|In silico screening of new potential TCR/CollagenII-MHCII inhibitors against rheumatoid arthritis|
Davide Pirolli, Francesco Ria, Bruno Giardina and Maria Cristina De Rosa
Residues 261-273 of type II collagen bound to the MHC class II allele HLA-DR4 play a crucial role in rheumatoid arthritis. The protein–protein interactions between TCR and CII-MHCII complex may therefore serve as targets for the development of new drugs against RA. The aim of this study is to develop a pharmacophore virtual screening followed by molecular docking and dynamics calculations leading to the identification of new TCR/CII-MHCII inhibitors.
|SuperNatural: A Database of Available Natural Compounds|
Melanie Füllbeck, Mathias Dunkel and Robert Preissner
The majority of marketed drugs are natural compounds or derivatives thereof. The compounds availability is often unclear. Therefore we have compiled a database of ~50,000 natural compounds. Starting point for in silico screenings are about 2,500 well-known, classified natural compounds or imported molecules. Possible medical applications can be detected and about three million conformers computed to account for the flexibility during usage of the 3D-superposition algorithm.
|An improved data processing pipe-line for comprehensive H-NMR and X/MS -omics data|
R. J. O. Torgrip, K. M. Åberg, E. Alm
In the post acqusition analysis of comprehensive -omics data the pre-processing pipe-line is crucial to extract the maximum possible amount of information from the data. Here we show a processing pipe-line for (1D)H-NMR and (2D)X/MS data comprising; feature detection, inter-sample feature alignment and internal-standard free normalization that outperforms today’s state-of-the-art processing schemes.
|Alignment of 1H-NMR data using a Generalized Fuzzy Hough Transform|
Erik Alm, Leonard Csenki, Ralf J.O. Torgrip, K. Magnus Åberg, Lars I. Nord, Ina Schuppe-Koistinen and Johan Lindberg
In metabolic profiling, multivariate data analysis techniques are used to interpret 1D 1H–NMR data. Multivariate data analysis techniques require that peaks are located in the same variables in every spectrum – this requirement is not met in native NMR spectra. Current state-of-the-art alignment algorithms are unable to align peaks when the spatial order of the peaks changes. We present the Fuzzy Generalized Hough Transform alignment which solves the alignment problem.
|1H NMR for the Accurate Quantification of Analytical Reference Standards|
Jan Schripsema, Denise Dagnino and Peter Verhaert
NMR can be used for the quantification of minute quantities of standard compounds. The high specificity of NMR signals permits absolute quantifications independent of the presence of impurities. The feasibility and limits of NMR application are demonstrated through the analysis of algal toxins and polar substances in butter.
|Single Cell Analysis of Voltage-gated Potassium Channels for Electrophysiological Properties of Rat Hypothalamic Paraventricular Nucleus Neurons|
Seul Ki Lee, Sora Lee, Seung Yub Shin, Pan Dong Ryu, So Yeong Lee
The hypothalamic paraventricular nucleus (PVN), an integrating site in the regulation of neuroendocrine and autonomic nervous systems, is composed of heterogeneous neurons, type I and type II, based on their electrophysiological properties. Single cell real-time RT-PCR analysis was made to investigate the molecular basis underlying the properties. The results suggest that Kv1.3, Kv4.2 and Kv4.3 potassium channels are the potential candidates in determining the electrophysiological properties in
|Fragment Screening Using Capillary Electrophoresis|
Simon Pettit, Carol Austin, Dallas Hughes, Sharon Magnolo, Leonid Raskovetsky
Capillary electrophoresis, which was pioneered for HTS in the 1990s, has recently been adapted to enable the screening of fragments. The technique is explained and the screening of fragments against a chaperone protein Hsp90 is presented as an example.
|High-Throughput Multiplexed Inflammation Assay Using Primary Cells|
Oksana Sirenko, Yen-Wen Chen, Jayne Hesley, Cathy Olsen, H. Roger Tang, Evan F. Cromwell*
An important event in the inflammation response is the expression of cell-surface antigens that facilitate binding of immune cells to blood vessels. The ability to monitor up-regulation of these molecules, such as VCAM, E-selectin, and HLADR on endothelial cells provides an important physiological read-out for cell-based models of inflammation.
|Maximizing cell wash performance with the AquaMax® 2000/4000 microplate washers|
Cathy Olsen, Iris Yang, and James Wasson
Many cell-based applications, including calcium flux assays, cell-based ELISAs, ion channel assays, and others require gentle but thorough washing of cells in order to ensure cell retention, cell integrity and optimal assay performance. The 96 cell wash head for AquaMax® 2000/4000 microplate washers from Molecular Devices uses angled pins to dispense fluid without disturbing cells. Adjustable dispense rate and aspiration height allow users to minimize disruption of even weakly adherent cells. We