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检索条件"主题词=Programming Language"

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Molecular Scaffold Hopping via Holistic Molecular Representation

Molecular Scaffold Hopping via Holistic Molecular Representa...

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作者： Francesca Grisoni Gisbert Schneider

Molecular descriptors encode a variety of molecular representations for computer-assisted drug discovery. Here, we focus on the Weighted Holistic Atom Localization and Entity Shape (WHALES) descriptors, which were originally designed for scaffold hopping from natural products to synthetic molecules. WHALES descriptors capture molecular shape and partial charges simultaneously. We introduce the key aspects of the WHALES concept and provide a step-by-step guide on how to use these descriptors for virtual compound screening and scaffold hopping. The results presented can be reproduced by using the code freely available from URL: ***/ETHmodlab/scaffold_hopping_whales . less

关键词： Virtual Screening Scaffold Hopping High-throughput Screening programming language Chemoinformatics Drug Natural product Weighted Holistic Atom Localization and Entity Shape (WHALES)

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Integrated Analysis of miRNA and mRNA Expression Profiles to Identify miRNA Targets

Integrated Analysis of miRNA and mRNA Expression Profiles to...

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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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Detection of Signatures of Selection Using

Detection of Signatures of Selection Using

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作者： Laercio R. Porto-Neto Seung Hwan Lee Hak Kyo Lee Cedric Gondro

Natural selection has molded the evolution of species across all taxa. Much more recently, on an evolutionary scale, human-oriented selection started to play an important role in shaping organisms, markedly so after the domestication of animals and plants. These selection processes have left traceable marks in the genome. Following from the recent advances in molecular genetics technologies, a number of methods have been developed to detect such signals, termed genomic signatures of selection. In this chapter we discuss a straightforward protocol based on the FST statistic to identify genomic regions that exhibit high variation in allelic frequency between groups, which is a characteristic of genomic regions that have gone through differential selection. How to define the borders of these regions and further explore its genetic content is then discussed. less

关键词： Statistical Calculation Genome Visualization Genotyping programming language Population genetics SNP Adaptation Speciation Evolution Divergence F-statistics

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Transcriptional Activation of Heterochromatin by Recruitment of dCas9 Activators

Transcriptional Activation of Heterochromatin by Recruitment...

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作者： Lukas Frank Robin Weinmann Fabian Erdel Jorge Trojanowski Karsten Rippe

The transition from silenced heterochromatin to a biologically active state and vice versa is a fundamental part of the implementation of cell type-specific gene expression programs. To reveal structure–function relationships and dissect the underlying mechanisms, experiments that ectopically induce transcription are highly informative. In particular, the approach to perturb chromatin states by recruiting fusions of the catalytically inactive dCas9 protein in a sequence-specific manner to a locus of interest has been used in numerous applications. Here, we describe how this approach can be applied to activate pericentric heterochromatin (PCH) in mouse cells as a prototypic silenced state by providing protocols for the following workflow: (a) Recruitment of dCas9 fusion constructs with the strong transcriptional activator VPR to PCH. (b) Analysis of the resulting changes in chromatin compaction, epigenetic marks, and active transcription by fluorescence microscopy-based readouts. (c) Automated analysis of the resulting images with a set of scripts in the R programming language. Furthermore, we discuss how parameters for chromatin decondensation and active transcription are extracted from these experiments and can be combined with other readouts to gain insights into PCH activation. less

关键词： CRISPR Fluorescence Microscopy Transfection Immunostaining Fiji Cell And Tissue Culture Image Analysis ImageJ Microscopy programming language Mus musculus Oryctolagus cuniculus Capra hircus Image quantification dCas9 Decondensation Chromocenter Pericentric heterochromatin Anti-rabbit anti-H3K27Ac

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Mathematical Modeling of Synaptic Patterns

Mathematical Modeling of Synaptic Patterns

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作者： Anastasios Siokis Philippe A. Robert Michael Meyer-Hermann

During antigen recognition by T cells, a specific spatial structure is formed at the contact face to an antigen-presenting cell (APC), called an immunological synapse (IS). The IS supports bidirectional signaling and release of effector molecules and is widely studied both biologically and numerically, in order to understand the process of T cell activation and signaling. This specialized structure harbors a central area (central supramolecular activation cluster, cSMAC) populated by T cell receptor-peptide-major histocompatibility complex (TCR-pMHC ) interactions, hedged by a peripheral ring (peripheral supramolecular activation cluster, pSMAC) of integrin lymphocyte function associated-1 interactions with its immunoglobulin superfamily ligand intercellular adhesion molecule-1 (LFA-1-ICAM-1). These two regions form the “bull’s eye” pattern characteristic of the mature IS. In theoretical studies, different modeling architectures, including partial differential equations (PDE) and agent-based modelsagent-based modeling , have been developed with the purpose to answer mechanistic questions about the IS dynamics. In this chapter, we explain possible physiological mechanisms that lead to the formation of ISs and technical issues that may occur in the course of development of agent-based models. less

关键词： Mathematical Modeling Cross-linking Fluorescence Microscopy programming language Computational biology Immunological synapse Agent-based modeling Patterns Partial differential equations (PDEs) Mechanics

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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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In Vivo Measurements of Cytosolic Calcium in

In Vivo Measurements of Cytosolic Calcium in

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作者： Claire Y. Allan Paul R. Fisher

The involvement of calcium signalling during chemotaxis in Dictyostelium discoideum is well documented. Spatiotemporal increases of intracellular calcium ([Ca2+]i) have been observed within seconds of stimulation with the chemoattractants folic acid and cAMP. This rise in [Ca2+]i localises to the rear cortex of the cell (J. Cell Sci. 109:2673–2678, 1996) and has been found to be not essential for chemotaxis, but likely to be involved in fine tuning of chemotactic responses (EMBO J. 19:4846–4854, 2000). Measurements of cytosolic Ca2+ ([Ca2+]c) responses have involved the use of different Ca2+ probes including ectopically expressed aequorin (a Ca2+-sensitive photoprotein), the fluorescent dye fura-2-dextran and the radioisotope 45Ca2+. The aequorin method (J. Cell Sci. 110:2845–2853, 1997) offers nonperturbing, real-time measurement of cytosolic free Ca2+ in suspensions of cells, but the low levels of light emission preclude measurements on individual cells. Fura-2 imaging (Cell Calcium 22:65–74, 1997; Eur. J. Cell Biol. 58:172–181, 1992; Biochem. J. 332:541–548, 1998; BMC Cell Biol. 6:13, 2005) has the advantage of allowing Ca2+ responses to be observed in individual cells so that the subcellular localisation of the response and differences amongst individual cells can be observed. However data collection is more labour intensive, much smaller numbers of cells are sampled, the cells are unavoidably damaged physically during loading and the time resolution (s) is much less than that provided by the aequorin method (ms). 45Ca2+ uptake assays (Cell Biol. Int. Rep. 2:71–79, 1978; J. Cell Biol. 112:103–110, 1991) allow measurement of Ca2+ influx from the medium by cell suspensions with a time resolution of the order of seconds. Radioactive Ca2+ uptake measurements are unsullied by but equally do not provide information about Ca2+ efflux, intracellular Ca2+ release or sequestration or changes in cytosolic free Ca2+ levels. less

关键词： Cell And Tissue Culture Cell Lysis Electroporation Fluorescence Microscopy Co-precipitation Chromatography programming language Dictyostelium Dictyostelium discoideum Saccharomyces cerevisiae Micrococcus luteus cAMP Calcium Folic acid Aequorin 45Ca2+ Fura-2-dextran

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Extracting Significant Comorbid Diseases from MeSH Index of PubMed

Extracting Significant Comorbid Diseases from MeSH Index of ...

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作者： Dheepa Anand Sharanya Manoharan Oviya Ramalakshmi Iyyappan Sadhanha Anand Kalpana Raja

Text mining is an important research area to be explored in terms of understanding disease associations and have an insight in disease comorbidities. The reason for comorbid occurrence in any patient may be genetic or molecular interference from any other processes. Comorbidity and multimorbidity may be technically different, yet still are inseparable in studies. They have overlapping nature of associations and hence can be integrated for a more rational approach. The association rule generally used to determine comorbidity may also be helpful in novel knowledge prediction or may even serve as an important tool of assessment in surgical cases. Another approach of interest may be to utilize biological vocabulary resources like UMLS/MeSH across a patient health information and analyze the interrelationship between different health conditions. The protocol presented here can be utilized for understanding the disease associations and analyze at an extensive level. less

关键词： Text Mining Natural language Processing programming language Python Statistical Calculation Information retrieval Information extraction Disease comorbidity

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Post-processing of Large Bioactivity Data

Post-processing of Large Bioactivity Data

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作者： Jason Bret Harris

Bioactivity data is a valuable scientific data type that needs to be findable, accessible, interoperable, and reusable (FAIR) (Wilkinson et al. Sci Data 3:160018, 2016). However, results from bioassay experiments often exist in formats that are difficult to interoperate across and reuse in follow-up research, especially when attempting to combine experimental records from many different sources. This chapter details common issues associated with the processing of large bioactivity data and methods for handling these issues in a post-processing scenario. Specifically described are observations from a recent effort (Harris, http://*** , 2017) to post-process massive amounts of bioactivity data from the NIH’s PubChem Bioassay repository (Wang et al., Nucleic Acids Res 42:1075–1082, 2014). less

关键词： GenBank programming language Bioassay PubChem Data integration Big data Bioactivity ScrubChem Hit-calls

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High-Throughput Screening to Examine the Dynamic of Stay-Green by an Imaging System

High-Throughput Screening to Examine the Dynamic of Stay-Gre...

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作者： Daniel Padilla-Chacón Cecilia B. Peña-Valdivia

The development of RGB (red, green, blue) sensors has opened the way for plant phenotyping. This is relevant because plant phenotyping allows us to visualize the product of the interaction between the plant ontogeny, anatomy, physiology, and biochemistry. Better yet, this can be achieved at any stage of plant development, i.e., from seedling to maturity. Here, we describe the use of phenotyping, based on the stay‐green trait, of common bean (Phaseolus vulgaris L.) plant, as a model, stressed by water deficit, to elucidate the result of that interaction. Description is based on interpretation of RGB digital images acquired using a phenomic platform and a specific software. These images allow us to obtain a data group related to the color parameters that quantify the changes and alterations in each plant growth and development. less

关键词： High-throughput Screening Image Analysis Statistical Calculation programming language Image Processing Senescence RGB Stay-green Common bean

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