Computational Evolution of Beta-2-Microglobulin Binding Peptides for Nanopatterned Surface Sensors

The bottom-up design of smart nanodevices largely depends on the accuracy by which each of the inherent nanometric components can be functionally designed with predictive methods. Here, we present a rationally designed, self-assembled nanochip capable of capturing a target protein by means of pre-selected binding sites. The sensing elements comprise computationally evolved peptides, designed to target an arbitrarily selected binding site on the surface of beta-2-Microglobulin (β2m), a globular protein that lacks well-defined pockets. The nanopatterned surface was generated by an atomic force microscopy (AFM)-based, tip force-driven nanolithography technique termed nanografting to construct laterally confined self-assembled nanopatches of single stranded (ss)DNA. These were subsequently associated with an ssDNA–peptide conjugate by means of DNA-directed immobilization, therefore allowing control of the peptide’s spatial orientation. We characterized the sensitivity of such peptide-containing systems against β2m in solution by means of AFM-based differential topographic imaging and surface plasmon resonance (SPR) spectroscopy. Our results show that the confined peptides are capable of specifically capturing β2m from the surface–liquid interface with micromolar affinity, hence providing a viable proof-of-concept for our approach to peptide design

Food-web structure in relation to environmental gradients and predator-prey ratios in tank-bromeliad ecosystems

Little is known of how linkage patterns between species change along environmental gradients. The small, spatially discrete food webs inhabiting tank-bromeliads provide an excellent opportunity to analyse patterns of community diversity and food-web topology (connectance, linkage density, nestedness) in relation to key environmental variables (habitat size, detrital resource, incident radiation) and predators: prey ratios. We sampled 365 bromeliads in a wide range of understorey environments in French Guiana and used gut contents of invertebrates to draw the corresponding 365 connectance webs. At the bromeliad scale, habitat size (water volume) determined the number of species that constitute food-web nodes, the proportion of predators, and food-web topology. The number of species as well as the proportion of predators within bromeliads declined from open to forested habitats, where the volume of water collected by bromeliads was generally lower because of rainfall interception by the canopy. A core group of microorganisms and generalist detritivores remained relatively constant across environments. This suggests that (i) a highly-connected core ensures food-web stability and key ecosystem functions across environments, and (ii) larger deviations in food-web structures can be expected following disturbance if detritivores share traits that determine responses to environmental changes. While linkage density and nestedness were lower in bromeliads in the forest than in open areas, experiments are needed to confirm a trend for lower food-web stability in the understorey of primary forests

Carbon Vacancies Steer the Activity in Dual Ni Carbon Nitride Photocatalysis

The manipulation of carbon nitride (CN) structures is one main avenue to enhance the activity of CN-based photocatalysts. Increasing the efficiency of photocatalytic heterogeneous materials is a critical step toward the realistic implementation of sustainable schemes for organic synthesis. However, limited knowledge of the structure/activity relationship in relation to subtle structural variations prevents a fully rational design of new photocatalytic materials, limiting practical applications. Here, the CN structure is engineered by means of a microwave treatment, and the structure of the material is shaped around its suitable functionality for Ni dual photocatalysis, with a resulting boosting of the reaction efficiency toward many C-X (X = N, S, O) couplings. The combination of advanced characterization techniques and first-principle simulations reveals that this enhanced reactivity is due to the formation of carbon vacancies that evolve into triazole and imine N species able to suitably bind Ni complexes and harness highly efficient dual catalysis. The cost-effective microwave treatment proposed here appears as a versatile and sustainable approach to the design of CN-based photocatalysts for a wide range of industrially relevant organic synthetic reactions

Overview of power exhaust experiments in the COMPASS divertor with liquid metals

Power handling experiments with a special liquid metal divertor module based on the capillary porous system technology were performed in the tokamak COMPASS. The performance of two metals (Li and LiSn alloy) were tested for the first time in a divertor under ELMy H-mode conditions. No damage of the capillary mesh and a good exhaust capability were observed for both metals in two separate experiments with up to 12 MW/m(2) of deposited perpendicular, inter-ELM steady-state heat flux and with ELMs of relative energy similar to 3% and a local peak energy fluence at the module similar to 15 kJ.m(-2). No droplets were directly ejected from the mesh top surface and for the LiSn experiment, no contamination of the core and SOL plasmas by Sn was observed. The elemental depth profile analysis of 14 stainless-steel samples located around the vacuum vessel for each experiment provides information about the migration of evaporated/redeposited liquid elements

Examining smoking-induced differential gene expression changes in buccal mucosa

<p>Abstract</p> <p>Background</p> <p>Gene expression changes resulting from conditions such as disease, environmental stimuli, and drug use, can be monitored in the blood. However, a less invasive method of sample collection is of interest because of the discomfort and specialized personnel necessary for blood sampling especially if multiple samples are being collected. Buccal mucosa cells are easily collected and may be an alternative sample material for biomarker testing. A limited number of studies, primarily in the smoker/oral cancer literature, address this tissue's efficacy as an RNA source for expression analysis. The current study was undertaken to determine if total RNA isolated from buccal mucosa could be used as an alternative tissue source to assay relative gene expression.</p> <p>Methods</p> <p>Total RNA was isolated from swabs, reverse transcribed and amplified. The amplified cDNA was used in RT-qPCR and microarray analyses to evaluate gene expression in buccal cells. Initially, RT-qPCR was used to assess relative transcript levels of four genes from whole blood and buccal cells collected from the same seven individuals, concurrently. Second, buccal cell RNA was used for microarray-based differential gene expression studies by comparing gene expression between a group of female smokers and nonsmokers.</p> <p>Results</p> <p>An amplification protocol allowed use of less buccal cell total RNA (50 ng) than had been reported previously with human microarrays. Total RNA isolated from buccal cells was degraded but was of sufficient quality to be used with RT-qPCR to detect expression of specific genes. We report here the finding of a small number of statistically significant differentially expressed genes between smokers and nonsmokers, using buccal cells as starting material. Gene Set Enrichment Analysis confirmed that these genes had a similar expression pattern to results from another study.</p> <p>Conclusions</p> <p>Our results suggest that despite a high degree of degradation, RNA from buccal cells from cheek mucosa could be used to detect differential gene expression between smokers and nonsmokers. However the RNA degradation, increase in sample variability and microarray failure rate show that buccal samples should be used with caution as source material in expression studies.</p

Modeling of COMPASS tokamak divertor liquid metal experiments

Two small liquid metal targets based on the capillary porous structure were exposed to the divertor plasma of the tokamak COMPASS. The first target was wetted by pure lithium and the second one by a lithium-tin alloy, both releasing mainly lithium atoms (sputtering and evaporation) when exposed to plasma. Due to poorly conductive target material and steep surface inclination (implying the surface-perpendicular plasma heat flux 12-17 MW/m(2)) for 0.1-0.2 s, the LiSn target has reached 900 degrees C under ELMy H-mode. A model of heat conduction is developed and serves to evaluate the lithium sputtering and evaporation and, thus, the surface cooling by the released lithium and consequent radiative shielding. In these conditions, cooling of the surface by the latent heat of vapor did not exceed 1 MW/m(2). About 10(19) lithium atoms were evaporated (comparable to the COMPASS 1 m(3) plasma deuterium content), local Li pressure exceeded the deuterium plasma pressure. Since the radiating Li vapor cloud spreads over a sphere much larger than the hot spot, its cooling effect is negligible (0.2 MW/m(2)). We also predict zero lithium prompt redeposition, consistent with our observation.

The influence of partial timber harvesting in riparian buffers on macroinvertebrate and fish communities in small streams in Minnesota, USA

Relatively few evaluations of aquatic macroinvertebrate and fish communities have been published in peer-reviewed literature detailing the effect of varying residual basal area (RBA) after timber harvesting in riparian buffers. Our analysis investigated the effects of partial harvesting within riparian buffers on aquatic macroinvertebrate and fish communities in small streams from two experiments in northern Minnesota northern hardwood-aspen forests. Each experiment evaluated partial harvesting within riparian buffers. In both experiments, benthic macroinvertebrates and fish were collected 1 year prior to harvest and in each of 3 years after harvest. We observed interannual variation for the macroinvertebrate abundance, diversity and taxon richness in the single-basin study and abundance and diversity in the multiple-basin study, but few effects related to harvest treatments in either study. However, interannual variation was not evident in the fish communities and we detected no significant changes in the stream fish communities associated with partially harvested riparian buffers in either study. This would suggest that timber harvesting in riparian management zones along reaches ≤200m in length on both sides of the stream that retains RBA≥12.4±1.3m2 ha−1 or on a single side of the stream that retains RBA≥8.7±1.6m2 ha−1 may be adequate to protect macroinvertebrate and fish communities in our Minnesota study systems given these specific timber harvesting techniques

Search for charged Higgs decays of the top quark using hadronic tau decays

We present the result of a search for charged Higgs decays of the top quark, produced in $p\bar{p}$ collisions at $\surd s =$ 1.8 TeV. When the charged Higgs is heavy and decays to a tau lepton, which subsequently decays hadronically, the resulting events have a unique signature: large missing transverse energy and the low-charged-multiplicity tau. Data collected in the period 1992-1993 at the Collider Detector at Fermilab, corresponding to 18.7$\pm$0.7~pb$^{-1}$, exclude new regions of combined top quark and charged Higgs mass, in extensions to the standard model with two Higgs doublets.Comment: uuencoded, gzipped tar file of LaTeX and 6 Postscript figures; 11 pp; submitted to Phys. Rev.