Analysis of proteolytic degradation of a crude protein mixture using a surface acoustic wave sensor.

Degradation of a crude protein mixture by proteases with pH optima from acidic to basic was followed in real time using a surface acoustic wave biosensor in Love-wave geometry. Proteases EC 3.4.23.18 from Aspergillus saitoi, EC 3.4.21.62 from Bacillus licheniformis, and Novozyme from Bacillus sp. have been used. Kinetic constants extracted from the curves resulted for comparable protease concentrations in maximal degradation rates between 1.1 x 10(-2) and 1.5 x 10(-2)s(-1). For the three proteases investigated, similar amounts of up to about two-thirds of the estimated 28 ng/cm2 bound molecules were proteolyzed. The residual material not degraded by the proteases was removed from the surface with 0.5% SDS. The analysis of the sensor signal allows: (1) estimation of the total mass of protein bound to the sensor surface and of the degradable fraction; (2) extraction of the pure mass signal; and (3) kinetic evaluation.

Detection of Rev peptides with impedance-sensors--comparison of device-geometries.

Two different impedance-sensor geometries have been compared for the detection of Rev peptides with a molecular weight of 2.4 kDa. Planar, two-dimensional interdigitated capacitor (IDC) sensors with electrode separations of 1.1 microm as well as three-dimensional nanogap-sensors with an electrode separation of 75 nm have been used. Both sensors have been operated at a fixed frequency of 980 MHz. We discuss the specific interaction of the Rev peptide to an immobilized RNA anti-Rev aptamer (9.2 kDa) for peptide concentrations in the range of 100 nM-2 microM. For the IDC sensor, only peptide concentrations above 500 nM gave detectable signals. For the nanogap sensor, the binding process was clearly visible for all concentrations applied. The higher sensitivity of the nanogap compared to the IDC is ascribed to the improved surface-to-volume ratio.

GermOnline, a cross-species community knowledgebase on germ cell differentiation.

GermOnline provides information and microarray expression data for genes involved in mitosis and meiosis, gamete formation and germ line development across species. The database has been developed, and is being curated and updated, by life scientists in cooperation with bioinformaticists. Information is contributed through an online form using free text, images and the controlled vocabulary developed by the GeneOntology Consortium. Authors provide up to three references in support of their contribution. The database is governed by an international board of scientists to ensure a standardized data format and the highest quality of GermOnline's information content. Release 2.0 provides exclusive access to microarray expression data from Saccharomyces cerevisiae and Rattus norvegicus, as well as curated information on approximately 700 genes from various organisms. The locus report pages include links to external databases that contain relevant annotation, microarray expression and proteome data. Conversely, the Saccharomyces Genome Database (SGD), S.cerevisiae GeneDB and Swiss-Prot link to the budding yeast section of GermOnline from their respective locus pages. GermOnline, a fully operational prototype subject-oriented knowledgebase designed for community annotation and array data visualization, is accessible at http://www.germonline.org. The target audience includes researchers who work on mitotic cell division, meiosis, gametogenesis, germ line development, human reproductive health and comparative genomics.

High-pressure Raman study of debundled single-walled carbon nanotubes.

We report the pressure dependence for the radial (omega R) and tangential (omega T) band frequencies in debundled single-walled carbon nanotubes (SWNTs) derived from laser-synthesized SWNT bundles. As previously described, a chemical procedure was used to prepare debundled SWNTs from as-prepared, large SWNT bundles. The normalized pressure coefficient for omega R in the debundled sample was compared with the corresponding value in the bundled sample to quantify the strength of van der Waals interactions between tubes in these nanotube materials. Furthermore, the pressure dependences for the radial (omega R) and tangential (omega T) band frequencies in debundled tubes were also compared with corresponding dependences predicted for isolated SWNTs, obtained with generalized tight binding molecular dynamic (GTBMD) simulations described in our previous work. The results presented here collectively suggest that the van der Waals interaction is still strong in the debundled sample studied here, which contained predominantly small bundles of SWNTs rather than isolated tubes.

Comparison of antibody and aptamer receptors for the specific detection of thrombin with a nanometer gap-sized impedance biosensor.

Nanogap-impedance biosensors with electrode separations of 75 nm have been fabricated by means of standard optical lithography and a sacrificial layer technique. Due to a large surface-to-volume ratio and high sensitivity, these sensors are superior compared to open interdigitated electrode structures. As a model, the blood coagulation factor thrombin was detected. As specific receptors, either an antibody or a RNA-aptamer have been used. The microwave frequency impedance measurements showed that both ligands were equally suitable for the specific detection of thrombin.

High-energy phonon branches of an individual metallic carbon nanotube.

We present excitation-energy dependent Raman measurements between 2.05 and 2.41 eV on the same individual carbon nanotube. We find a change in the Raman frequencies of both the D mode (63 cm(-1)/eV) and the high-energy modes. The observed frequencies of the modes at approximately 1600 cm(-1) as a function of laser-energy map the phonon dispersion relation of a metallic tube near the Gamma point of the Brillouin zone. Our results prove the entire first-order Raman spectrum in single-wall carbon nanotubes to originate from double-resonant scattering. Moreover, we confirm experimentally the phonon softening in metallic tubes by a Peierls-like mechanism.

Effect of van der Waals interactions on the Raman modes in single walled carbon nanotubes.

We have measured the Raman spectrum of individual single walled carbon nanotubes in solution and compare it to that obtained from the same starting material where the tubes are present in ordered bundles or ropes. Interestingly, the radial mode frequencies for the tubes in solution are found to be approximately 10 cm (-1) higher than those observed for tubes in a rope, in apparent contradiction to lattice dynamics predictions. We suggest that there is no such contradiction, and propose that the upshift is due rather to a decreased energy spacing of the Van Hove singularities in isolated tubes over the spacings in a rope, thereby allowing the same laser excitation to excite different diameter tubes in these two samples.

Database model and specification of GermOnline Release 2.0, a cross-species community annotation knowledgebase on germ cell differentiation.

UNLABELLED: GermOnline is a web-accessible relational database that enables life scientists to make a significant and sustained contribution to the annotation of genes relevant for the fields of mitosis, meiosis, germ line development and gametogenesis across species. This novel approach to genome annotation includes a platform for knowledge submission and curation as well as microarray data storage and visualization hosted by a global network of servers. AVAILABILITY: The database is accessible at http://www.germonline.org/. For convenient world-wide access we have set up a network of servers in Europe (http://germonline.unibas.ch/; http://germonline.igh.cnrs.fr/), Japan (http://germonline.biochem.s.u-tokyo.ac.jp/) and USA (http://germonline.yeastgenome.org/). SUPPLEMENTARY INFORMATION: Extended documentation of the database is available through the link 'About GermOnline' at the websites.