Deactivation of TEM-1 beta-Lactamase investigated by isothermal batch and non-isothermal continuous enzyme membrane reactor methods

The thermal deactivation of TEM-1 β-lactamase was examined using two experimental techniques: a series of isothermal batch assays and a single, continuous, non-isothermal assay in an enzyme membrane reactor (EMR). The isothermal batch-mode technique was coupled with the three-state Equilibrium Model of enzyme deactivation, while the results of the EMR experiment were fitted to a four-state molten globule model . The two methods both led to the conclusions that the thermal deactivation of TEM-1 β -lactamase does not follow the Lumry-Eyring model and that the Teq of the enzyme (the point at which active and inactive states are present in equal amounts due to thermodynamic equilibrium) is at least 10 °C from the Tm (melting temperature), contrary to the idea that the true temperature optimum of a biocatalyst is necessarily close to the melting temperature

The super-oscillating superlens

We demonstrate a lens that creates a sub-wavelength focal spot beyond the near-field by exploiting the phenomenon of super-oscillation

Infinite factorization of multiple non-parametric views

Combined analysis of multiple data sources has increasing application interest, in particular for distinguishing shared and source-specific aspects. We extend this rationale of classical canonical correlation analysis into a flexible, generative and non-parametric clustering setting, by introducing a novel non-parametric hierarchical mixture model. The lower level of the model describes each source with a flexible non-parametric mixture, and the top level combines these to describe commonalities of the sources. The lower-level clusters arise from hierarchical Dirichlet Processes, inducing an infinite-dimensional contingency table between the views. The commonalities between the sources are modeled by an infinite block model of the contingency table, interpretable as non-negative factorization of infinite matrices, or as a prior for infinite contingency tables. With Gaussian mixture components plugged in for continuous measurements, the model is applied to two views of genes, mRNA expression and abundance of the produced proteins, to expose groups of genes that are co-regulated in either or both of the views. Cluster analysis of co-expression is a standard simple way of screening for co-regulation, and the two-view analysis extends the approach to distinguishing between pre- and post-translational regulation

Extrapolation of neutron-rich isotope cross-sections from projectile fragmentation

Using the measured fragmentation cross sections produced from the 48Ca and 64Ni beams at 140 MeV per nucleon on 9Be and 181Ta targets, we find that the cross sections of unmeasured neutron rich nuclei can be extrapolated using a systematic trend involving the average binding energy. The extrapolated cross-sections will be very useful in planning experiments with neutron rich isotopes produced from projectile fragmentation. The proposed method is general and could be applied to other fragmentation systems including those used in other radioactive ion beam facilities.Comment: accepted for publication in Europhysics Letter

Kank Is an EB1 Interacting Protein that Localises to Muscle-Tendon Attachment Sites in Drosophila

Little is known about how microtubules are regulated in different cell types during development. EB1 plays a central role in the regulation of microtubule plus ends. It directly binds to microtubule plus ends and recruits proteins which regulate microtubule dynamics and behaviour. We report the identification of Kank, the sole Drosophila orthologue of human Kank proteins, as an EB1 interactor that predominantly localises to embryonic attachment sites between muscle and tendon cells. Human Kank1 was identified as a tumour suppressor and has documented roles in actin regulation and cell polarity in cultured mammalian cells. We found that Drosophila Kank binds EB1 directly and this interaction is essential for Kank localisation to microtubule plus ends in cultured cells. Kank protein is expressed throughout fly development and increases during embryogenesis. In late embryos, it accumulates to sites of attachment between muscle and epidermal cells. A kank deletion mutant was generated. We found that the mutant is viable and fertile without noticeable defects. Further analysis showed that Kank is dispensable for muscle function in larvae. This is in sharp contrast to C. elegans in which the Kank orthologue VAB-19 is required for development by stabilising attachment structures between muscle and epidermal cells

tRNAs: Cellular Barcodes for Amino Acids

The role of tRNA in translating the genetic code has received considerable attention over the last 50 years, and we now know in great detail how particular amino acids are specifically selected and brought to the ribosome in response to the corresponding mRNA codon. Over the same period, it has also become increasingly clear that the ribosome is not the only destination to which tRNAs deliver amino acids, with processes ranging from lipid modification to antibiotic biosynthesis all using aminoacyl‐tRNAs as substrates. Here we review examples of alternative functions for tRNA beyond translation, which together suggest that the role of tRNA is to deliver amino acids for a variety of processes that includes, but is not limited to, protein synthesis

Conformational effects on the Circular Dichroism of Human Carbonic Anhydrase II: a multilevel computational study

Circular Dichroism (CD) spectroscopy is a powerful method for investigating conformational changes in proteins and therefore has numerous applications in structural and molecular biology. Here a computational investigation of the CD spectrum of the Human Carbonic Anhydrase II (HCAII), with main focus on the near-UV CD spectra of the wild-type enzyme and it seven tryptophan mutant forms, is presented and compared to experimental studies. Multilevel computational methods (Molecular Dynamics, Semiempirical Quantum Mechanics, Time-Dependent Density Functional Theory) were applied in order to gain insight into the mechanisms of interaction between the aromatic chromophores within the protein environment and understand how the conformational flexibility of the protein influences these mechanisms. The analysis suggests that combining CD semi empirical calculations, crystal structures and molecular dynamics (MD) could help in achieving a better agreement between the computed and experimental protein spectra and provide some unique insight into the dynamic nature of the mechanisms of chromophore interactions

Monitoring international migration flows in Europe. Towards a statistical data base combining data from different sources

The paper reviews techniques developed in demography, geography and statistics that are useful for bridging the gap between available data on international migration flows and the information required for policy making and research. The basic idea of the paper is as follows: to establish a coherent and consistent data base that contains sufficiently detailed, up-to-date and accurate information, data from several sources should be combined. That raises issues of definition and measurement, and of how to combine data from different origins properly. The issues may be tackled more easily if the statistics that are being compiled are viewed as different outcomes or manifestations of underlying stochastic processes governing migration. The link between the processes and their outcomes is described by models, the parameters of which must be estimated from the available data. That may be done within the context of socio-demographic accounting. The paper discusses the experience of the U.S. Bureau of the Census in combining migration data from several sources. It also summarizes the many efforts in Europe to establish a coherent and consistent data base on international migration. The paper was written at IIASA. It is part of the Migration Estimation Study, which is a collaborative IIASA-University of Groningen project, funded by the Netherlands Organization for Scientific Research (NWO). The project aims at developing techniques to obtain improved estimates of international migration flows by country of origin and country of destination

Quantifying signal changes in nano-wire based biosensors

In this work, we present a computational methodology for predicting the change in signal (conductance sensitivity) of a nano-BioFET sensor (a sensor based on a biomolecule binding another biomolecule attached to a nano-wire field effect transistor) upon binding its target molecule. The methodology is a combination of the screening model of surface charge sensors in liquids developed by Brandbyge and co-workers [Sørensen et al., Appl. Phys. Lett., 2007, 91, 102105], with the PROPKA method for predicting the pH-dependent charge of proteins and protein-ligand complexes, developed by Jensen and co-workers [Li et al., Proteins: Struct., Funct., Bioinf., 2005, 61, 704-721, Bas et al., Proteins: Struct., Funct., Bioinf., 2008, 73, 765-783]. The predicted change in conductance sensitivity based on this methodology is compared to previously published data on nano-BioFET sensors obtained by other groups. In addition, the conductance sensitivity dependence from various parameters is explored for a standard wire, representative of a typical experimental setup. In general, the experimental data can be reproduced with sufficient accuracy to help interpret them. The method has the potential for even more quantitative predictions when key experimental parameters (such as the charge carrier density of the nano-wire or receptor density on the device surface) can be determined (and reported) more accurately. © 2011 The Royal Society of Chemistry

Multiwavelength VLBI observations of Sagittarius A*

The compact radio source Sgr\,A*, associated with the super massive black hole at the center of the Galaxy, has been studied with VLBA observations at 3 frequencies (22, 43, 86\,GHz) performed on 10 consecutive days in May 2007. The total VLBI flux density of Sgr\,A* varies from day to day. The variability is correlated at the 3 observing frequencies with higher variability amplitudes appearing at the higher frequencies. For the modulation indices, we find 8.4\,% at 22\,GHz, 9.3\,% at 43\,GHz, and 15.5\,% at 86\,GHz. The radio spectrum is inverted between 22 and 86\,GHz, suggesting inhomogeneous synchrotron self-absorption with a turnover frequency at or above 86\,GHz. The radio spectral index correlates with the flux density, which is harder (more inverted spectrum) when the source is brighter. The average source size does not appear to be variable over the 10-day observing interval. However, we see a tendency for the sizes of the minor axis to increase with increasing total flux, whereas the major axis remains constant. Towards higher frequencies, the position angle of the elliptical Gaussian increases, indicative of intrinsic structure, which begins to dominate the scatter broadening. At cm-wavelength, the source size varies with wavelength as $\lambda^{2.12\pm0.12}$, which is interpreted as the result of interstellar scatter broadening. After removal of this scatter broadening, the intrinsic source size varies as $\lambda^{1.4 ... 1.5}$. The VLBI closure phases at 22, 43, and 86\,GHz are zero within a few degrees, indicating a symmetric or point-like source structure. In the context of an expanding plasmon model, we obtain an upper limit of the expansion velocity of about 0.1\,c from the non-variable VLBI structure. This agrees with the velocity range derived from the radiation transport modeling of the flares from the radio to NIR wavelengths.}Comment: 14pages, 14 Figures, Accepted for publication in A&