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  1. Bacterial cells alter gene expression in response to changes in population density in a process called quorum sensing (QS). In Vibrio harveyi, LuxO, a low cell density activator of sigma factor-54 (RpoN), is required for transcription of five non-coding regulatory sRNAs, Qrr1-Qrr5, which each repress translation of the master QS regulator LuxR. Vibrio parahaemolyticus, the leading cause of bacterial seafood-borne gastroenteritis, also contains five Qrr sRNAs that control OpaR (the LuxR homolog), controlling capsule polysaccharide (CPS), motility, and metabolism. We show that in a Δ luxO deletion mutant, opaR was de-repressed and CPS and biofilm were produced. However, in amore »Δ rpoN mutant, opaR was repressed, no CPS was produced, and less biofilm production was observed compared to wild type. To determine why opaR was repressed, expression analysis in Δ luxO showed all five qrr genes were repressed, while in Δ rpoN the qrr2 gene was significantly de-repressed. Reporter assays and mutant analysis showed Qrr2 sRNA can act alone to control OpaR. Bioinformatics analysis identified a sigma-70 (RpoD) -35 -10 promoter overlapping the canonical sigma-54 (RpoN) -24 -12 promoter in the qrr2 regulatory region. The qrr2 sigma-70 promoter element was also present in additional Vibrio species indicating it is widespread. Mutagenesis of the sigma-70 -10 promoter site in the Δ rpoN mutant background, resulted in repression of qrr2. Analysis of qrr quadruple deletion mutants, in which only a single qrr gene is present, showed that only Qrr2 sRNA can act independently to regulate opaR . Mutant and expression data also demonstrated that RpoN and the global regulator, Fis, act additively to repress qrr2 . Our data has uncovered a new mechanism of qrr expression and shows that Qrr2 sRNA is sufficient for OpaR regulation. Importance The quorum sensing non-coding sRNAs are present in all Vibrio species but vary in number and regulatory roles among species. In the Harveyi clade, all species contain five qrr genes, and in V. harveyi these are transcribed by sigma-54 and are additive in function. In the Cholerae clade, four qrr genes are present, and in V. cholerae the qrr genes are redundant in function. In V. parahaemolyticus , qrr2 is controlled by two overlapping promoters. In an rpoN mutant, qrr2 is transcribed from a sigma-70 promoter that is present in all V. parahaemolyticus strains and in other species of the Harveyi clade suggesting a conserved mechanism of regulation. Qrr2 sRNA can function as the sole Qrr sRNA to control OpaR.« less
    Free, publicly-accessible full text available October 11, 2022
  2. Photosynthetic O 2 evolution is catalyzed by the Mn 4 CaO 5 cluster of the water oxidation complex of the photosystem II (PSII) complex. The photooxidative self-assembly of the Mn 4 CaO 5 cluster, termed photoactivation, utilizes the same highly oxidizing species that drive the water oxidation in order to drive the incorporation of Mn 2+ into the high-valence Mn 4 CaO 5 cluster. This multistep process proceeds with low quantum efficiency, involves a molecular rearrangement between light-activated steps, and is prone to photoinactivation and misassembly. A sensitive polarographic technique was used to track the assembly process under flash illuminationmore »as a function of the constituent Mn 2+ and Ca 2+ ions in genetically engineered membranes of the cyanobacterium Synechocystis sp. PCC6803 to elucidate the action of Ca 2+ and peripheral proteins. We show that the protein scaffolding organizing this process is allosterically modulated by the assembly protein Psb27, which together with Ca 2+ stabilizes the intermediates of photoactivation, a feature especially evident at long intervals between photoactivating flashes. The results indicate three critical metal-binding sites: two Mn and one Ca, with occupation of the Ca site by Ca 2+ critical for the suppression of photoinactivation. The long-observed competition between Mn 2+ and Ca 2+ occurs at the second Mn site, and its occupation by competing Ca 2+ slows the rearrangement. The relatively low overall quantum efficiency of photoactivation is explained by the requirement of correct occupancy of these metal-binding sites coupled to a slow restructuring of the protein ligation environment, which are jointly necessary for the photooxidative trapping of the first stable assembly intermediate.« less
  3. The trend of offshore wind energy in deeper water that is expected to shift from fixed to floating platforms requires a cost-effective anchor solution for floating offshore wind turbines (FOWTs). Multiline ring anchor (MRA) has been developed as a cost-effective solution for FOWTs due to its capability of anchoring multiple mooring lines, its high efficiency, and its availability to a wide range of soils and loading conditions. While previous preliminary studies on the anchor performance provide useful insights on how the potential advantages of the MRA can improve load capacity, these studies are limited to focusing on optimizing the anchormore »design in certain soil and loading conditions. By contrast, the MRA will be installed in seabeds under more complex conditions that depend on geological location, water depth of at-place, and environmental conditions, of which wind, current, and wave are major components. These may result in additional substantial extra capital costs, delays in the projects, and safety issues, when the complex conditions are not properly considered. Specifically, the installation time and expenses of the offshore anchor are very susceptible to anchor types, installation methods, and environmental conditions. For this reason, this paper compares two existing offshore anchor installation methods and different anchor types on the basis of their performance under the same severe environmental condition. In evaluating the installability of the MRA, this paper conducts a comparative scenario study. The results show that the anchor installations and anchor handling vessel (AHV) operations are sensitive to weather conditions and AHV sizes. In view of total weather standby, the results show that anchor types or installation methods have little effect on it due to their relatively shorter duration than other work sequences. However, the MRA can benefit in substantially reducing transport time and costs due to its compact size. The MRA can be more efficient and cost-effective than other alternatives under complex and severe weather conditions.« less
  4. Abstract The ATLAS experiment at the Large Hadron Collider has a broad physics programme ranging from precision measurements to direct searches for new particles and new interactions, requiring ever larger and ever more accurate datasets of simulated Monte Carlo events. Detector simulation with Geant4 is accurate but requires significant CPU resources. Over the past decade, ATLAS has developed and utilized tools that replace the most CPU-intensive component of the simulation—the calorimeter shower simulation—with faster simulation methods. Here, AtlFast3, the next generation of high-accuracy fast simulation in ATLAS, is introduced. AtlFast3 combines parameterized approaches with machine-learning techniques and is deployed tomore »meet current and future computing challenges, and simulation needs of the ATLAS experiment. With highly accurate performance and significantly improved modelling of substructure within jets, AtlFast3 can simulate large numbers of events for a wide range of physics processes.« less
    Free, publicly-accessible full text available December 1, 2023
  5. Free, publicly-accessible full text available May 1, 2023
  6. Free, publicly-accessible full text available May 1, 2023