Showing papers in "Methods in 2013"

TL;DR: Normal reference ranges for circulating miRNAs in serum and plasma as well as a hemolysis indicator based on microRNA expression are developed.

TL;DR: Flexibility in assay design qualifies MST for analysis of biomolecular interactions in complex experimental settings, which is demonstrated by addressing typically challenging types of binding events from various fields of life science.

TL;DR: A comprehensive and integrated set of tools for the analysis of data from large scale sequencing experiments, which supports adapter detection and removal, demultiplexing of barcodes, paired-end data, a range of read architectures and the efficient removal of sequence redundancy.

TL;DR: This book discusses exosome function in the tumor microenvironment and cancer progression, and the role of exosomes in this environment and its role in cancer progression.

TL;DR: Developing a framework for robust and unbiased assessment of curve analysis performance whereby various publicly available curve analysis methods were thoroughly compared using a previously published large clinical data set is aimed at.

TL;DR: A selection of techniques to detect cell death and to distinguish necrosis from apoptosis is presented, based on pharmacologic and transgenic approaches in combination with several biochemical and morphological criteria.

TL;DR: The current status of digital PCR is discussed, highlighting its advantages and focusing on how it can be utilized in biomarker development and analysis, including the use of individualized biomarkers.

TL;DR: A practical guide to quantify the adhesive strength of living animal cells to various substrates using atomic force microscopy (AFM)-based single-cell force spectroscopy (SCFS).

TL;DR: This work reports that microfluidic arrays enable analysis of 96 qPCR assays on 1440 single cells and data from sufficient cells to address noise inherent in single-cell transcription.

TL;DR: It is shown that the elastic modulus (aka the Young's modulus) of cells is independent of the indentation depth up to 10-20% deformation for the eukaryotic cells studied here.

TL;DR: Two functional assays for same-day analysis of cell lines or primary tissue samples are developed using defined inputs in the form of peptides derived primarily from the BH3 domains of pro-apoptotic members of the BCL2 family to invoke a response in the mitochondria in the forms of mitochondrial outer membrane permeabilization measured indirectly using potential sensitive dyes.

TL;DR: This paper demonstrates how to infer a Boolean network model from the available experimental data, analyze the network using graph-theoretical measures, and convert it into a predictive dynamic model, and illustrates these steps on a toy network and in the context of the Drosophila melanogaster segment polarity gene network.

TL;DR: A number of assays are highlighted, utilizing both microscopy and flow cytometry, to determine whether cells have undergone apoptosis or alternative modes of cell death.

TL;DR: It is predicted that the combination of ultra-low-cost fabrication with the advantages of easy-to-use dipsticks and swabs and the option of lateral flow concentration position ink-jet printed SERS substrates as a technology which will enable the application of SERS in solving critical problems for chemical detection in the field.

TL;DR: It is concluded that samples should be stored at low temperatures in order to maintain cytokine stability, and various factors influencing the levels of cytokines measured in plasma, serum, dried blood spots and tissue biopsies are described.

TL;DR: This review presents detailed protocols for the use of yeast surface display to isolate de novo binding proteins from combinatorial libraries, and subsequent biophysical characterization of binders.

TL;DR: This study demonstrates the consistency of the NanoVelcro Chip assay over time for CTC enumeration and shows that continuous monitoring of CTC numbers can be employed to follow responses to different treatments and monitor disease progression.

TL;DR: Recent contributions of directed evolution to synthetic biology at the protein, pathway, network, and whole cell levels are reviewed.

TL;DR: It appears that the quality and depth of the more recent quantitative proteomics studies is beginning to shed light on a number of aspects of neuroscience that relates to normal brain function as well as of the changes in protein expression and regulation that occurs in neuropsychiatric and neurodegenerative disorders.

TL;DR: Immunostimulatory properties of nanovaccines including their immunogenicity, adjuvant properties, inflammatory responses and the mechanisms of uptake and stimulation of immune cells are reviewed.

TL;DR: Current understanding of the interdependent structural features that define the quadruplex fold is described, and a tutorial for the use and application of the formalism developed for unimolecular quadruplexes of three loops is provided.

TL;DR: Current methods for identifying lncRNAs using large-scale sequencing data from RNA-seq experiments are reviewed and analytical considerations that are required when undertaking such projects are highlighted.

TL;DR: This study investigates whether ddPCR can be used to assess HER2 transcript levels in formalin-fixed paraffin embedded (FFPE) human breast tumors and whether these dd PCR measurements agree with prior assessments of these same samples by pathologists using immunohistochemistry (IHC) and in some cases fluorescence in situ hybridization (FISH).

TL;DR: In summary, the methods described here demonstrate how NGS analysis enhances quality control of complex antibody libraries as well as facilitates the antibody discovery process.

TL;DR: This work provides a strategy, using a combination of dynamic light scattering and analytical ultracentrifugation, for the biophysical characterization of unmodified nanodiscs and characterize the hydrodynamically resolvednanodisc of interest in terms of its sedimentation coefficient, Stokes' radius and overall protein and lipid stoichiometry.

TL;DR: Detailed protocols are presented for the robotic injection of zebrafish embryos at very high accuracy with a speed of up to 2000 embryos per hour for several applications, including the injection of human cancer cells as a model for tumor progression.

TL;DR: The goal of this article is to review the innovative methods that have been emerged in genosensor and aptasensor during recent years, with particular attention given to recent advances and trends in selection of biorecognition element, DNA immobilization strategies and sensing formats.

TL;DR: A set of phage display sorting strategies and validation methodologies are presented that are capable of producing high performance synthetic antibodies (sABs) with customized properties that open myriad opportunities to study complex macromolecular processes inaccessible to traditional affinity reagent technology.

TL;DR: The relationship between the methylation status of these miRNA genes and their relative expression in tumor samples was verified and a method based on Differential High Resolution Melting (D-HRM) was adopted for the quantification of DNA methylation.

TL;DR: The basic physics of the measurements, the model that is used for data interpretation, and the ways to extract the bond information from the experimental data are reviewed to help the planning and analysis of single molecule force spectroscopy experiments.