TMB-Hunt: An amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins

BACKGROUND: Beta-barrel transmembrane (bbtm) proteins are a functionally important and diverse group of proteins expressed in the outer membranes of bacteria (both gram negative and acid fast gram positive), mitochondria and chloroplasts. Despite recent publications describing reasonable levels of accuracy for discriminating between bbtm proteins and other proteins, screening of entire genomes remains troublesome as these molecules only constitute a small fraction of the sequences screened. Therefore, novel methods are still required capable of detecting new families of bbtm protein in diverse genomes. RESULTS: We present TMB-Hunt, a program that uses a k-Nearest Neighbour (k-NN) algorithm to discriminate between bbtm and non-bbtm proteins on the basis of their amino acid composition. By including differentially weighted amino acids, evolutionary information and by calibrating the scoring, an accuracy of 92.5% was achieved, with 91% sensitivity and 93.8% positive predictive value (PPV), using a rigorous cross-validation procedure. A major advantage of this approach is that because it does not rely on beta-strand detection, it does not require resolved structures and thus larger, more representative, training sets could be used. It is therefore believed that this approach will be invaluable in complementing other, physicochemical and homology based methods. This was demonstrated by the correct reassignment of a number of proteins which other predictors failed to classify. We have used the algorithm to screen several genomes and have discussed our findings. CONCLUSION: TMB-Hunt achieves a prediction accuracy level better than other approaches published to date. Results were significantly enhanced by use of evolutionary information and a system for calibrating k-NN scoring. Because the program uses a distinct approach to that of other discriminators and thus suffers different liabilities, we believe it will make a significant contribution to the development of a consensus approach for bbtm protein detection

TMB-Hunt: a web server to screen sequence sets for transmembrane β-barrel proteins

TMB-Hunt is a program that uses a modified k-nearest neighbour (k-NN) algorithm to classify protein sequences as transmembrane β-barrel (TMB) or non-TMB on the basis of whole sequence amino acid composition. By including differentially weighted amino acids, evolutionary information and by calibrating the scoring, a discrimination accuracy of 92.5% was achieved, as tested using a rigorous cross-validation procedure. The TMB-Hunt web server, available at , allows screening of up to 10 000 sequences in a single query and provides results and key statistics in a simple colour coded format

Graphene-Based Electromechanical Thermal Switches

Thermal management is an important challenge in modern electronics, avionics, automotive, and energy storage systems. While passive thermal solutions (like heat sinks or heat spreaders) are often used, actively modulating heat flow (e.g. via thermal switches or diodes) would offer additional degrees of control over the management of thermal transients and system reliability. Here we report the first thermal switch based on a flexible, collapsible graphene membrane, with low operating voltage, < 2 V. We also employ active-mode scanning thermal microscopy (SThM) to measure the device behavior and switching in real time. A compact analytical thermal model is developed for the general case of a thermal switch based on a double-clamped suspended membrane, highlighting the thermal and electrical design challenges. System-level modeling demonstrates the thermal trade-offs between modulating temperature swing and average temperature as a function of switching ratio. These graphene-based thermal switches present new opportunities for active control of fast (even nanosecond) thermal transients in densely integrated systems

Proteomic analysis of the human skin proteome after in vivo treatment with sodium dodecyl sulphate

BACKGROUND: Skin has a variety of functions that are incompletely understood at the molecular level. As the most accessible tissue in the body it often reveals the first signs of inflammation or infection and also represents a potentially valuable source of biomarkers for several diseases. In this study we surveyed the skin proteome qualitatively using gel electrophoresis, liquid chromatography tandem mass spectrometry (GeLC-MS/MS) and quantitatively using an isobaric tagging strategy (iTRAQ) to characterise the response of human skin following exposure to sodium dodecyl sulphate (SDS).RESULTS: A total of 653 skin proteins were assigned, 159 of which were identified using GeLC-MS/MS and 616 using iTRAQ, representing the most comprehensive proteomic study in human skin tissue. Statistical analysis of the available iTRAQ data did not reveal any significant differences in the measured skin proteome after 4 hours exposure to the model irritant SDS.CONCLUSIONS: This study represents the first step in defining the critical response to an irritant at the level of the proteome and provides a valuable resource for further studies at the later stages of irritant exposure

The First RSBI (ISA-TAB) Workshop:“Can a Simple Format Work for Complex Studies?”

This article summarizes the motivation for, and the proceedings of, the first ISA-TAB workshop held December 6–8, 2007, at the EBI, Cambridge, UK. This exploratory workshop, organized by members of the Microarray Gene Expression Data (MGED) Society's Reporting Structure for Biological Investigations (RSBI) working group, brought together a group of developers of a range of collaborative systems to discuss the use of a common format to address the pressing need of reporting and communicating data and metadata from biological, biomedical, and environmental studies employing combinations of genomics, transcriptomics, proteomics, and metabolomics technologies along with more conventional methodologies. The expertise of the participants comprised database development, data management, and hands-on experience in the development of data communication standards. The workshop's outcomes are set to help formalize the proposed Investigation, Study, Assay (ISA)-TAB tab-delimited format for representing and communicating experimental metadata. This article is part of the special issue of OMICS on the activities of the Genomics Standards Consortium (GSC)