Sickeningly sweet : L-rhamnose stimulates Flavobacterium columnare biofilm formation and virulence

Flavobacterium columnare, the causative agent of columnaris disease, causes substantial mortality worldwide in numerous freshwater finfish species. Due to its global significance and impact on the aquaculture industry continual efforts to better understand basic mechanisms that contribute to disease are urgently needed. The current work sought to evaluate the effect of L-rhamnose on the growth characteristics of F. columnare. While we initially did not observe any key changes during the total growth of F. columnare isolates tested when treated with L-rhamnose, it soon became apparent that the difference lies in the ability of this carbohydrate to facilitate the formation of biofilms. The addition of different concentrations of L-rhamnose consistently promoted the development of biofilms among different F. columnare isolates; however, it does not appear to be sufficient as a sole carbon source for biofilm growth. Our data also suggest that iron acquisition machinery is required for biofilm development. Finally, the addition of different concentrations of L-rhamnose to F. columnare prior to a laboratory challenge increased mortality rates in channel catfish (Ictalurus punctatus) as compared to controls. These results provide further evidence that biofilm formation is an integral virulence factor in the initiation of disease in fish

Scale interactions between the MJO and the western maritime continent

State-of-the-art regional climate model simulations that are able to resolve key mesoscale circulations are used, for the first time, to understand the interaction between the large-scale convective environment of the MJO and processes governing the strong diurnal cycle over the islands of the Maritime Continent (MC). Convection is sustained in the late afternoon just inland of the coasts due to sea breeze convergence. Previous work has shown that the variability in MC rainfall associated with the MJO is manifested in changes to this diurnal cycle; land-based rainfall peaks before the active convective envelope of the MJO reaches the MC, whereas oceanic rainfall rates peak whilst the active envelope resides over the region. The model simulations show that the main controls on oceanic MC rainfall in the early active MJO phases are the large-scale environment and atmospheric stability, followed by high oceanic latent heat flux forced by high near-surface winds in the later active MJO phases. Over land, rainfall peaks before the main convective envelope arrives (in agreement with observations), even though the large-scale convective environment is only moderately favourable for convection. The causes of this early rainfall peak are convective triggers from land-sea breeze circulations that are strong due to high surface insolation and surface heating. During the peak MJO phases cloud cover increases and surface insolation decreases, which weakens the strength of the mesoscale circulations and reduces land-based rainfall, even though the large-scale environment remains favourable for convection at this time. Hence, scale interactions are an essential part of the MJO transition across the MC

The catfish genome database cBARBEL: an informatic platform for genome biology of ictalurid catfish

The catfish genome database, cBARBEL (abbreviated from catfish Breeder And Researcher Bioinformatics Entry Location) is an online open-access database for genome biology of ictalurid catfish (Ictalurus spp.). It serves as a comprehensive, integrative platform for all aspects of catfish genetics, genomics and related data resources. cBARBEL provides BLAST-based, fuzzy and specific search functions, visualization of catfish linkage, physical and integrated maps, a catfish EST contig viewer with SNP information overlay, and GBrowse-based organization of catfish genomic data based on sequence similarity with zebrafish chromosomes. Subsections of the database are tightly related, allowing a user with a sequence or search string of interest to navigate seamlessly from one area to another. As catfish genome sequencing proceeds and ongoing quantitative trait loci (QTL) projects bear fruit, cBARBEL will allow rapid data integration and dissemination within the catfish research community and to interested stakeholders. cBARBEL can be accessed at http://catfishgenome.org

Evaluation of multi-season convection-permitting atmosphere – mixed-layer ocean simulations of the Maritime Continent

A multi-season convection-permitting regional climate simulation of the Maritime Continent (MC) using the Met Office Unified Model (MetUM) with 2.2 km grid spacing is presented and evaluated. The simulations pioneer the use of atmosphere–ocean coupling with the multi-column K profile parametrisation (KPP) mixed-layer ocean model in atmospheric convection-permitting climate simulations. Comparisons are made against a convection-parametrised simulation in which it is nested and which in turn derives boundary conditions from the ERA5 reanalysis. This paper describes the configuration, performance of the mean state and variability in the two simulations compared against observational datasets. The models have both minor sea surface temperature (SST) and wet precipitation biases. The diurnal cycle, representation of equatorial waves, and relationship between SST and precipitation are all improved in the convection-permitting model compared to the convection-parametrised model. The Madden–Julian oscillation (MJO) is present in both models with a faster-than-observed propagation speed. However, it is unclear whether fidelity of the MJO simulation is inherent to the model or whether it predominantly arises from the forcing at the boundaries

A local-to-large scale view of Maritime Continent rainfall: control by ENSO, MJO, and equatorial waves

The canonical view of the Maritime Continent (MC) diurnal cycle is deep convection occurring over land during the afternoon and evening, tending to propagate offshore overnight. However, there is considerable day-to-day variability in the convection, and the mechanism of the offshore propagation is not well understood. We test the hypothesis that large-scale drivers such as ENSO, the MJO, and equatorial waves, through their modification of the local circulation, can modify the direction or strength of the propagation, or prevent the deep convection from triggering in the first place. Taking a local-to-large scale approach, we use in situ observations, satellite data, and reanalyses for five MC coastal regions, and show that the occurrence of the diurnal convection and its offshore propagation is closely tied to coastal wind regimes that we define using the k-means cluster algorithm. Strong prevailing onshore winds are associated with a suppressed diurnal cycle of precipitation, while prevailing offshore winds are associated with an active diurnal cycle, offshore propagation of convection, and a greater risk of extreme rainfall. ENSO, the MJO, equatorial Rossby waves, and westward mixed Rossby–gravity waves have varying levels of control over which coastal wind regime occurs, and therefore on precipitation, depending on the MC coastline in question. The large-scale drivers associated with dry and wet regimes are summarized for each location as a reference for forecasters

Evaluation of multi-season convection permitting atmosphere - mixed layer ocean simulations of the Maritime Continent

A multi-season convection permitting regional climate simulation of the Maritime Continent using the Met Office Unified Model with 2.2-km grid spacing is presented and evaluated. The simulations pioneer the use of atmosphere-ocean coupling with the multi-column K profile parametrisation (KPP) mixed layer ocean model in atmospheric convection permitting climate simulations. Comparisons are made against a convection parametrised simulation in which it is nested, and which in turn derives boundary conditions from ERA5 reanalysis. This paper describes the configuration, performance of the mean state and variability of the two simulations compared against observational datasets. The models both have minor sea surface temperature (SST) and wet precipitation biases. The diurnal cycle, representation of equatorial waves and relationship between SST and precipitation are all improved in the convection permitting model compared to the convection parametrised model. The MJO is present in both models with a faster than observed propagation speed. However, it is unclear whether fidelity of the MJO simulation is inherent to the model or whether it predominantly arises from the forcing at the boundaries

Novel Fine-Structure in the Low-Energy Excitation Spectrum of a High-Tc Superconductor by Polarization Dependent Photoemission

Angle-resolved photoemission spectroscopy is performed on single crystals of the single-layer high-Tc superconductor Bi(2)Sr(2-x)La(x)CuO(6+d) at optimal doping (x=0.4) in order to study in great detail the Zhang-Rice (ZR) singlet band at the Fermi level. Besides the high crystal quality the advantages of a single-layer material are the absence of bilayer effects and the distinct reduction of thermal broadening. Due to the high energy and angle resolution and, most important, due to the controlled variation of the polarization vector of the synchrotron radiation the emission from the ZR singlet band reveals a distinct fine-structure. It consists of two maxima, the first showing only weak and the second at EF extremely strong polarization dependence. However, our observation has enormous consequences for line shape analyses and the determination of pseudo gaps by photoemission.Comment: 10 pages, 2 figures. to appear in PRB (Rapid Comm.

Impact of the Madden–Julian oscillation and equatorial waves on tracked mesoscale convective systems over southeast Asia

Southeast Asia is a region dominated by high-impact weather, but numerical weather prediction here is a challenge owing to the complex orography and interactions between small- and large-scale phenomena. Localised mesoscale convective systems (MCSs) can produce intense precipitation. Here, we track MCSs over a 5-year period in Himawari satellite data, characterise the distribution of MCSs in the region, and investigate how they are modulated by the Madden–Julian oscillation (MJO) and equatorial waves. Between 10°S and 10°N in southeast Asia, MCSs account for 45–70% of the precipitation during boreal extended winter (November–April). Over most of the region, the fractional MCS contribution to rainfall is higher than average on days with extreme rainfall (>55%). Long-lived (>12 hr) MCSs contribute disproportionately, providing 85% of the rainfall despite comprising only 34% of all MCSs. Variability in MCS rainfall accounts for >50% of the total rainfall variability during an MJO cycle, mostly due to larger numbers of MCSs in convectively active MJO phases. Variations in MCS size and mean rain rate due to shifts in the stratiform proportion provide compensating effects. In the west of the region, a shift to faster moving MCSs in active MJO phases and slower moving MCSs in inactive phases resulted in fast-moving MCSs having the greatest impact on the MJO-associated variability. Variability is larger in the west than in the east. Equatorial Kelvin waves modulate MCS rainfall, with MCSs accounting for 20–50% of local rainfall anomalies. This variability is again enhanced in the west. By contrast, rainfall anomalies due to westward-propagating mixed Rossby–gravity waves and Rossby-1 waves are dominated by tropical-cyclone-related rainfall. Skill at local scales may be extracted from forecasts of subseasonal drivers such as the MJO and Kelvin waves, by understanding how these modulate the number and characteristics of MCSs

Updating requirements for Endangered, Threatened and Protected species MSC Fisheries Standard v3.0 to operationalise best practices

Bycatch in fisheries is a key threat to non-target marine species, particularly for those species that have life histories with low productivity or poor conservation status. In this paper, the requirements of the new Marine Stewardship Council (MSC) Fisheries Standard (hereafter “the Standard”) are summarised relevant to Endangered, Threatened and Protected (ETP) species. This covers both how species are designated as ETP, and how performance of management is assessed with respect to ETP species, when scoring fisheries against the Standard. The process used to select these requirements is described, including a review of the requirements for earlier versions of the Standard and the scoring of these requirements in assessment reports for a selection of fisheries that have achieved MSC certification. The review identified a lack of consistency in the implementation of scoring guidelines, which was in part due to a lack of clarity in the requirements of the Standard. The revised Standard has been designed to achieve more consistent implementation of the requirements with respect to management of impacts on ETP species, and to align the requirements more closely with global best practice. The requirements may be used as a template for fisheries managers seeking to prioritise bycatch species for improved management and setting more specific and measurable objectives in relation to population status and minimising mortalities

Sea-breeze dynamics and convection initiation: the influence of convective parameterization in weather and climate model biases

There are some long-established biases in atmospheric models that originate from the representation of tropical convection. Previously, it has been difficult to separate cause and effect because errors are often the result of a number of interacting biases. Recently, researchers have gained the ability to run multiyear global climate model simulations with grid spacings small enough to switch the convective parameterization off, which permits the convection to develop explicitly. There are clear improvements to the initiation of convective storms and the diurnal cycle of rainfall in the convection-permitting simulations, which enables a new process-study approach to model bias identification. In this study, multiyear global atmosphere-only climate simulations with and without convective parameterization are undertaken with the Met Office Unified Model and are analyzed over the Maritime Continent region, where convergence from sea-breeze circulations is key for convection initiation. The analysis shows that, although the simulation with parameterized convection is able to reproduce the key rain-forming sea-breeze circulation, the parameterization is not able to respond realistically to the circulation. A feedback of errors also occurs: the convective parameterization causes rain to fall in the early morning, which cools and wets the boundary layer, reducing the land–sea temperature contrast and weakening the sea breeze. This is, however, an effect of the convective bias, rather than a cause of it. Improvements to how and when convection schemes trigger convection will improve both the timing and location of tropical rainfall and representation of sea-breeze circulations