Showing papers in "Methods in 2008"

TL;DR: Methods for the isolation, expansion and differentiation of ASCs are presented and described in detail and can be applied to adipose tissues from other species with minimal modifications.

TL;DR: A selection of techniques that can be used to identify necrosis and to discriminate it from apoptosis are presented and a recently developed approach based on the use of fluid phase tracers and different kind of microscopy, transmission electron and fluorescence microscopy is described to characterize the mechanisms used by phagocytes to internalize dying cells.

TL;DR: By profiling over 200 precursor and mature miRNAs in HL60 cells induced to differentiate with 12-O-tetradecanoylphorbol-13-acetate, it was possible to identify mi RNAs who's processing is regulated during differentiation and become the gold standard of nucleic acid quantification.

TL;DR: This chapter discusses some of the most common chemicalCa2+ indicators that are widely used for the investigation of intracellular Ca2+ signaling and their advantages and limitations.

TL;DR: The in situ proximity ligation assays (in situ PLA) are described, a method that is suitable for visualizing protein interactions in both tissue sections and in vitro cell lines, and research tasks when this or other method may be selected are discussed.

TL;DR: Methods to prepare cDNA libraries from pools of small RNAs isolated from organisms, tissues or cells are described, which enable the identification of new members or new classes of smallRNAs, and they are also suitable to obtain miRNA expression profiles based on clone count frequencies.

TL;DR: It is proposed that multiple criteria should be met before miRNA target validation should be considered "confirmed," and several methods by which to validate miRNA targets are outlined.

TL;DR: The perturbation methods for measuring cerebral haemodynamic responses within resting and exercise conditions in humans are examined and how NIRS can be used to image the moving brain is examined.

TL;DR: The work done to evaluate the effectiveness of various chemically modified AMOs for use in cultured cells and rodent models is summarized, and important issues to consider when inhibiting miRNAs with antisense oligonucleotides are outlined.

TL;DR: The field of apoptosis or cell death research is advancing rapidly and it is becoming increasingly evident that apoptosis and necrosis represent two extremes of cell death and that many variations now exist.

TL;DR: Polymersomes hold enormous potential as nanostructured biomaterials for future in vivo drug delivery and diagnostic imaging applications, especially for therapeutic pharmaceuticals and contrast imaging agents.

TL;DR: The combined application of ion-trap mass spectrometry and peptide-specific antibodies for the isolation and structural analysis of collagen cross-linking domains is illustrated with examples of results from various types of collagen with the emphasis on bone and cartilage.

TL;DR: This Chapter describes the variant based on strand breaks labeling with Br-dUTP that is subsequently detected immunocytochemically withBr-dUAb, and offers the greatest sensitivity in detecting DNA breaks.

TL;DR: This paper discusses how empirical studies have generally tackled the problem of movement artifact by adopting alternative paradigms which avoid recording during actual physical exertion, and suggests a knowledge of practical aspects of EEG recording along with the advent of new technology and increasingly sophisticated processing models offer a promising approach to minimising theproblem of obtaining reliable EEG data during motion.

TL;DR: Practical methods involving fluorescentCa2+ indicators and electrophysiological approaches for dissecting the observed intracellular Ca2+ signal to reveal characteristics of store-operated Ca2- entry are described, highlighting the advantages, and limitations, of these approaches.

TL;DR: This paper describes strategies how to make use of single molecule trajectories for deducing information about nanoscopic structures in a live cell context and focuses on elucidating the plasma membrane organization by single molecule tracking.

TL;DR: The theoretical background and practical aspects of static light scattering analysis of membrane proteins are reviewed using a number of examples from their lab to highlight potential pitfalls and a detailed protocol of how the authors perform light scattering analyses is provided.

TL;DR: Though improvement of cognitive functions through noninvasive brain stimulation is promising, it still remains an exciting challenge to extend the use of TMS and tDCS from research tools in neuroscience to the treatment of neurological and psychiatric patients.

TL;DR: The development of a set of modular components that can be assembled into biomimetic materials that meet the minimum number of components necessary to allow cells to rebuild and replicate a given tissue is described.

TL;DR: Two different methods for the in situ detection of miR in paraffin embedded, formalin fixed tissues are described and one can easily determine the specific subcellular compartmentalization of the precursor and mature forms which may provide insight into the modulation of these important regulatory molecules and their targets.

TL;DR: A practical guide on how to set-up the basic technique to study OXPHOS defects in patient-derived cells and tissues is provided.

TL;DR: These techniques are described in isolation and in the context of transgenic and dietary animal models that have been used as tools to study the regulation of mitochondria biogenesis and its role in disease pathology.

TL;DR: Methods for studying phagocytosis of apoptotic cells are described, which reveal an active and highly regulated process that not only serves to remove potentially histotoxic cells from the inflammatory milieu, but also directs the phenotype of thephagocytic cell to be anti-inflammatory.

TL;DR: Recent progress in the development of GECIs is reviewed, highlighting which indicators are most appropriate for measuring calcium in specific organelles and localized domains in mammalian tissue culture cells.

TL;DR: This review focuses on the methodologies that are found to be successful with cartilage and bone marrow sources of human cells and comments on the many factors which may enable improved phenotypic performance once the cells are in a fully chondrogenic environment.

TL;DR: Application of these methods to any aaRS system allows the investigator to derive detailed kinetic mechanisms for the activation and aminoacyl transfer reactions, permitting issues of substrate specificity, stereochemical mechanism, and inhibitor interaction to be addressed in a rigorous and quantitative fashion.

TL;DR: The most common approaches for purification of insoluble elastin and tropoelastin are described and key aspects of studying tropoELastin production in cultured cells are addressed, whereElastin expression is highly dependent upon cell type, culture conditions, and passage number.

TL;DR: Determining the dimensions of protein-detergent micelles may facilitate membrane protein purification and crystallization by defining the accessibility of the protein surface.

TL;DR: An assay technique for the electrical characterization of electrogenic transport proteins on solid supported membranes that opens up new possibilities where conventional electrophysiology fails like transporters or ion channels from bacteria and from intracellular compartments.

TL;DR: The theoretical basis of FCS is described and some practical implications for its application in membrane studies are discussed, including sources of potential artifacts, such as membrane undulations, positioning of the detection volume, and photobleaching.