Monodisperse measurement of the biotin-streptavidin interaction strength in a well-defined pulling geometry

The widely used interaction of the homotetramer streptavidin with the small molecule biotin has been intensively studied by force spectroscopy and has become a model system for receptor ligand interaction. However, streptavidin's tetravalency results in diverse force propagation pathways through the different binding interfaces. This multiplicity gives rise to polydisperse force spectroscopy data. Here, we present an engineered monovalent streptavidin tetramer with a single cysteine in its functional subunit that allows for site-specific immobilization of the molecule, orthogonal to biotin binding. Functionality of streptavidin and its binding properties for biotin remain unaffected. We thus created a stable and reliable molecular anchor with a unique high-affinity binding site for biotinylated molecules or nanoparticles, which we expect to be useful for many single-molecule applications. To characterize the mechanical properties of the bond between biotin and our monovalent streptavidin, we performed force spectroscopy experiments using an atomic force microscope. We were able to conduct measurements at the single-molecule level with 1: 1-stoichiometry and a well-defined geometry, in which force exclusively propagates through a single subunit of the streptavidin tetramer. For different force loading rates, we obtained narrow force distributions of the bond rupture forces ranging from 200 pN at 1,500 pN/s to 230 pN at 110,000 pN/s. The data are in very good agreement with the standard Bell-Evans model with a single potential barrier at Delta x(0) = 0.38 nm and a zero-force off-rate k(off,0) in the 10(-6) s(-1) range

Performance Evaluation of Pseudospectral Ultrasound Simulations on a Cluster of Xeon Phi Accelerators

The rapid development of novel procedures in medical ultrasonics, including treatment planning in therapeutic ultrasound and image reconstruction in photoacoustic tomography, leads to increasing demand for large-scale ultrasound simulations. However, routine execution of such simulations using traditional methods, e.g., finite difference time domain, is expensive and often considered intractable due to the computational and memory requirements. The k-space corrected pseudospectral time domain method used by the k-Wave toolbox allows for significant reductions in spatial and temporal grid resolution. These improvements are achieved at the cost of all-to-all communication, which are inherent to the multi-dimensional fast Fourier transforms. To improve data locality, reduce communication and allow efficient use of accelerators, we recently implemented a domain decomposition technique based on a local Fourier basis. In this paper, we investigate whether it is feasible to run the distributed k-Wave implementation on the Salomon cluster equipped with 864 Intel Xeon Phi (Knight’s Corner) accelerators. The results show the immaturity of the KNC platform with issues ranging from limited support of Infiniband and LustreFS in Intel MPI on this platform to poor performance of 3D FFTs achieved by Intel MKL on the KNC architecture. Yet, we show that it is possible to achieve strong and weak scaling comparable to CPU-only platforms albeit with the runtime 1.8× to 4.3× longer. However, the accounting policy for Salomon’s accelerators is far more favorable and thus their employment reduces the computational cost significantly

Impact of the TCR Signal on Regulatory T Cell Homeostasis, Function, and Trafficking

Signaling through the T cell antigen receptor (TCR) is important for the homeostasis of naïve and memory CD4+ T cells. The significance of TCR signaling in regulatory T (Treg) cells has not been systematically addressed. Using an Ox40-cre allele that is prominently expressed in Treg cells, and a conditional null allele of the gene encoding p56Lck, we have examined the importance of TCR signaling in Treg cells. Inactivation of p56Lck resulted in abnormal Treg homeostasis characterized by impaired turnover, preferential redistribution to the lymph nodes, loss of suppressive function, and striking changes in gene expression. Abnormal Treg cell homeostasis and function did not reflect the involvement of p56Lck in CD4 function because these effects were not observed when CD4 expression was inactivated by Ox40-cre.The results make clear multiple aspects of Treg cell homeostasis and phenotype that are dependent on a sustained capacity to signal through the TCR

Persistent cAMP-Signals Triggered by Internalized G-Protein–Coupled Receptors

Real-time monitoring of G-protein-coupled receptor (GPCR) signaling in native cells suggests that the receptor for thyroid stimulating hormone remains active after internalization, challenging the current model for GPCR signaling

TFAA chemical derivatization and XPS: Analysis of OH and NHx polymers

The determination of functional groups on complex polymer surfaces by X-ray photoelectron spectroscopy (XPS) can be improved considerably by derivatization reactions. Simple polymers containing hydroxyl groups or amino groups were investigated as reference materials for the derivatization with trifluoroacetic anhydride (TFAA). Poly(vinyl alcohol) (PVA), poly(hydroxyethyl methacrylate) (PHEMA), poly(vinyl butyral) (PVB), poly(allylamine) (PAAm), and poly(diallyl amine) (PDAAm) were derivatized using TFAA and analyzed with XPS. Polyethylene (PE) was used as an independent external reference for the binding energy (BE). Applying this procedure, the BE scales of all measurements were referenced to the carbon atoms of PE. It was found that the BE of the CF3 component in the C1s region is different when bonded as an acetate or as an amide. The CF3 BE is also influenced by the density of these groups in the polymer molecule. In TFAA-PVA, where every second main chain carbon atom carries a trifluoroacetate (TFAc) group, the BE is 294.3 eV while in TFAA-PVB with only isolated groups, the BE is 293.6 eV. The BE of the CF3 Component in the trifluoroacetamides (TFAAms) prepared from PAAm and PDAAm was found to be 292.5 and 292.3 eV, respectively. Compared with the analog fluorine free compounds, the BE is shifted toward higher values also for the ester carbon atom, the amide carbon atom, and the carbon atom to which the ester or amide is bonded. The data suggest that the gas phase reaction of TFAA with a polymer surface is diffusion limited. The actual ester or amide formation is a fast reaction and runs as a wave into the surface

Properties of tin/plasma polymer nanocomposites

Thin composite layers (tin in plasma polymer matrix) were prepared in a stainless steel vacuum chamber. An RF powered magnetron with tin target was used to excite the discharge and to activate the monomer species (n-hexane). The gas mixture introduced comprised At and n-hexane vapours. The properties of the films and chemical composition were characterized by AFM (surface morphology), TEM and Electron tomography (bulk structure characterization), XPS and FTIR spectroscopy (chemical composition analyses). Current-voltage characteristics were measured to examine the electrical properties of the layers and their dependence on the deposition parameters