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Bovine isolates of Streptococcus agalactiae (n ‫؍‬ 76), Streptococcus dysgalactiae subsp. dysgalactiae (n ‫؍‬ 32), and Streptococcus uberis (n ‫؍‬ 101) were analyzed for the presence of different integrative and conjugative elements (ICEs) and their association with macrolide, lincosamide, and tetracycline resistance. The diversity of the isolates included in this study was demonstrated by multilocus sequence typing for S. agalactiae and pulsedfield gel electrophoresis for S. dysgalactiae and S. uberis. Most of the erythromycin-resistant strains carry an ermB gene. Five strains of S. uberis that are resistant to lincomycin but susceptible to erythromycin carry the lin(B) gene, and one has both linB and lnuD genes. In contrast to S. uberis, most of the S. agalactiae and S. dysgalactiae tetracycline-resistant isolates carry a tet(M) gene. A tet(S) gene was also detected in the three species. A Tn916-related element was detected in 30 to 50% of the tetracycline-resistant strains in the three species. Tetracycline resistance was successfully transferred by conjugation to an S. agalactiae strain. Most of the isolates carry an ICE integrated in the rplL gene. In addition, half of the S. agalactiae isolates have an ICE integrated in a tRNA lysine (tRNA Lys ) gene. Such an element is also present in 20% of the isolates of S. dysgalactiae and S. uberis. A circular form of these ICEs was detected in all of the isolates tested, indicating that these genetic elements are mobile. These ICEs could thus also be a vehicle for horizontal gene transfer between streptococci of animal and/or human origin.

Vision restoration is an ideal medical application for optogenetics, because the eye provides direct optical access to the retina for stimulation. Optogenetic therapy could be used for diseases involving photoreceptor degeneration, such as retinitis pigmentosa or age-related macular degeneration. We describe here the selection, in non-human primates, of a specific optogenetic construct currently tested in a clinical trial. We used the microbial opsin ChrimsonR, and showed that the AAV2.7m8 vector had a higher transfection efficiency than AAV2 in retinal ganglion cells (RGCs) and that ChrimsonR fused to tdTomato (ChR-tdT) was expressed more efficiently than ChrimsonR. Light at 600 nm activated RGCs transfected with AAV2.7m8 ChR-tdT, from an irradiance of 1015 photons.cm−2.s−1. Vector doses of 5 × 1010 and 5 × 1011 vg/eye transfected up to 7000 RGCs/mm2 in the perifovea, with no significant immune reaction. We recorded RGC responses from a stimulus duration of 1 ms upwards. When using the recorded activity to decode stimulus information, we obtained an estimated visual acuity of 20/249, above the level of legal blindness (20/400). These results lay the groundwork for the ongoing clinical trial with the AAV2.7m8 - ChR-tdT vector for vision restoration in patients with retinitis pigmentosa.

SummaryIn Gram-negative bacteria, the TonB -ExbB-ExbD inner membrane multiprotein complex is required for active transport of diverse molecules through the outer membrane. We present evidence that Serratia marcescens, like several other Gram-negative bacteria, has two TonB proteins: the previously characterized TonB SM , and also HasB, a newly identified component of the has operon that encodes a haemophore-dependent haem acquisition system. This system involves a soluble extracellular protein (the HasA haemophore) that acquires free or haemoprotein-bound haem and presents it to a specific outer membrane haemophore receptor (HasR). TonB SM and HasB are significantly similar and can replace each other for haem acquisition. However, TonB SM , but not HasB, mediates iron acquisition from iron sources other than haem and haemoproteins, showing that HasB and TonB SM only display partial redundancy. The reconstitution in Escherichia coli of the S. marcescens Has system demonstrated that haem uptake is dependent on the E. coli ExbB, ExbD and TonB proteins and that HasB is non-functional in E. coli. Nevertheless, a mutation in the HasB transmembrane anchor domain allows it to replace TonB EC for haem acquisition. As the change affects a domain involved in specific TonB EC -ExbB EC interactions, HasB may be unable to interact with ExbB EC , and the HasB mutation may allow this interaction. In E. coli, the HasB mutant protein was functional for haem uptake but could not complement the other TonB EC -dependent functions, such as iron siderophore acquisition, and phage DNA and colicin uptake. Our findings support the emerging hypothesis that TonB homologues are widespread in bacteria, where they may have specific functions in receptor-ligand uptake systems.

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In situ measurement of grain-scale fluvial morphology is important for studies on grain roughness, sediment transport and the interactions between animals and the geomorphology, topics relevant to many river practitioners. Close-range digital photogrammetry (CRDP) and terrestrial laser scanning (TLS) are the two most common techniques to obtain high-resolution digital elevation models (DEMs) from fluvial surfaces. However, field application of topography remote sensing at the grain scale is presently hindered mainly by the tedious workflow challenges that one needs to overcome to obtain high-accuracy elevation data. A recommended approach for CRDP to collect high-resolution and high-accuracy DEMs has been developed for gravel-bed flume studies. The present paper investigates the deployment of the laboratory technique on three exposed gravel bars in a natural river environment. In contrast to other approaches, having the calibration carried out in the laboratory removes the need for independently surveyed groundcontrol targets, and makes for an efficient and effective data collection in the field. Optimization of the gravel-bed imagery helps DEM collection, without being impacted by variable lighting conditions. The benefit of a light-weight three-dimensional printed gravel-bed model for DEM quality assessment is shown, and confirms the reliability of grain roughness data measured with CRDP. Imagery and DEM analysis evidences sedimentological contrasts between gravel bars within the reach. The analysis of the surface elevations shows the effect variable grain-size and sediment sorting have on the surface roughness. By plotting the twodimensional structure functions and surface slopes and aspects we identify different grain arrangements and surface structures. The calculation of the inclination index allows determining the surface-forming flow direction(s). We show that progress in topography remote sensing is important to extend our knowledge on fluvial morphology processes at the grain scale, and how a technique customized for use by fluvial geomorphologists in the field benefits this progress.

There is a growing consensus that gravel‐bed roughness should be parameterized based on bed‐surface topography, not only sediment size. One benefit is the possible identification of various spatial scales of surface roughness and evaluation of their respective contributions to flow resistance (and also to bedload transport). The absence of relationships between roughness at the different scales is apparent in previous work, which currently limits roughness parameterization from topography and application in flow modeling. This study examines the use of moving‐window detrending on gravel‐bed digital elevation models (DEMs) for isolating roughness scales and their respective signatures. A large data set of 35 water‐worked gravel‐bed patches from both the laboratory and the field was used for the analysis. The measured bed topography was separated into two distinct DEMs: one representing grains, the other representing small bedforms. For all DEMs, bed‐elevation parameters measuring vertical roughness, imbrication, and spatial correlations were determined. Our results show distinct topographic signatures between grain and bedform DEMs. We show strong positive linear relationships between grain vertical roughness and the size of the bed‐surface material. Surface sediment arrangement also determined bedform shape, with groupings of coarse sediment forming humps on the surface, and finer sediment sheltered in hollows. Patch‐scale vertical roughness could not be estimated simply as the sum of grain and bedform vertical roughness. Instead, our results suggest weighted summation and the existence of universal weighting coefficients. Practical applications for studies on gravel‐bed roughness and flow modeling using DEMs are discussed.