Showing papers in "Methods in 2014"

TL;DR: The purpose here is to review and assess methods for multiplexed, quantitative, image analysis based approaches, using new multicolor immunohistochemistry methods, automated multispectral slide imaging, and advanced trainable pattern recognition software.

TL;DR: The improved iCLIP protocol is described and critical optimization and control experiments that are required when applying the method to new RBPs are discussed.

TL;DR: Major methods used to conduct research using Drosophila melanogaster, including protocols for dietary interventions, measurements of triglycerides, cholesterol, glucose, trehalose, and glycogen, stains for lipid detection, and the use of gas chromatography-mass spectrometry to detect major polar metabolites are reviewed.

TL;DR: A detailed and easy-to-use protocol of using exomePeak R/Bioconductor package along with other software programs for analysis of MeRIP-Seq data, which covers raw reads alignment, RNA methylation site detection, motif discovery, differentialRNA methylation analysis, and functional analysis.

TL;DR: The MeDALL allergen-chip is introduced which has been developed for the specific and sensitive monitoring of IgE and IgG reactivity profiles towards more than 170Allergen molecules in sera collected in European birth cohorts.

TL;DR: A brief overview of the current “state of play” in fixation and focus on the effect fixation, and particularly the effect of the newer brand of “molecular fixatives” have on morphology, histochemistry, immunohistochemistry and RNA/DNA analysis.

TL;DR: There is still no suitable therapy available against cow’s milk allergy except avoidance, therefore research needs to focus on the development of suitable and safe immunotherapies that do not elicit severe side effect.

TL;DR: The need to integrate digital image analysis data with epidemiological, clinical and genomic data in order to fully understand the relationship between genotype and phenotype and to drive discovery and the delivery of personalized medicine is discussed.

TL;DR: This review summarizes the use of TALENs and RNA-guided nucleases in the field of zebrafish genetics with a special focus on knock-in approaches.

TL;DR: To specifically monitor RNA synthesis and degradation genome-wide, Bru-Seq and BruChase-Sequ are developed, based on metabolic pulse-chase labeling of RNA using bromouridine (Bru), which highlight their usefulness in assessingRNA synthesis and stability as well as splicing kinetics with examples of specific genes from different human cell lines.

TL;DR: The Fc variant of IgG2 was engineered with V234A/G237A /P238S/H268A/V309L/A330S/P331S substitutions to eliminate affinity for Fcγ receptors and C1q complement protein and consequently, immune effector functions, and shows minimal immunogenic potential by T-cell epitope analysis and structural perturbations of the Fc provide a rationale for the loss of function.

TL;DR: Molecular imaging using engineered antibodies and fragments provides a general approach for assessing cell surface phenotype in vivo and stands to play an increasingly important role in cancer diagnosis, treatment selection, and monitoring of molecularly targeted therapeutics.

TL;DR: This review covers techniques for assessing the kinetics and efficiency of immune responses quantitatively and qualitatively, such as survival analysis, bacterial persistence, antimicrobial peptide gene expression, phagocytosis and melanisation assays.

TL;DR: An optimized mammalian transient expression system, capable of producing up to 400mg/L of native secreted antibodies in less than a week, is described, composed of commercially available components and based on expression in the fast growing suspension cell line, FreeStyle™ 293-F (HEK-293F).

TL;DR: Qualitative aspects of this work are reviewed and technical considerations when using Drosophila to study aging and age-related diseases are highlighted.

TL;DR: A simple and efficient technique to generate and detect novel mutations in desired target genes in Drosophila melanogaster by injections of mRNA encoding the Cas9 endonuclease and in vitro transcribed synthetic guide RNA is described.

TL;DR: An overview of methods for monitoring autophagy in Drosophila, with a special emphasis on the larval fat body, can be used to investigate whether observed vesicles are of autophagic origin, and to determine a relative rate of Autophagic degradation.

TL;DR: This paper defines a set of in vitro, DNA-based molecular transformations that can be linked to each other in such a way that the product of one transformation can activate or inhibit the production of one or several other DNA compounds, and shows how these reactions can be wired in arbitrary networks.

TL;DR: An overview of the important developmental steps to build Drosophila body muscle in embryos, larvae and pupae is provided and key methods, including muscle histology, live imaging and genetics, to study these steps are described.

TL;DR: An updated protocol to enable much faster library preparation, and reduce the cost by pooling indexed samples together for sequencing, has been devised and has been successfully used in the laboratory to validate miRNA targets in a variety of plant species.

TL;DR: Methods to set up and monitor experiments to determine worm lifespan are described, procedures used for classical, small-scale lifespan assays that are generally performed on solid media are reviewed, and recent advances in high-throughput, automated longevity experiments conducted in liquid culture and microfluidic devices are reviewed.

TL;DR: The experimental results showed that the priori knowledge of known essential proteins was effective for improving the predicted precision and the predicted precisions of CPPK and CEPPK clearly exceeded that of the previously proposed essential protein discovery methods.

TL;DR: Drosophila oogenesis is an excellent system for the study of developmental cell biology and many available reagents and key methods for research in oogenesis are provided.

TL;DR: This guideline seeks to provide a stepwise approach for the validation of an antibody for immunohistochemical assays, reflecting the views of a consortium of academic and pharmaceutical based histopathology researchers.

TL;DR: A review of the Drosophila hematopoietic system at different developmental stages is described, the major useful cell markers and tools for each stage are summarized, and basic protocols for practical analysis of circulating blood cells and of the lymph gland, the larval hematoplastic organ are provided.

TL;DR: The characteristics and properties of purified recombinant allergens and hypoallergenic derivatives are described and their potential use in diagnosis and therapy of weed pollen allergy is discussed.

TL;DR: This review summarizes the existing structural information on allergens and their classification in protein fold families and discusses established methods for linear and conformational epitope mapping, putting special emphasis on a recently developed approach which uses the structural similarity of proteins in combination with the experimental cross-reactivity data for epitope prediction.

TL;DR: The “hyb” bioinformatics pipeline, which is developed to analyse high-throughput cDNA sequencing data from CLASH experiments, and examined the sensitivity and specificity of chimera detection in a test dataset using the BLAST, BLAST+, BLAT, pBLAT and Bowtie2 read alignment programs.

TL;DR: This review will cover a wide range of techniques that have been instrumental to the understanding of Drosophila circadian rhythms, and that are essential for current and future research.

TL;DR: A ribonucleoprotein (RNP) footprinting approach recently developed for identifying occupancy sites of both individual RBPs and multi-subunit RNP complexes that is particularly suited for studying dynamic RNP assemblages whose composition evolves as gene expression proceeds.