Tracking marine mammals in 3D using electronic tag data

1. Information about at-depth behaviour of marine mammals is fundamental yet very hard to obtain from direct visual observation. Animal-borne multisensor electronic tags provide a unique window of observation into such behaviours. 2. Electronic tag sensors allow the estimation of the animal's 3-dimensional (3D) orientation, depth and speed. Using tag flow noise level to provide an estimate of animal speed, we extend existing approaches of 3D track reconstruction by allowing the direction of movement to differ from that of the animal's longitudinal axis. 3. Data are processed by a hierarchical Bayesian model that allows processing of multisource data, accounting for measurement errors and testing hypotheses about animal movement by comparing models. 4. We illustrate the approach by reconstructing the 3D track of a 52-min deep dive of a Blainville's beaked whale Mesoplodon densirostris adult male fit with a digital tag (DTAG) in the Bahamas. At depth, the whale alternated regular movements at large speed (>1·5 m s-1) and more complex movements at lower speed (<1·5 m s-1) with differences between movement and longitudinal axis directions of up to 28°. The reconstructed 3D track agrees closely with independent acoustic-based localizations. 5. The approach is potentially applicable to study the underwater behaviour (e.g. response to anthropogenic disturbances) of a wide variety of species of marine mammals fitted with triaxial magnetometer and accelerometer tags.PostprintPeer reviewe

Small Molecule Inhibitors of the BfrB-Bfd Interaction Decrease Pseudomonas aeruginosa Fitness and Potentiate Fluoroquinolone Activity

© 2019 American Chemical Society. All rights reserved. The iron storage protein bacterioferritin (BfrB) is central to bacterial iron homeostasis. The mobilization of iron from BfrB, which requires binding by a cognate ferredoxin (Bfd), is essential to the regulation of cytosolic iron levels in P. aeruginosa. This paper describes the structure-guided development of small molecule inhibitors of the BfrB-Bfd protein-protein interaction. The process was initiated by screening a fragment library and followed by obtaining the structure of a fragment hit bound to BfrB. The structural insights were used to develop a series of 4-(benzylamino)- A nd 4-((3-phenylpropyl)amino)-isoindoline-1,3-dione analogs that selectively bind BfrB at the Bfd binding site. Challenging P. aeruginosa cells with the 4-substituted isoindoline analogs revealed a dose-dependent growth phenotype. Further investigation determined that the analogs elicit a pyoverdin hyperproduction phenotype that is consistent with blockade of the BfrB-Bfd interaction and ensuing irreversible accumulation of iron in BfrB, with concomitant depletion of iron in the cytosol. The irreversible accumulation of iron in BfrB prompted by the 4-substituted isoindoline analogs was confirmed by visualization of BfrB-iron in P. aeruginosa cell lysates separated on native PAGE gels and stained for iron with Ferene S. Challenging P. aeruginosa cultures with a combination of commercial fluoroquinolone and our isoindoline analogs results in significantly lower cell survival relative to treatment with either antibiotic or analog alone. Collectively, these findings furnish proof of concept for the usefulness of small molecule probes designed to dysregulate bacterial iron homeostasis by targeting a protein-protein interaction pivotal for iron storage in the bacterial cell

Architecture of Pseudomonas aeruginosa glutamyl-tRNA synthetase defines a subfamily of dimeric class Ib aminoacyl-tRNA synthetases

The aminoacyl-tRNA synthetases (AaRSs) are an ancient family of structurally diverse enzymes that are divided into two major classes. The functionalities of most AaRSs are inextricably linked to their oligomeric states. While GluRSs were previously classified as monomers, the current investigation reveals that the form expressed in Pseudomonas aeruginosa is a rotationally pseudosymmetrical homodimer featuring intersubunit tRNA binding sites. Both subunits display a highly bent, "pipe strap" conformation, with the anticodon binding domain directed toward the active site. The tRNA binding sites are similar in shape to those of the monomeric GluRSs, but are formed through an approximately 180-degree rotation of the anticodon binding domains and dimerization via the anticodon and D-arm binding domains. As a result, each anticodon binding domain is poised to recognize the anticodon loop of a tRNA bound to the adjacent protomer. Additionally, the anticodon binding domain has an α-helical C-terminal extension containing a conserved lysine-rich consensus motif positioned near the predicted location of the acceptor arm, suggesting dual functions in tRNA recognition. The unique architecture of PaGluRS broadens the structural diversity of the GluRS family, and member synthetases of all bacterial AaRS subclasses have now been identified that exhibit oligomerization

Diversity and dispersal of a ubiquitous protein family: acyl-CoA dehydrogenases

Acyl-CoA dehydrogenases (ACADs), which are key enzymes in fatty acid and amino acid catabolism, form a large, pan-taxonomic protein family with at least 13 distinct subfamilies. Yet most reported ACAD members have no subfamily assigned, and little is known about the taxonomic distribution and evolution of the subfamilies. In completely sequenced genomes from approximately 210 species (eukaryotes, bacteria and archaea), we detect ACAD subfamilies by rigorous ortholog identification combining sequence similarity search with phylogeny. We then construct taxonomic subfamily-distribution profiles and build phylogenetic trees with orthologous proteins. Subfamily profiles provide unparalleled insight into the organisms’ energy sources based on genome sequence alone and further predict enzyme substrate specificity, thus generating explicit working hypotheses for targeted biochemical experimentation. Eukaryotic ACAD subfamilies are traditionally considered as mitochondrial proteins, but we found evidence that in fungi one subfamily is located in peroxisomes and participates in a distinct β-oxidation pathway. Finally, we discern horizontal transfer, duplication, loss and secondary acquisition of ACAD genes during evolution of this family. Through these unorthodox expansion strategies, the ACAD family is proficient in utilizing a large range of fatty acids and amino acids—strategies that could have shaped the evolutionary history of many other ancient protein families

Navigating through the r packages for movement

The advent of miniaturized biologging devices has provided ecologists with unprecedented opportunities to record animal movement across scales, and led to the collection of ever-increasing quantities of tracking data. In parallel, sophisticated tools have been developed to process, visualize and analyse tracking data; however, many of these tools have proliferated in isolation, making it challenging for users to select the most appropriate method for the question in hand. Indeed, within the r software alone, we listed 58 packages created to deal with tracking data or 'tracking packages'. Here, we reviewed and described each tracking package based on a workflow centred around tracking data (i.e. spatio-temporal locations (x, y, t)), broken down into three stages: pre-processing, post-processing and analysis, the latter consisting of data visualization, track description, path reconstruction, behavioural pattern identification, space use characterization, trajectory simulation and others. Supporting documentation is key to render a package accessible for users. Based on a user survey, we reviewed the quality of packages' documentation and identified 11 packages with good or excellent documentation. Links between packages were assessed through a network graph analysis. Although a large group of packages showed some degree of connectivity (either depending on functions or suggesting the use of another tracking package), one third of the packages worked in isolation, reflecting a fragmentation in the r movement-ecology programming community. Finally, we provide recommendations for users when choosing packages, and for developers to maximize the usefulness of their contribution and strengthen the links within the programming community

An Analysis of the Water Quality Problems of the Safford Valley, Arizona

A marked change in ground water quality in the Safford Valley of Graham County, Arizona, averaging approximately +0.129 x 103 mhos electrical conductivity per year and +35 parts per million chloride per year, has been documented between 1940 and 1972 with data from ten long -term sample wells. A chloride change map constructed between these two years shows a general increase of 200 to 400 ppm chloride. The 1972 iso- chemical maps show areas of up to 1600 ppm chloride and 8.0 x 103 mhos electrical conductivity, which is extremely saline and considered threshold level for agricultural waters. The Safford Valley, a structural trough with approximately east -west orientation, averages 12 miles in width and 30 miles in length in the study area. Bounded by typical basin and range province mountains on the northeast and southwest, the valley contains a perennial stream flowing toward the west. A bi- aquifer system constitutes the ground water reservoir of the area with a deep, artesian aquifer of several thousand feet thickness overlaid by a water table aquifer averaging 400 feet in thickness and with the water table rarely over fifty feet from the surface on the eastern end of the valley, deepening to over 5000 feet at the western end. This bedrock -alluvium interface is the lower vertical constraint for the artesian system, thus the thickness of this aquifer increases downstream (to the west). The basin fill consists of a basal conglomerate overlaid by lacustrine evaporite beds, the aquifer cap beds, and recent alluvial material. The artesian aquifer is shown to be up to ten times as saline as the water table aquifer, and appears to increase in temperature and salinity in a downstream direction (corresponding to increasing thicknesses of lacustrine beds included in the extent of this aquifer). The decrement in the water quality of the surficial aquifer seems to be attributable to four major mechanisms. An increase in salinity may be expected from leakage of saline water from the artesian aquifer. Suck leakage would be stimulated by pumping- caused reduction of confining pressure, and by the puncture of the cap beds by deep wells. Water reaching the aquifer from natural recharge may contribute salts to the system. Such recharging water, if passed through soluble beds, could contribute to the salt content of the aquifer. Lateral movement of water through similar deposits may be a contribution, and the concentration and infiltration of agricultural water could also add to aquifer salinity. Ground water applied to the land surface is concentrated by evaporation and dissolves salts in the unsaturated zone as it re- enters the water table aquifer. Iso- salinity and salinity -change maps show the quality situation of the water table aquifer to be broken up into three major sections. From the eastern limit of the study area to Safford, the quality is relatively high and stable. From Safford to Pima there appears a uniform increase of low magnitude but continued decrement. Beyond Pima the area exhibits extremely irregular salinity conditions with marked increases and high salinity gradients. The salinity pattern corresponds to the extent of the underlying artesian aquifer but may be influenced to an unknown extent by the down- gradient transport of salts. The 1972 iso -chemical maps show chevrons of high quality water protruding into the aquifer at points corresponding to the locations of washes. Such wash bottoms are the principal zones of recharge in arid regions. Recharge from the Gila River is of extremely high quality relative to the salinity of the aquifer. There appear no configurations of iso -chemical lines which are attributable to internal movement through saline deposits. The hydraulic gradient of the water table aquifer is relatively constant and follows the gradient of the land surface. Concentration of irrigation water by evaporation and subsequent leaching while in conveyance to the water table seems to increase the salinity of this percolating water by approximately three -fold. The magnitude of this increase at any one point in space and time is a function of the volume of water applied to the land surface, the amount of evaporation, the initial chemical composition of the water, the chemical characteristics of the unsaturated zone through which it penetrates, and the transmission properties of the aquifer. The salinity increase seems significant but the extent of the contribution to the salinity of the aquifer is dependent on the amount of infiltration to the aquifer. This amount is currently undetermined, but is probably a sizable volume -- especially from pre- irrigation applications. A sociologic investigation based on responses from a detailed questionnaire - interview program of 41 farmers (25 percent of the farming population), indicated that there is an awareness of the high salinity of ground water being used for irrigation but relatively little concern about the rate of increase of that salinity. The farmers seem reluctant to leave the area and are willing to take somewhat greater economic losses than expected. Since the farmers of the area are principally Mormon, there may be a tie to this historically Mormon region which is stronger than usual. The economic analysis of the Safford Valley based on the modeling of a "Representative Farm" analog indicates that cotton will remain economical to produce on the basis of the projected salinity trends and ceteris paribus conditions, for a significant time beyond limits of prediction. The analysis indicates that the optimum salt-resistant crops for the area are being cultivated, and that of these, alfalfa, the least tolerant, will cease to be productive in large areas of the valley by 1990. The entire valley will not be able to economically produce alfalfa by 2040, but will remain in production since it is a necessary crop for cotton and the cotton profits should be sufficient to cover the alfalfa losses. Pumping is the only element in the operation of the social, physical and economic systems by which salinity change could be influenced significantly. The area east of Safford is the optimal pumping region while that west of Pima is the worst. The employment of surface water should be maximized, and salt- oriented field methods should be employed. Although agriculture does not seem in danger in predictable time, these practices would increase yield (or slow the decrease) and postpone the day when farming will no longer by profitable in the Safford Valley of Graham County, Arizona.This title from the Hydrology & Water Resources Technical Reports collection is made available by the Department of Hydrology & Atmospheric Sciences and the University Libraries, University of Arizona. If you have questions about titles in this collection, please contact [email protected]