Acoustic characterization of sensors used for marine environmental monitoring

Acknowledgements The authors wish to acknowledge Benjamin Brand for his assistance with the Acoustic Test Facility set-up, Jessica Noe for her assistance designing sonar mounts, James Joslin for his assistance with cables for sonar operation, and Mark Wood for his assistance with icListen hydrophones. This study would not have been possible without their contributions. Funding This work was funded by the US Department of Energy [grant number DE-EE0007827]. Emma Cotter is supported by a National Science Foundation Graduate Research Fellowship [grant number DGE-1762114].Peer reviewedPostprin

Frequency- and depth-dependent target strength measurements of individual mesopelagic scatterers

Author Posting. © Acoustical Society of America, 2020. This article is posted here by permission of Acoustical Society of America for personal use, not for redistribution. The definitive version was published in Journal of the Acoustical Society of America 148(2),(2020): EL153-EL158, doi:10.1121/10.0001745.Recent estimates based on shipboard echosounders suggest that 50% or more of global fish biomass may reside in the mesopelagic zone (depths of ∼200–1000 m). Nonetheless, little is known about the acoustic target strengths (TS) of mesopelagic animals because ship-based measurements cannot resolve individual targets. As a result, biomass estimates of mesopelagic organisms are poorly constrained. Using an instrumented tow-body, broadband (18–90 kHz) TS measurements were obtained at depths from 70 to 850 m. A comparison between TS measurements at-depth and values used in a recent global estimate of mesopelagic biomass suggests lower target densities at most depths.Development of Deep-See was funded by the National Science Foundation (Grant No. OCE MRI 1626087), field work was funded by NOAA, and ongoing support is provided by the WHOI Audacious/TED Project. Mike Jech (NOAA NWFSC) and WHOI collaborators Bob Pettit, Kaitlyn Tradd, Peter Weibe, and Joel Llopiz contributed to development and fieldwork

Antioxidant-mediated inhibition of the heat shock response leads to apoptosis

AbstractWe examined the hypothesis that reactive oxygen species (ROS) contribute to the induction of heat shock proteins (hsps) during stress response. Exposure of HL-60 human myelocytic cells to 42°C induced both hsp72 and hsp27. In the presence of the antioxidant molecules pyrrolidine dithiocarbamate or 1,10-phenanthroline induction of hsp72 and 27 was significantly decreased, while N-acetyl-l-cysteine caused a slight reduction. Prevention of hsp induction was associated with heat sensitization and increased caspase activity, indicating that the cells were undergoing apoptosis. These data suggest that ROS contribute to the induction of hsps and furthermore, that hsp induction and apoptosis are mutually exclusive events within the same cell

Bordetella pertussis Autotransporter Vag8 Binds Human C1 Esterase Inhibitor and Confers Serum Resistance

Bordetella pertussis employs numerous strategies to evade the immune system, including the ability to resist killing via complement. Previously we have shown that B. pertussis binds a complement regulatory protein, C1 esterase inhibitor (C1inh) to its surface in a Bvg-regulated manner (i.e. during its virulence phase), but the B. pertussis factor was not identified. Here we set out to identify the B. pertussis C1inh-binding factor. Using a serum overlay assay, we found that this factor migrates at approximately 100 kDa on an SDS-PAGE gel. To identify this factor, we isolated proteins of approximately 100 kDa from wild type strain BP338 and from BP347, an isogenic Bvg mutant that does not bind C1inh. Using mass spectrometry and bioinformatics, we identified the autotransporter protein Vag8 as the putative C1inh binding protein. To prove that Vag8 binds C1inh, vag8 was disrupted in two different B. pertussis strains, namely BP338 and 18–323, and the mutants were tested for their ability to bind C1inh in a surface-binding assay. Neither mutant strain was capable of binding C1inh, whereas a complemented strain successfully bound C1inh. In addition, the passenger domain of Vag8 was expressed and purified as a histidine-tagged fusion protein and tested for C1inh-binding in an ELISA assay. Whereas the purified Vag8 passenger bound C1inh, the passenger domain of BrkA (a related autotransporter protein) failed to do so. Finally, serum assays were conducted to compare wild type and vag8 mutants. We determined that vag8 mutants from both strains were more susceptible to killing compared to their isogenic wild type counterparts. In conclusion, we have discovered a novel role for the previously uncharacterized protein Vag8 in the immune evasion of B. pertussis. Vag8 binds C1inh to the surface of the bacterium and confers serum resistance

Ras GTPase-like protein MglA, a controller of bacterial social-motility in Myxobacteria, has evolved to control bacterial predation by Bdellovibrio

Bdellovibrio bacteriovorus invade Gram-negative bacteria in a predatory process requiring Type IV pili (T4P) at a single invasive pole, and also glide on surfaces to locate prey. Ras-like G-protein MglA, working with MglB and RomR in the deltaproteobacterium Myxococcus xanthus, regulates adventurous gliding and T4P-mediated social motility at both M. xanthus cell poles. Our bioinformatic analyses suggested that the GTPase activating protein (GAP)-encoding gene mglB was lost in Bdellovibrio, but critical residues for MglABd GTP-binding are conserved. Deletion of mglABd abolished prey-invasion, but not gliding, and reduced T4P formation. MglABd interacted with a previously uncharacterised tetratricopeptide repeat (TPR) domain protein Bd2492, which we show localises at the single invasive pole and is required for predation. Bd2492 and RomR also interacted with cyclic-di-GMP-binding receptor CdgA, required for rapid prey-invasion. Bd2492, RomRBd and CdgA localize to the invasive pole and may facilitate MglA-docking. Bd2492 was encoded from an operon encoding a TamAB-like secretion system. The TamA protein and RomR were found, by gene deletion tests, to be essential for viability in both predatory and non-predatory modes. Control proteins, which regulate bipolar T4P-mediated social motility in swarming groups of deltaproteobacteria, have adapted in evolution to regulate the anti-social process of unipolar prey-invasion in the “lone-hunter” Bdellovibrio. Thus GTP-binding proteins and cyclic-di-GMP inputs combine at a regulatory hub, turning on prey-invasion and allowing invasion and killing of bacterial pathogens and consequent predatory growth of Bdellovibrio

Advanced Environmental Monitoring for Marine Renewable Energy

Thesis (Ph.D.)--University of Washington, 2019Marine renewable energy has the potential to provide clean, reliable power to coastal communities and offshore facilities. However, the effects that marine energy development might have on the environment are not yet well understood. One environmental risk of particular concern is that of collision between an animal and a marine energy converter, but conducting the requisite environmental monitoring to understand this risk has presented a challenge at marine energy sites around the world for several reasons. First, if collision does occur, it is likely to be a rare event, meaning that detection requires continuous monitoring over extended deployments. Second, there is no single sensor that can provide all of the necessary information, and a combination of active acoustic, passive acoustic, and optical sensors is required. Third, these sensors can rapidly accrue vast volumes of data (petabyte-scale), making it difficult to extract insight from collected data. Finally, waves and currents at marine energy sites complicate the deployment of any monitoring instrumentation. Integrated instrumentation platforms that combine sensors into a single platform can address some of these challenges, because they can provide all of the necessary data and reduce deployment complexity. However, operation of such a platform must meet three directives in order to be most effective: 1) avoid biasing animal behavior through the use of instrumentation, 2) reliably detect rare events, and 3) avoid collection of unmanageable volumes of data. In this thesis, it is demonstrated that it is possible to simultaneously meet all three of these directives. This is demonstrated using the Adaptable Monitoring Package (AMP), an integrated instrumentation platform that combines multibeam sonars, optical cameras, hydrophones, and an acoustic Doppler current profiler. Artificial illumination is necessary to collect data from optical cameras when ambient light is not available. However, this light can either attract or repel animals. To minimize these effects (e.g., meet directive 1), the AMP uses detection, tracking, and classification of targets in the multibeam sonar data to restrict the use of artificial illumination to periods when a target of interest is present and might be detectable by the optical cameras. Information about target presence is also used to limit data archival to periods when a target of interest is present and avoid curation of data that does not contain any useful information (e.g., meeting directives 2 and 3). To benchmark this capability, real-time target detection and tracking are used to limit data archival to periods when any target of potential interest is present during a deployment of the AMP in Sequim Bay, WA. The target detection and tracking approach was found to have a true negative rate of 0.99 (e.g., an estimated 1% of targets of interest were not recorded), but 45% of recorded data did not contain a biological target. To address this relatively high false positive rate, recorded data were used to train machine learning classification of tracked targets. Three machine learning algorithms, trained using varying parameters and features, were evaluated for this task. A random forest algorithm was found to perform best, and the resulting classification model was able to distinguish between biological targets (e.g., seals, fish) and non-biological targets (e.g., acoustic artifacts) with a true positive rate of 0.97 and a false negative rate of 0.13. This model was then implemented in real-time during a second deployment of the AMP and used to limit data acquisition to periods when biological targets were predicted to be present. The model achieved the same true positive rate and a false positive rate of 0.23 in real-time after re-training with site specific data. From these results, general recommendations are made for implementation of real-time classification of biological targets in multibeam sonar data at new marine energy sites. All active acoustic sensors used on the Adaptable Monitoring Package, including the multibeam sonar used for real-time classification, have operating frequencies above the upper limit of marine mammal hearing. However, high-frequency transducers can still produce sound at lower frequencies audible to marine mammals. A comprehensive evaluation of the acoustic emissions of four active acoustic transducers used on the Adaptable Monitoring Package was conducted to understand whether they might cause hearing damage or bias marine mammal hearing (e.g., violating directive 1). All four transducers were found to produce measurable sound below 160 kHz, the reported upper limit of marine mammal hearing. A spatial map of the acoustic emissions of each sonar was used to evaluate potential effects on marine mammal hearing if the transducer were continuously operated from a stationary platform. Based on the cumulative sound exposure level metric, the acoustic emissions from any of the the transducers are unlikely to cause hearing damage to marine mammals. However, the extent of audibility is estimated to be on the order of 100 m, and further research is needed to understand how this might affect marine mammal behavior. In sum, this thesis provides a framework for effective environmental monitoring that can be used to reduce the the uncertainty surrounding the environmental effects of marine renewable energy. Further, many aspects are widely applicable to the ocean instrumentation community. Automatic classification of fauna in multibeam sonar data had not been previously demonstrated, and has applications in biological research. The methods developed for evaluation of the acoustic emissions of active acoustic sensors allow for effective comparison between transducers, which can be used to inform sensor selection and government regulation of their use

Dataset to supplement the PhD dissertation "Advanced Environmental Monitoring for Marine Renewable Energy" http://hdl.handle.net/1773/44376

Supplemental data for: Detection and Classification Capabilities of Two Multibeam Sonars, by Emma Cotter and Brian Polagye, accepted for publication in Limnology and Oceanography Methods (2020

Automatic Classification of Biological Targets in a Tidal Channel using a Multibeam Sonar: Data Set

The paper this data set supports is titled "Automatic Classification of Biological Targets in a Tidal Channel using a Multibeam Sonar" by Emma Cotter and Brian Polagye, and will be published in the Journal of Atmospheric and Oceanic TechnologyThese files accompany the manuscript "Automatic Classification of Biological Targets in a Tidal Channel using a Multibeam Sonar." The files include three data sets of target tracks from multibeam sonar data collected in Sequim, WA. The data were used to train machine learning classification models. Each target track is classified as a non-biological target, a seal, a school of fish, a diving bird, or an unclassified small target. The data format is described in detail in the README files

Subspecies diversity in bacteriocin production by intestinal Lactobacillus salivarius strains

peer-reviewedAddendum to: O’Shea EF, O’Connor PM, Raftis EJ, O’Toole PW, Stanton C, Cotter PD, Ross RP, et al. Production of multiple bacteriocins from a single locus by gastrointestinal strains of Lactobacillus salivarius. J Bacteriol 2011; 193:6973-84A recent comparative genomic hybridisation study in our laboratory revealed considerable plasticity within the bacteriocin locus of gastrointestinal strains of Lactobacillus salivarius. Most notably these analyses led to the identification of two novel unmodified bacteriocins salivaricin L and salivaricin T produced by the neonatal isolate L. salivarius DPC6488 with immunity, regulatory and export systems analogous to those of abp118, a two-component bacteriocin produced by the well characterized reference strain L. salivarius UCC118. In this addendum we discuss the intraspecific diversity of our seven bacteriocin-producing L. salivarius isolates on a genome-wide level, and more specifically, with respect to their salivaricin loci.Food Institutional Research Measure, Department of Agriculture, Fisheries and Food (grant no. 04R & DC); Alimentary Pharmabiotic Centre; Science Foundation Ireland (SFI) (grant no. 07/CE/B1368