

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作者： A. Florence Keller Jean-Marie C. Bouteiller Theodore W. Berger

Modern laboratory techniques allow studying NMDA receptors (NMDAR) either anatomically with specific antibodies coupled to sophisticated confocal microscopy, or physiologically by live imaging or electrophysiological techniques. However, NMDARs are not fixed in time and space and changes in their composition and/or distribution on the post-synaptic membrane may significantly impact the synaptic strength and overall function. The computational modeling approach therefore constitutes a complementary tool for investigating the properties of biological systems based on the knowledge provided by the lab experiments. Here, we describe a general computational method aiming at developing kinetic Markov-chain based models of NMDARs subtypes capable of reproducing various experimental results. These models are then used to make predictions on additional (non-obvious) properties and on their role in synaptic function under various physiological and pharmacological conditions. For the purpose of this book chapter, we will focus on the method used to develop a NMDAR model that includes pharmacological site of action of different compounds. Notably, this elementary model can subsequently be included in a neuron model (not described in detail here) to explore the impact of their differential distribution on synaptic functions. less

关键词： Confocal Microscopy Live Cell Imaging Data Mining Data analysis programming language Python Pharmacology Computational model Ordinary differential equation kinetic models NMDA receptors model Synaptic function Optimization algorithm

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Chromatin Immunoprecipitation Followed by Next-Generation Sequencing (ChIP-Seq) Analysis in Ewing Sarcoma

Chromatin Immunoprecipitation Followed by Next-Generation Se...

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作者： Gwenneg Kerdivel Valentina Boeva

ChIP-seq is the method of choice for profiling protein–DNA interactions, and notably for characterizing the landscape of transcription factor binding and histone modifications. This technique has been widely used to study numerous aspects of tumor biology and led to the development of several promising cancer therapies. In Ewing sarcoma research, ChIP-seq provided important insights into the mechanism of action of the major oncogenic fusion protein EWSR1-FLI1 and related epigenetic and transcriptional changes. In this chapter, we provide a detailed pipeline to analyze ChIP-seq experiments from the preprocessing of raw data to tertiary analysis of detected binding sites. We also advise on best practice to prepare tumor samples prior to sequencing. less

关键词： ChIP-seq ChIP Assay Peak Calling Library Preparation Immunoprecipitation Variant Calling PCR Genome Visualization RNA-seq Statistical Calculation Genome Assembly Genomics programming language Transcription factors Binding sites Histone modifications Ewing sarcoma Motif analysis

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Predicting Gene Expression Noise from Gene Expression Variations

Predicting Gene Expression Noise from Gene Expression Variat...

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作者： Xiaojian Shao Ming-an Sun

The level of gene expression is known to vary from cell to cell and even in the same cell over time. This variability provides cells with the ability to mitigate environmental stresses and genetic perturbations, and facilitates gene expression evolution. Recently, many valuable gene expression noise data measured at the single-cell level and gene expression variation measured for cell populations have become available. In this chapter, we show how to perform integrative analysis using these data. Specifically, we introduce how to apply a machine learning technique (support vector regression) to explore the relationship between gene expression variations and stochastic noise. less

关键词： Machine Learning Statistical Calculation MATLAB Flow Cytometry RNA-seq Microarray Image Processing Data analysis programming language Saccharomyces cerevisiae Feature selection Single-cell Support vector regression Gene expression variation Intrinsic noise

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Genome-Scale Metabolic Network Reconstruction

Genome-Scale Metabolic Network Reconstruction

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作者： Marco Fondi Pietro Liò

Bacterial metabolism is an important source of novel products/processes for everyday life and strong efforts are being undertaken to discover and exploit new usable substances of microbial origin. Computational modeling and in silico simulations are powerful tools in this context since they allow the exploration and a deeper understanding of bacterial metabolic circuits. Many approaches exist to quantitatively simulate chemical reaction fluxes within the whole microbial metabolism and, regardless of the technique of choice, metabolic model reconstruction is the first step in every modeling pipeline. Reconstructing a metabolic network consists in drafting the list of the biochemical reactions that an organism can carry out together with information on cellular boundaries, a biomass assembly reaction, and exchange fluxes with the external environment. Building up models able to represent the different functional cellular states is universally recognized as a tricky task that requires intensive manual effort and much additional information besides genome sequence. In this chapter we present a general protocol for metabolic reconstruction in bacteria and the main challenges encountered during this process. less

关键词： Genome Annotation Genomics Extrusion Text Mining Sequence Comparison Genome Sequencing Python programming language Escherichia coli Flux balance analysis Metabolic modeling Metabolic model reconstruction

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Read Depth Analysis to Identify CNV in Bacteria Using CNOGpro

Read Depth Analysis to Identify CNV in Bacteria Using CNOGpr...

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作者： Ola Brynildsrud

Whole-genome sequencing with short-read technologies is well suited for calling single nucleotide polymorphisms, but has major problems with the detection of structural variants larger than the read length. One such type of variation is copy number variation (CNV), which entails deletion or duplication of genomic regions, and the expansion or contraction of repeated elements. Duplicated and deleted regions will typically be collapsed during de novo assembly of sequence data, or ignored when mapping reads toward a reference. However, signatures of the copy number variation can be detected in the resultant read depth at each position in the genome. We here provide instructions on how to analyze this read depth signal with the R package CNOGpro, allowing for estimation of copy numbers with uncertainty for each feature in a genome. less

关键词： Whole-genome Sequencing Read Depth Analysis Copy Number Variation Profiling PCR Library Preparation Genomics GenBank programming language Bacteria Read depth CNV Coverage CNOGpro

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Functional Imaging of Retinal Photoreceptors and Inner Neurons Using Stimulus-Evoked Intrinsic Optical Signals

Functional Imaging of Retinal Photoreceptors and Inner Neuro...

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作者： Xin-Cheng Yao Yi-Chao Li

Retinal development is a dynamic process both anatomically and functionally. High-resolution imaging and dynamic monitoring of photoreceptors and inner neurons can provide important information regarding the structure and function of the developing retina. In this chapter, we describe intrinsic optical signal (IOS) imaging as a high spatiotemporal resolution method for functional study of living retinal tissues. IOS imaging is based on near infrared (NIR) light detection of stimulus-evoked transient change of inherent optical characteristics of the cells. With no requirement for exogenous biomarkers, IOS imaging is totally noninvasive for functional mapping of stimulus-evoked spatiotemporal dynamics of the photoreceptors and inner retinal neurons. less

关键词： Electrophysiology Optical Imaging Image Processing Genetic Mapping Decapitation Dissection MATLAB programming language Xenopus Photoreceptor Neuron Ganglion Intrinsic optical signal Retinal function

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High-resolution structural and functional deep brain imaging using adaptive optics three-photon microscopy

High-resolution structural and functional deep brain imaging...

引用

作者： Lina Streich Juan Carlos Boffi Ling Wang Khaleel Alhalaseh Matteo Barbieri Ronja Rehm Senthilkumar Deivasigamani Cornelius T. Gross Amit Agarwal Robert Prevedel

Multiphoton microscopy has become a powerful tool with which to visualize the morphology and function of neural cells and circuits in the intact mammalian brain. However, tissue scattering, optical aberrations and motion artifacts degrade the imaging performance at depth. Here we describe a minimally invasive intravital imaging methodology based on three-photon excitation, indirect adaptive optics (AO) and active electrocardiogram gating to advance deep-tissue imaging. Our modal-based, sensorless AO approach is robust to low signal-to-noise ratios as commonly encountered in deep scattering tissues such as the mouse brain, and permits AO correction over large axial fields of view. We demonstrate near-diffraction-limited imaging of deep cortical spines and (sub)cortical dendrites up to a depth of 1.4 mm (the edge of the mouse CA1 hippocampus). In addition, we show applications to deep-layer calcium imaging of astrocytes, including fibrous astrocytes that reside in the highly scattering corpus callosum. less

关键词： Calcium Imaging Fluorescence Microscopy Multiphoton Microscopy Microscopy Brain Slice Preparation Electrocardiogram MATLAB Affinity Chromatography Titration Real-time PCR Surgery In Vivo Imaging Machine Learning Adaptive optics Intravital Microscopy programming language Glial biology

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DNA Microarrays as a Tool for Neurosciences Research

DNA Microarrays as a Tool for Neurosciences Research

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作者： James D. Eudy Lynette Smith

DNA microarray technology is a useful tool to further our understanding of underlying biological pathways governing the behavior of cells and tissues. In fact, microarrays have evolved over the last 10 years or so to become one of the major technologies utilized in biomedical research. This chapter will provide a brief history of the development of DNA microarray technology, a brief survey of widely accepted microarray platforms, and then expand upon critical components of DNA microarray experimentation necessary to ensure optimal outcomes in a given microarray experiment. Topics covered will include the necessity of a good initial experimental design, quality control issues with respect to input RNA or DNA, appropriate use of biological replicates relevant to a given biological question, and analysis strategies employed to extract meaningful results from a microarray *** microarray technology is a useful tool to further our understanding of underlying biological pathways governing the behavior of cells and tissues. In fact, microarrays have evolved over the last 10 years or so to become one of the major technologies utilized in biomedical research. This chapter will provide a brief history of the development of DNA microarray technology, a brief survey of widely accepted microarray platforms, and then expand upon critical components of DNA microarray experimentation necessary to ensure optimal outcomes in a given microarray experiment. Topics covered will include the necessity of a good initial experimental design, quality control issues with respect to input RNA or DNA, appropriate use of biological replicates relevant to a given biological question, and analysis strategies employed to extract meaningful results from a microarray experiment.

关键词： Nucleic Acid Microarray Image Analysis Cell And Tissue Culture RNA Extraction Agarose Gel Electrophoresis Ultraviolet Spectrophotometry Contact Lithography Photolithography Affymetrix SNP Array In Vitro Transcription Column Chromatography Gene Expression Analysis Principal Component Analysis Differential Expression Analysis Microarray Data analysis programming language DNA RNA Hybridization Analysis Normalization Gene expression

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