Showing papers in "Methods in 2005"

TL;DR: In the following report, several methods to measure GRP78 induction are presented, which can be achieved by measuring the Grp78 promoter activity or by measuringThe level of Grp 78 transcripts or GRp78 protein.

TL;DR: An improved protocol that performs RNA linker ligation before the SDS-PAGE step is presented, and its application to the specific purification and amplification of RNA ligands of Nova in neurons is described.

TL;DR: The simplicity and sensitivity of the method, coupled with the widespread availability of tandem mass spectrometers, make the AQUA strategy a highly useful procedure for measuring the levels of proteins and post-translational modifications directly from cell lysates.

TL;DR: This review describes a series of protocols that have been developed for the relatively rapid analysis of all of the molecular species from 3-ketosphinganines through sphingomyelins and some glycosphingolipids using normal- and reverse-phase LC to separate isometric and isobaric species.

TL;DR: Reported AAR to murine, mouse-human chimeric, and humanized antibodies shows replacement of mouse immunoglobulin constant regions with human ones effects the largest immunogenicity reduction.

TL;DR: Two new approaches to obtaining active proteins are described: the use of molecular chaperones, and modification of the reaction conditions of the PURE system.

TL;DR: The most widely used ion activation and dissociation process, gas-phase collision-activated dissociation (CAD), is discussed from a practical point of view and the influence of instrumental methods on the fragmentation pathways and final spectra are discussed.

TL;DR: Two cell migration assays are described that allow the quantification of tumor cell invasion, a versatile transwell Matrigel invasion assay and an organotypic assay that examines the invasion of glioma cells through a rat brain slice are described.

TL;DR: The power of peptide mass fingerprinting for protein identification was described here, as exemplified by the identification of protein species with high molecular masses, low molecular masses (elongation factor EF-TU fragments), splice variants (alpha A crystallin), aggregates with disulfide bridges (alkylhydroperoxide reductase), and phosphorylated proteins (heat shock protein 27).

TL;DR: A procedure to humanize xenogeneic antibodies has been described that is based on grafting, onto the human frameworks, only the specificity determining residues (SDRs), the CDR residues that are most crucial in the antibody-ligand interaction.

TL;DR: Approaches and strategies for using minigenes to define the cis-acting elements that determine splice site usage and to identify and characterize the trans-acting factors that bind to these elements and regulate alternative splicing are described.

TL;DR: The newly developed quantitative and qualitative methods to detect IRE1 activity-dependent XBP1 mRNA splicing will be fast and accurate tools to show the activation of the UPR.

TL;DR: This paper reports application of a recently developed multichannel SPR sensor based on spectroscopy of surface plasmons and wavelength division multiplexing of sensing channels to multi-analyte detection.

TL;DR: A new method of humanizing antibodies by complementarity determining region (CDR) grafting is reported, which chooses human framework sequences from the set of human germline genes based on the structural similarity of the human CDRs to those of the mouse antibody to be humanized.

TL;DR: The most recent advances in methodologies for protein identification by mass spectrometry are described and the limitations of the application of the technologies are described.

TL;DR: An overview of Lipases and esterases is presented, along with protocols for common assays performed in solution, with an emphasis on assays for enzymes that can hydrolyze triacylglycerols.

TL;DR: Comparison of the complementary information contained in proteomic and mRNA data sets poses considerable analytical challenges, but several analytical approaches, methods, and tools that have proven to be helpful in the face of this important challenge are outlined.

TL;DR: This new humanization approach allows to rapidly identify various human framework combinations able to support the structural feature(s) of the CDRs which are essential for binding and functional activity.

TL;DR: This article will provide a brief review of various signaling aptamer design strategies as well as a detailed description of methods that can be used to generate, by both rational design and in vitro selection, a special class of signaling aptamers dubbed "structure-switching signalingaptamers."

TL;DR: All the different substrate-trapping mutants that have successfully been used or that hold interesting promises are described and the methodology to identify substrates in vivo (co-immunoprecipitation and in vitro (GST pulldown) and a current list of substrates that have been identified using these technologies are provided.

TL;DR: An overview of lipid-dependent polytopic membrane protein topogenesis is provided, with particular emphasis on Escherichia coli strains genetically altered in their lipid composition and strategies for experimentally determining the transmembrane organization of proteins.

TL;DR: Guided selection has successfully been used for the generation of a number of human versions of rodent antibodies, including HUMIRA, an inhibitor of tumour necrosis factor-alpha which is approved for the treatment of moderate to severe rheumatoid arthritis in over 40 countries.

TL;DR: Activity assays for tyrosine phosphatases include the determinations of the rate of dephosphorylation and calculations of kinetic constants such as k(cat) and K(M) that are commonly used to evaluate the efficiency of inhibitors.

TL;DR: Recent advances that make it possible to add new building blocks systematically to the genetic codes of bacteria, yeast and mammalian cells are described, which will enable the detailed investigation of protein structure and function, which is not possible with conventional mutagenesis.

TL;DR: Instrumentation and application of LAPS to multi-ion sensing and imaging are described and potentiometric imaging of a microfluidic channel is proposed.

TL;DR: Methods for the production and processing of aptamer microarrays are described, including detailed procedures for the high-throughput, enzymatic synthesis of 5' RNA biotinylated aptamers and for arraying them onto streptavidin-coated glass slides.

TL;DR: Procedures for antibody humanization with an emphasis on strategies for designing humanized antibodies with the aid of computer-guided modeling of antibody variable domains are described, using as an example the humanized anti-CD25 monoclonal antibody, Zenapax.

TL;DR: Current methods for the enrichment of phosphopeptides that are compatible with mass spectrometry for assignment of phosphorylation sites are described and hold the potential for rapid and sensitive profiling of phosphoproteins from a variety of sources and cellular conditions.

TL;DR: In this article, the effects of oxidative stress on the oxidation of macromolecules have been studied in mammalian cells and the protection of a small heat shock protein against the deleterious effects induced by oxidative stress.

TL;DR: A novel biosensing approach incorporating nanoscale chemical structures such as self-assembled monolayers with electrochemical biosensors is designed and achieved rapid, ultra-low concentration sensitivities without target amplification.