2D label-free imaging of resonant grating biochips in ultraviolet

International audience2D images of label-free biochips exploiting resonant waveguide grating (RWG) are presented. They indicate sensitivities on the order of 1 pg/mm2 for proteins in air, and hence 10 pg/mm2 in water can be safely expected. A 320×256 pixels Aluminum-Gallium-Nitride-based sensor array is used, with an intrinsic narrow spectral window centered at 280 nm. The additional role of characteristic biological layer absorption at this wavelength is calculated, and regimes revealing its impact are discussed. Experimentally, the resonance of a chip coated with protein is revealed and the sensitivity evaluated through angular spectroscopy and imaging. In addition to a sensitivity similar to surface plasmon resonance (SPR), the RWGs resonance can be flexibly tailored to gain spatial, biochemical, or spectral sensitivity

An examination of point-particle Lagrangian simulations for assessing time-resolved hydroacoustic particle flux measurements in sediment-laden flows

Accurate modelling and prediction of sediment transport in aquatic environments is essential for sustainable coastal and riverine management. Current capabilities rely on physical process-based numerical models and fine-scale sedi�ment flux measurements. High-resolution hydroacoustic instrumentation has emerged as a promising tool for such measurements. However, challenges arise due to the inherent complexity of ultrasound scattering processes. This study introduces a numerical modelling using a point-particle approach to simulate the echoes backscattered by such instrumentation in sediment-laden flow conditions. The model considers geometric, statistical, particle cloud, and flow-induced effects on sediment velocity, concentration, and flux estimates using an acoustic concentration and velocity profiler as a reference. The model performance is assessed here under unidirectional constant flow condi�tions in terms of velocity, concentration, and time-resolved sediment flux estimates for a large range of the particles’ advection speed and sampled volume sizes. Application to the estimation of the measurement accuracy of sediment flux in these flows is also considered, with a final error on the flux seen to be partially controlled by the residence time of particles within the sampled volumes. The proposed model provides insights into scattering processes and offers a tool for investigating robust sediment flux estimation techniques in various flow conditions

Wave boundary layer hydrodynamics and sheet flow properties under large-scale plunging-type breaking waves

Wave boundary layer (WBL) dynamics are measured with an Acoustic Concentration and Velocity Profiler (ACVP) across the sheet flow-dominated wave-breaking region of regular large-scale waves breaking as a plunger over a developing breaker bar. Acoustic sheet flow measurements are first evaluated quantitatively in comparison to Conductivity Concentration Meter (CCM+) data used as a reference. The near-bed orbital velocity field exhibits expected behaviors in terms of wave shape, intrawave WBL thickness, and velocity phase leads. The observed fully turbulent flow regime all across the studied wave-breaking region supports the model-predicted transformation of free-stream velocity asymmetry into near-bed velocity skewness inside the WBL. Intrawave concentration dynamics reveal the existence of a lower pickup layer and an upper sheet flow layer similar to skewed oscillatory sheet flows, and with similar characteristics in terms of erosion depth and sheet flow layer thickness. Compared to the shoaling region, differences in terms of sheet flow and hydrodynamic properties of the flow are observed at the plunge point, attributed to the locally enhanced wave breaker turbulence. The ACVP-measured total sheet flow transport rate is decomposed into its current-, wave-, and turbulence-driven components. In the shoaling region, the sand transport is found to be fully dominated by the onshore skewed wave-driven component with negligible phase lag effects. In the outer surf zone, the total net flux exhibits a three-layer vertical structure typical of skewed oscillatory sheet flows. However, in the present experiments this structure originates from offshore-directed undertow-driven flux, rather than from phase lag effects.Peer ReviewedPostprint (published version

Wave Boundary Layer Hydrodynamics and Sheet Flow Properties under Large-Scale Plunging-Type Breaking Waves

The authors wish to thank the staff of CIEMLAB, in particular Joaquim Sospedra, Oscar Galego and Ricardo Torres, for their hospitality and hard work during the experimental campaign. This research was funded by the European Community’s Horizon 2020 Programme through the Integrated Infrastructure Initiative HYDRALAB+ COMPLEX (no. 654110), the French DGA funded ANR Astrid Maturation project MESURE (no. ANR-16- ASMA-0005-01) and the SINBAD project funded by STW (12058) in the Netherlands and by EPSRC (EP/J00507X/1, EPJ005541/1) in the UK. Data of this study are available at U. Twente repository doi (10.4121/uuid:753f1d84-36e5-47fa-b74b-55c288545b9b). Comments and remarks raised by the two anonymous reviewers helped to improve the quality of the paper.Peer reviewedPublisher PD

Why high-error-rate random mutagenesis libraries are enriched in functional and improved proteins

Recently, several groups have used error-prone polymerase chain reactions to construct mutant libraries containing up to 27 nucleotide mutations per gene on average, and reported a striking observation: although retention of protein function initially declines exponentially with mutations as has previously been observed, orders of magnitude more proteins remain viable at the highest mutation rates than this trend would predict. Mutant proteins having improved or novel activity were isolated disproportionately from these heavily mutated libraries, leading to the suggestion that distant regions of sequence space are enriched in useful cooperative mutations and that optimal mutagenesis should target these regions. If true, these claims have profound implications for laboratory evolution and for evolutionary theory. Here, we demonstrate that properties of the polymerase chain reaction can explain these results and, consequently, that average protein viability indeed decreases exponentially with mutational distance at all error rates. We show that high-error-rate mutagenesis may be useful in certain cases, though for very different reasons than originally proposed, and that optimal mutation rates are inherently protocol-dependent. Our results allow optimal mutation rates to be found given mutagenesis conditions and a protein of known mutational robustness.Comment: Optimality results improved. 26 pages, 4 figures, 3 table

Hydrodynamics under Large-Scale Waves Breaking over a Barred Beach

This paper shows preliminary results of experiments obtained in a large-scale wave flume under monochromatic waves plunging over a fixed bar. Velocity measurements were conducted using acoustic and optical instruments at 22 cross-shore locations ranging from the final part of the shoaling zone up to the inner surf zone. The measurements included the bottom boundary layer and the lower part of the water column and provided insights on the mean velocity distribution, turbulent velocity fluctuations and Reynolds stresses. The mean velocity is generally seaward directed. Magnitudes of the mean velocity are small in the shoaling region and increase above the bar crest, especially in the higher part of the water column, while magnitudes in the boundary layer are relatively small. Fluid from the inner surf zone is transported offshore by the undertow and pushed up near the shoreward face of the bar, thus largely feeding the onshore mass transport above trough level. As a result a large recirculation cell located just above the trough of the bar is generated where currents and turbulent velocity fluctuations are strong

ruvA Mutants that resolve Holliday junctions but do not reverse replication forks

RuvAB and RuvABC complexes catalyze branch migration and resolution of Holliday junctions (HJs) respectively. In addition to their action in the last steps of homologous recombination, they process HJs made by replication fork reversal, a reaction which occurs at inactivated replication forks by the annealing of blocked leading and lagging strand ends. RuvAB was recently proposed to bind replication forks and directly catalyze their conversion into HJs. We report here the isolation and characterization of two separation-of-function ruvA mutants that resolve HJs, based on their capacity to promote conjugational recombination and recombinational repair of UV and mitomycin C lesions, but have lost the capacity to reverse forks. In vivo and in vitro evidence indicate that the ruvA mutations affect DNA binding and the stimulation of RuvB helicase activity. This work shows that RuvA's actions at forks and at HJs can be genetically separated, and that RuvA mutants compromised for fork reversal remain fully capable of homologous recombination

Исследование оптических спектров химически модифицированного поливинилиденфторида

The present study aims to extend insights of surf zone turbulence dynamics to wave groups. In a large-scale wave flume, bichromatic wave groups were produced with 31.5 s group period, 4.2 s mean wave period, and a 0.58 m maximum wave height near the paddle. This condition resulted in plunging-type wave breaking over a fixed, gravel-bed, barred profile. Optic, acoustic and electromagnetic instruments were used to measure the flow and the spatial and temporal distributions of turbulent kinetic energy (TKE). The measurements showed that turbulence in the shoaling region is primarily bed-generated and decays almost fully within one wave cycle, leading to TKE variations at the short wave frequency. The wave breaking-generated turbulence, in contrast, decays over multiple wave cycles, leading to a gradual increase and decay of TKE during a wave group cycle. In the wave breaking region, TKE dynamics are driven by the production and subsequent downward transport of turbulence under the successive breaking waves in the group. Consequently, the maximum near-bed TKE in the breaking region can lag the highest breaking wave by up to 2.5 wave cycles. The net cross-shore transport of TKE is in the shoaling region primarily driven by short-wave velocities and is shoreward-directed; in the wave breaking region, the TKE transport is seaward-directed by the undertow and the long-wave velocities. Downward transport of TKE is driven by the vertical component of the time-averaged flow. The cross-shore and vertical diffusive transport rates are small relative to the advective transport rates

Quantifying annual spatial consistency in chick-rearing seabirds to inform important site identification

Animal tracking has afforded insights into patterns of space use in numerous species and thereby informed area-based conservation planning. A crucial consideration when estimating spatial distributions from tracking data is whether the sample of tracked animals is representative of the wider population. However, it may also be important to track animals in multiple years to capture changes in distribution in response to varying environmental conditions. Using GPS-tracking data from 23 seabird species, we assessed the importance of multi-year sampling for identifying important sites for conservation during the chick-rearing period, when seabirds are most spatially constrained. We found a high degree of spatial overlap among distributions from different years in most species. Multi-year sampling often captured a significantly higher portion of reference distributions (based on all data for a population) than sampling in a single year. However, we estimated that data from a single year would on average miss only 5 % less of the full distribution of a population compared to equal-sized samples collected across three years (min: −0.3 %, max: 17.7 %, n = 23). Our results suggest a key consideration for identifying important sites from tracking data is whether enough individuals were tracked to provide a representative estimate of the population distribution during the sampling period, rather than that tracking necessarily take place in multiple years. By providing an unprecedented multi-species perspective on annual spatial consistency, this work has relevance for the application of tracking data to informing the conservation of seabirds