Showing papers in "Methods in 2017"

TL;DR: TrackMate is an extensible platform where developers can easily write their own detection, particle linking, visualization or analysis algorithms within the TrackMate environment and is validated for quantitative lifetime analysis of clathrin-mediated endocytosis in plant cells.

TL;DR: This paper examines several standard algorithms used in deconvolution microscopy, notably: Regularized inverse filter, Tikhonov regularization, Landweber, T Sheikhonov-Miller, Richardson-Lucy, and fast iterative shrinkage-thresholding and distinguishes the algorithms in terms of image quality, performance, usability and computational requirements.

TL;DR: The ribosome profiling method has undergone continuing development and important improvements include: the incorporation of sample barcodes to enable library multiplexing, the incorporate of unique molecular identifiers to enable to removal of duplicated sequences, and the replacement of a gel-purification step with the enzymatic degradation of unligated linker.

TL;DR: This protocol combines chromatin digestion and frequently cutting enzymes to obtain kilobase (kb) resolution and includes steps to reduce random ligation and the generation of uninformative molecules, such as unligated ends, to improve the amount of valid intra-chromosomal read pairs.

TL;DR: A protocol to create precise edits in the C. elegans genome using direct injection of CRISPR-Cas9 ribonucleo-protein complexes and use of linear DNAs with short homology arms as repair templates is developed.

TL;DR: The effect of antibody immobilization approaches on the parameters on the performance of an immunoassay is discussed and the main challenges associated with these approaches are discussed.

TL;DR: Detailed methods for genome editing using the RNP approach with synthetic guide RNAs using lipofection or electroporation in mammalian cells or using microinjection in murine zygotes, with or without addition of a single-stranded HDR template DNA are provided.

TL;DR: DiAna offers a complete and intuitive 3D image analysis tool for biologists that computes the distribution of distances between objects in 3D and introduces an original method, which allows for estimating the statistical significance of object co-localization.

TL;DR: Methods to produce and deliver Cas9 RNPs as a preformed ribonucleoprotein (RNP) complex minimize some of the pitfalls of alternative editing modalities and is rapidly being adopted by the genome editing community.

TL;DR: New strategies to generate cDNA edited or tagged insertions are proposed, which once established will constitute a new and versatile toolbox for CRISPR/Cas9-based knock-ins in zebrafish.

TL;DR: The C-Circle Assay has satisfied the need for a rapid, robust and quantitative ALT assay that responds quickly to changes in ALT activity.

TL;DR: This paper proposes a framework for drug-target interaction prediction leveraging both feature dimensionality reduction and ensemble learning, and compared the proposed methods with various state-of-the-art methods under 5-fold cross validation.

TL;DR: The development of micro- and nanoscaled UCA is summarized and recent advances in diagnostic and therapeutic applications, which are ready for translation into the clinic are highlighted.

TL;DR: Imaging flow cytometry, as performed with the ImagestreamX MKII, with its combination of increased fluorescence sensitivity, low background, image confirmation ability and powerful data analysis tools, provides a great tool to accurately evaluate EVs.

TL;DR: This review will examine the four predominant methods that have been used to measure autophagy via multispectral imaging flow cytometry.

TL;DR: The stress granule core isolation protocol provides a starting point for assisting future endeavors aimed at discovering conserved RNA regulatory mechanisms and potential links between RNP aggregation and degenerative disease.

TL;DR: FET PET can provide important diagnostic information in crucial situations such as the definition of biopsy site, the delineation of cerebral gliomas for therapy planning, sensitive monitoring of treatment response and an improved differentiation of tumour recurrence from treatment-related changes.

TL;DR: A detailed approach to perform single-molecule tracking (SMT) of transcription factors in living cells to obtain key binding characteristics, namely their residence time and bound fractions is described.

TL;DR: This paper describes a machine learning workflow that identifies phenotypes in imaging flow cytometry using open-source software and does not require computational expertise.

TL;DR: The immense potential of imaging flow cytometry for microalgal research is highlighted, but also the limitations and future developments are discussed.

TL;DR: This work presents strategies and protocols for designing, producing and screening CRISPR/Cas9 edited founders and genotyping their offspring according to desired allele type (indel, point mutation and deletion).

TL;DR: A detailed overview on affinity chromatography and the components involved in purification is provided to provide a detailed overview of antibody purification methodologies and their underlying working principles.

TL;DR: A 3D level set protocol is used to accurately segment cells using only the signal from fluorescently labelled receptor, and a strategy for the visualisation of co-occurrence is presented, which provides an unbiased alternative to colour overlays.

TL;DR: Characteristics of PPI interfaces and their known binders are summarized and existing in silico structure-based approaches for discovering small molecules that bind to P PI interfaces are reviewed.

TL;DR: Methods to study the structure and conformational dynamics of protein-RNA complexes in solution starting from the identification of interaction partners in a given RNP are illustrated.

TL;DR: The aim of this review is to provide an overview of available image analysis methods for live cell imaging, in particular required preprocessing image segmentation, cell tracking and data visualisation methods.

TL;DR: Experimental and computational methods to determine transcriptome-wide RNA stabilities using both pharmacological inhibition of transcription and metabolic labeling are described and broader application of these approaches will further the understanding of mRNA decay and illuminate its contribution to different biological processes.

TL;DR: An overview on the methodology of how RT-qPCR and primer pairs that are specific for different subtelomeric sequences can be used to detect and quantify TERRA expressed from different chromosome ends is presented.

TL;DR: Strategies to assist in predicting the pathogenicity of ARS variants are outlined and cautious evaluation of genetic and functional data is urged prior to linking an ARS mutation to a human disease phenotype.