Showing papers in "Methods in 2007"

TL;DR: The resazurin assay utilising microtitre-plate has been modified to achieve more accuracy in the determination of the minimum inhibitory concentration values of natural products, including crude extracts, chromatographic fractions or purified compounds against various bacterial strains.

TL;DR: The use of detergents for the structural study of membrane proteins is discussed with an emphasis on practical issues relating to membrane solubilization, protein aggregation, detergent purity and detergent quantitation.

TL;DR: In this article four case studies are presented to indicate the strengths and limitations of CD in investigations of the properties of quadruplex structures formed by telomere repeat sequences.

TL;DR: Two new (related) methods to embed a protein in a lipid bilayer are introduced, which minimize equilibration time and can be almost completely automated, nearly eliminating one time consuming step in MD simulations of membrane proteins.

TL;DR: The FRET method used to measure the stabilization and selectivity of quadruplex ligands towards the human telomeric G-quadruplex is analysed and the stabilization value depends on the nature of the fluorescent tags, the incubation buffer, and the method chosen for T(m) calculation, complicating a direct comparison of the results obtained by different laboratories.

TL;DR: The sulphorhodamine B (SRB) assay is described in detail as the preferred method and a novel approach has been developed which is based on the hypothesis that, in some circumstances, the naturally occurring compounds act as prodrugs rather than active compounds in their own right.

TL;DR: This review will focus on the eight classes of scavenger receptors (class A-H) in terms of their structure, expression and recognition of host-derived ligands.

TL;DR: The methods used in the laboratory to construct small RNA cDNA libraries for high-throughput sequencing using technologies such as MPSS, 454 or SBS are described.

TL;DR: Much more work is needed in order to establish reliable and valid measures of creative thinking, in particular measures of novelty or originality of creative insights.

TL;DR: The basics of the SPR technique are presented, suggestions for experimental design are provided, and data processing and analysis of results are illustrated, showing the reproducibility of the binding constants and agreement from both steady-state and kinetic analyses.

TL;DR: Methods for the detection of membrane-bound and extracellular HSPs and methods for determining their immunological functions are discussed.

TL;DR: A detailed method for experimental identification of microRNA targets based on affinity purification of tagged microRNAs associated with their targets is presented.

TL;DR: Following release of heat shock protein 70, it has been shown that Hsp70 binds to adjacent cells, suggesting that the secreted protein participates in paracrine or autocrine interactions with adjacent cell surfaces, suggesting the role for endolysosomes.

TL;DR: Specific examples of creative cognition studies are described in detail with a particular focus on research concerned with accessing conceptual information at varying levels of abstraction and combining previously separate concepts.

TL;DR: A model of CVB3-induced myocarditis presented here allows dissection of the contribution of viral infection and xenobiotics on immune dysregulation and inflammation in the heart to represent a clear challenge for immunotoxicologists.

TL;DR: Standard methods recommended by the Clinical and Laboratory Standards Institute are compared with a microtitre assay using a metabolic colour indicator Alamar blue, which enables high throughput screening, under similar conditions and is less wasteful of plant material.

TL;DR: The local lymph node assay, when conducted according to published guidelines, provides a robust method for skin sensitization testing that not only provides reliable hazard identification information but also data necessary for effective risk assessment and risk management.

TL;DR: The data suggest a strategy of selective increases in cationicity concomitant with decreases in helicity and hydrophobicity in the transformation of naturally-occurring antimicrobial peptides into non-toxic therapeutic agents.

TL;DR: Advances in ITC experiments can be designed such that previously inaccessible parameters can be evaluated, and some of these advances are outlined, including exploiting different experimental conditions; low affinity systems; (3) high affinity systems and displacement assays.

TL;DR: Computational approaches that tackle membrane protein structure and function prediction, including sequence alignment, motif search, functional residue identification, transmembrane segment and protein topology predictions, homology and ab initio modeling are surveyed.

TL;DR: A set of problems developed by the authors, and the use of solvers' self reports of insight, are presented to argue that advances in the understanding of insight are being unnecessarily stifled by over reliance on traditional insight problems and a widespread failure to determine whether insight has occurred on a solution-by-solution basis.

TL;DR: This review describes the use of DNase I and hydroxyl radicals, the most commonly used footprinting probes, in footprinting experiments.

TL;DR: An overview of the methods currently applied to structural, dynamics, thermodynamics, and kinetics studies of nucleic acid quadruplexes and associated cations can be found in this paper.

TL;DR: Two affinity-purification protocols compatible with subsequent mass spectrometry, namely FLAG purification, and the tandem affinity purification (TAP) are presented, successfully used for the identification of binding partners for PP2A, PP4 and PP6 and they should be amenable to the analysis of interactors for other phosphatases.

TL;DR: The ideas outlined here can be seen as a sustained and disciplined demolition project aimed at sanitizing the authors' bad habits of thinking about creativity, and are grounded in current understanding of cognitive and neural processes.

TL;DR: Major aspects of performing research using EEG/ERP based experiments including the recording of the signals, removing noise, estimating ERP signals, and signal analysis are discussed for better understanding of the neural correlates of processes involved in creativity.

TL;DR: The methodological challenges that brain research on insight poses are discussed and how the authors dealt with these challenges in their recent studies on insight problem solving is described.

TL;DR: In this article, the authors describe complementary methods that utilize the incorporation of nucleotide analogs combined with microscopic examination, and also describe the use of a technique for the synchronization of adherent cells in mitosis by simple mechanical agitation.

TL;DR: This review provides a critical assessment of the advantages and limitations of modeling methods available for guanine quadruplex (G-DNA) molecules and characterize the relations of simulations to the experimental techniques and explain the actual meaning and significance of the results.

TL;DR: The place of mathematical modeling is justified as a standard method for studying molecular regulatory networks and the non-expert is guided to initiate modeling projects in order to gain a systems-level perspective for complex control systems.