Envisat - taking the measure of North Atlantic storms

Envisat carries a number of sensors able to provide quantitative information on raining clouds: AATSR delivers information on cloud microphysics (particle size, temperature etc.), MWR-2 gives columnar totals for liquid and vapour forms of water, and RA-2 yields rain rate and wind speed. This paper examines the complementarity of these sensors, with a focussed study on significant rain events in the N. Atlantic, covering both coherent large storms and fronts with smaller scale structure. The difference in liquid water estimates from the infra-red and passive systems appears to be related to the temperature and sizes of drops being detected

Measuring rainfall from above and below the sea surface

Satellites play a major role in the determination of the rainfall at sea. Researchers at Southampton Oceanography Centre (SOC) have been involved in two projects addressing this task. First they have been instrumental in developing techniques to retrieve rain rate information from the 10+ years of dual-frequency altimeter data. The TOPEX radar measures rainfall via the attenuation it causes, producing a climatology that is independent of those derived from passive microwave (PM) and infrared (IR) sensors. Because TOPEX is an active microwave sensor, it can have a much smaller footprint than PM sensors. Therefore it can be used to estimate the size of rain cells, showing that the ITCZ and mid-latitude storm tracks are characterized by larger rain systems than elsewhere. TOPEX’s simultaneous recording of wind and wave data reveal that, for mid-latitude systems, rain is most likely in association with developing seas.All satellite-based datasets require validation, and SOC's work on the development and testing of acoustic rain gauges is the second aspect of this paper. By listening at a range of frequencies, an underwater hydrophone may distinguish the spectra of wind, rain, shipping etc., and estimate the wind speed or rain rate according to the magnitude of the signals. All our campaigns have shown a good acoustic response to changes in wind speed. However the quantitative inversion for recent trials has given values that are too high, possibly because of significant acoustic reflection from the sea bottom. The changes in spectral slope often agree with other observations of rain, although validation experiments in coastal regions are hampered by the extraneous sources present. Acoustic rain gauges would eventually see service not only for routine satellite validation, but also for real-time monitoring of locations of interest

Weathering the storm: developments in the acoustic sensing of wind and rain

An Acoustic Rain Gauge (ARG) analyses the underwater sound levels across a wide frequency range, classifies the observed spectrum according to likely source and then determines the local wind speed or rain rate as appropriate. Thispaper covers a trial on the Scotian Shelf off Canada, comparing the geophysical information derived from the acoustic signals with those obtained from other sources

Vertical variation of mixing within porous sediment beds below turbulent flows

River ecosystems are influenced by contaminants in the water column, in the pore water and adsorbed to sediment particles. When exchange across the sediment-water interface (hyporheic exchange) is included in modelling, the mixing coefficient is often assumed to be constant with depth below the interface. Novel fibre-optic fluorometers have been developed and combined with a modified EROSIMESS system to quantify the vertical variation in mixing coefficient with depth below the sediment-water interface. The study considered a range of particle diameters and bed shear velocities, with the permeability Péclet number, image between 1,000 and 77,000 and the shear Reynolds number, image between 5 and 600. Different parameterisation of both an interface exchange coefficient and a spatially variable in-sediment mixing coefficient are explored. The variation of in-sediment mixing is described by an exponential function applicable over the full range of parameter combinations tested. The empirical relationship enables estimates of the depth to which concentrations of pollutants will penetrate into the bed sediment, allowing the region where exchange will occur faster than molecular diffusion to be determined

A One-Dimensional Model for Turbulent Mixing in the Benthic Biolayer of Stream and Coastal Sediments

In this paper, we develop and validate a rigorous modeling framework, based on Duhamel’s Theorem, for the unsteady one-dimensional vertical transport of a solute across a flat sediment-water interface (SWI) and through the benthic biolayer of a turbulent stream. The modeling framework is novel in capturing the two-way coupling between evolving solute concentrations above and below the SWI and in allowing for a depth-varying diffusivity. Three diffusivity profiles within the sediment (constant, exponentially decaying, and a hybrid model) are evaluated against an extensive set of previously published laboratory measurements of turbulent mass transfer across the SWI. The exponential diffusivity profile best represents experimental observations and its reference diffusivity scales with the permeability Reynolds Number, a dimensionless measure of turbulence at the SWI. The depth over which the turbulence-enhanced diffusivity decays is of the order of centimeters and comparable to the thickness of the benthic biolayer. Thus, turbulent mixing across the SWI may serve as a universal transport mechanism, supplying the nutrient and energy fluxes needed to sustain microbial growth, and nutrient processing, in the benthic biolayer of stream and coastal sediments

Extremely fast amelioration of plasmid fitness costs by multiple functionally diverse pathways

The acquisition of plasmids is often accompanied by fitness costs such that compensatory evolution is required to allow plasmid survival, but it is unclear whether compensatory evolution can be extensive or rapid enough to maintain plasmids when they are very costly. The mercury-resistance plasmid pQBR55 drastically reduced the growth of its host, Pseudomonas fluorescens SBW25, immediately after acquisition, causing a small colony phenotype. However, within 48 h of growth on agar plates we observed restoration of the ancestral large colony morphology, suggesting that compensatory mutations had occurred. Relative fitness of these evolved strains, in lab media and in soil microcosms, varied between replicates, indicating different mutational mechanisms. Using genome sequencing we identified that restoration was associated with chromosomal mutations in either a hypothetical DNA-binding protein PFLU4242, RNA polymerase or the GacA/S two-component system. Targeted deletions in PFLU4242, gacA or gacS recapitulated the ameliorated phenotype upon plasmid acquisition, indicating three distinct mutational pathways to compensation. Our data shows that plasmid compensatory evolution is fast enough to allow survival of a plasmid despite it imposing very high fitness costs upon its host, and indeed may regularly occur during the process of isolating and selecting individual plasmid-containing clones

Positive selection inhibits plasmid coexistence in bacterial genomes

Plasmids play an important role in bacterial evolution by transferring niche-adaptive functional genes between lineages, thus driving genomic diversification. Bacterial genomes commonly contain multiple, coexisting plasmid replicons, which could fuel adaptation by increasing the range of gene functions available to selection and allowing their recombination. However, plasmid coexistence is difficult to explain because the acquisition of plasmids typically incurs high fitness costs for the host cell. Here, we show that plasmid coexistence was stably maintained without positive selection for plasmid-borne gene functions and was associated with compensatory evolution to reduce fitness costs. In contrast, with positive selection, plasmid coexistence was unstable despite compensatory evolution. Positive selection discriminated between differential fitness benefits of functionally redundant plasmid replicons, retaining only the more beneficial plasmid. These data suggest that while the efficiency of negative selection against plasmid fitness costs declines over time due to compensatory evolution, positive selection to maximize plasmid-derived fitness benefits remains efficient. Our findings help to explain the forces structuring bacterial genomes: coexistence of multiple plasmids in a genome is likely to require either rare positive selection in nature or nonredundancy of accessory gene functions among the coexisting plasmids

Test-Retest Repeatability of Microperimetry at the Border of Deep Scotomas

Citation: Wu Z, Jung CJ, Ayton LN, Luu CD, Guymer RH. Test-retest repeatability of microperimetry at the border of deep scotomas. Invest Ophthalmol Vis Sci. 2015;56:2606-2611. DOI:10.1167/iovs.14-15977 PURPOSE. The purpose of this study was to examine the test-retest repeatability of microperimetric sensitivity at the border of deep scotomas. METHODS. Thirty normal participants underwent two examinations, each on the Macular Integrity Assessment (MAIA) microperimeter and on the MP-1 microperimeter (four examinations in total). A customized stimulus pattern allowed microperimetric sensitivity to be measured at the border of the optic nerve head (ONH), which acted as a model for the border of a deep scotoma-and also at the macular and peripapillary region. RESULTS. There were no significant changes in average point-wise sensitivity (PWS) values between the two examinations for all three regions using the MAIA microperimeter (P ‡ 0.262). The PWS coefficient of repeatability (CoR) was 612.99 dB at the border of the ONH, which was significantly larger than points in the macular and peripapillary regions (P > 0.001). A significant decrease in average PWS, using the MP-1 microperimeter at the macular and peripapillary region (P < 0.001), meant that the PWS CoR could not be determined in these regions. No significant changes in average PWS were observed at the border of the ONH (P ¼ 0.223), and the PWS CoR was 67.52 dB in this region. CONCLUSIONS. Microperimetric test-retest repeatability at the border of a deep scotoma was worse than at other areas of normal retina, and this highlights the limitation of applying a single estimate of test-retest repeatability to determine whether significant functional decline has occurred at the border of a deep scotoma