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

Crystal Structure of VapBC-1 from Nontypeable \u3ci\u3eHaemophilus influenzae\u3c/i\u3e and the Effect of Pin Domain Mutations on Survival During Infection

Toxin-antitoxin (TA) gene pairs have been identified in nearly all bacterial genomes sequenced to date and are thought to facilitate persistence and antibiotic tolerance. TA loci are classified into various types based upon the characteristics of their antitoxins, with those in type II expressing proteic antitoxins. Many toxins from type II modules are ribonucleases that maintain a PilT N-terminal (PIN) domain containing conserved amino acids considered essential for activity. The vapBC (virulence-associated protein) TA system is the largest subfamily in this class and has been linked to pathogenesis of nontypeable Haemophilus influenzae (NTHi). In this study, the crystal structure of the VapBC-1 complex from NTHi was determined to 2.20 Å resolution. Based on this structure, aspartate-to-asparagine and glutamate-to-glutamine mutations of four conserved residues in the PIN domain of the VapC-1 toxin were constructed and the effects of the mutations on protein-protein interactions, growth of Escherichia coli, and pathogenesis ex vivo were tested. Finally, a novel model system was designed and utilized that consists of an NTHi ΔvapBC-1 strain complemented in cis with the TA module containing a mutated or wild-type toxin at an ectopic site on the chromosome. This enabled the analysis of the effect of PIN domain toxin mutants in tandem with their wild-type antitoxin under the control of the vapBC-1 native promoter and in single copy. This is the first report of a system facilitating the study of TA mutant operons in the background of NTHi during infections of primary human tissues ex vivo

The structure of the BfrB-Bfd complex reveals protein-protein interactions enabling iron release from bacterioferritin

This document is the Accepted Manuscript version of a Published Work that appeared in final form in the Journal of the American Chemical Society, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://doi.org/10.1021/ja305180n.Ferritin-like molecules are unique to cellular iron homeostasis because they can store iron at concentrations much higher than those dictated by the solubility of Fe3+. Very little is known about the protein interactions that deliver iron for storage, or promote the mobilization of stored iron from ferritin-like molecules. Here, we report the X-ray crystal structure of Pseudomonas aeruginosa bacterioferritin (Pa-BfrB) in complex with bacterioferritin-associated ferredoxin (Pa-Bfd) at 2.0 Å resolution. As the first example of a ferritin-like molecule in complex with a cognate partner, the structure provides unprecedented insight into the complementary interface that enables the [2Fe-2S] cluster of Pa-Bfd to promote heme-mediated electron transfer through the BfrB protein dielectric (~18 Å), a process that is necessary to reduce the core ferric mineral and facilitate mobilization of Fe2+. The Pa-BfrB-Bfd complex also revealed the first structure of a Bfd, thus providing a first view to what appears to be a versatile metal binding domain ubiquitous to the large Fer2_BFD family of proteins and enzymes with diverse functions. Residues at the Pa-BfrB-Bfd interface are highly conserved in Bfr and Bfd sequences from a number of pathogenic bacteria, suggesting that the specific recognition between Pa-BfrB and Pa-Bfd is of widespread significance to the understanding of bacterial iron homeostasis

Etching effects during the chemical vapor deposition of (100) diamond

Current theories of CVD growth on (100) diamond are unable to account for the numerous experimental observations of slow-growing, locally smooth (100)(2×1)(100)(2×1) films. In this paper we use quantum mechanical calculations of diamond surface thermochemistry and atomic-scale kinetic Monte Carlo simulations of deposition to investigate the efficacy of preferential etching as a mechanism that can help to reconcile this discrepancy. This etching mechanism allows for the removal of undercoordinated carbon atoms from the diamond surface. In the absence of etching, simulated growth on the (100)(2×1)(100)(2×1) surface is faster than growth on the (110) and (111) surfaces, and the (100) surface is atomically rough. When etching is included in the simulations, the (100) growth rates decrease to values near those observed experimentally, while the rates of growth on the other surfaces remain largely unaffected and similar to those observed experimentally. In addition, the etching mechanism promotes the growth of smooth (100) surface regions in agreement with numerous scanning probe studies. © 1999 American Institute of Physics.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/70606/2/JCPSA6-111-9-4291-1.pd

Reconfiguration of the proteasome during chaperone-mediated assembly

The proteasomal ATPase ring, comprising Rpt1-Rpt6, associates with the heptameric α ring of the proteasome core particle (CP) in the mature proteasome, with the Rpt C-terminal tails inserting into pockets of the α ring1–4. Rpt ring assembly is mediated by four chaperones, each binding a distinct Rpt subunit5–10. We report that the base subassembly of the proteasome, which includes the Rpt ring, forms a high affinity complex with the CP. This complex is subject to active dissociation by the chaperones Hsm3, Nas6, and Rpn14. Chaperone-mediated dissociation was abrogated by a nonhydrolyzable ATP analog, indicating that chaperone action is coupled to nucleotide hydrolysis by the Rpt ring. Unexpectedly, synthetic Rpt tail peptides bound α pockets with poor specificity, except for Rpt6, which uniquely bound the α2/α3 pocket. Although the Rpt6 tail is not visualized within an α pocket in mature proteasomes2–4, it inserts into the α2/α3 pocket in the base-CP complex and is important for complex formation. Thus, the Rpt-CP interface is reconfigured when the lid complex joins the nascent proteasome to form the mature holoenzyme

Making the Connection Between Microstructure and Mechanics

The purpose of microstructural control is to optimize materials properties. To that end, they have developed sophisticated and successful computational models of both microstructural evolution and mechanical response. However, coupling these models to quantitatively predict the properties of a given microstructure poses a challenge. This problem arises because most continuum response models, such as finite element, finite volume, or material point methods, do not incorporate a real length scale. Thus, two self-similar polycrystals have identical mechanical properties regardless of grain size, in conflict with theory and observations. In this project, they took a tiered risk approach to incorporate microstructure and its resultant length scales in mechanical response simulations. Techniques considered include low-risk, low-benefit methods, as well as higher-payoff, higher-risk methods. Methods studied include a constitutive response model with a local length-scale parameter, a power-law hardening rate gradient near grain boundaries, a local Voce hardening law, and strain-gradient polycrystal plasticity. These techniques were validated on a variety of systems for which theoretical analyses and/or experimental data exist. The results may be used to generate improved constitutive models that explicitly depend upon microstructure and to provide insight into microstructural deformation and failure processes. Furthermore, because mechanical state drives microstructural evolution, a strain-enhanced grain growth model was coupled with the mechanical response simulations. The coupled model predicts both properties as a function of microstructure and microstructural development as a function of processing conditions

Coupled Simulations of Mechanical Deformation and Microstructural Evolution Using Polycrystal Plasticity and Monte Carlo Potts Models

The microstructural evolution of heavily deformed polycrystalline Cu is simulated by coupling a constitutive model for polycrystal plasticity with the Monte Carlo Potts model for grain growth. The effects of deformation on boundary topology and grain growth kinetics are presented. Heavy deformation leads to dramatic strain-induced boundary migration and subsequent grain fragmentation. Grain growth is accelerated in heavily deformed microstructures. The implications of these results for the thermomechanical fatigue failure of eutectic solder joints are discussed

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

Costameric integrin and sarcoglycan protein levels are altered in a Drosophila model for Limb-girdle muscular dystrophy type 2H

Mutations in two different domains of the ubiquitously expressed TRIM32 protein give rise to two clinically separate diseases, one of which is Limb-girdle muscular dystrophy type 2H (LGMD2H). Uncovering the muscle-specific role of TRIM32 in LGMD2H pathogenesis has proven difficult, as neurogenic phenotypes, independent of LGMD2H pathology, are present in TRIM32 KO mice. We previously established a platform to study LGMD2H pathogenesis using Drosophila melanogaster as a model. Here we show that LGMD2H disease-causing mutations in the NHL domain are molecularly and structurally conserved between fly and human TRIM32. Furthermore, transgenic expression of a subset of myopathic alleles (R394H, D487N, and 520fs) induce myofibril abnormalities, altered nuclear morphology, and reduced TRIM32 protein levels, mimicking phenotypes in patients afflicted with LGMD2H. Intriguingly, we also report for the first time that the protein levels of βPS integrin and sarcoglycan δ, both core components of costameres, are elevated in TRIM32 disease-causing alleles. Similarly, murine myoblasts overexpressing a catalytically inactive TRIM32 mutant aberrantly accumulate α- and β-dystroglycan and α-sarcoglycan. We speculate that the stoichiometric loss of costamere components disrupts costamere complexes to promote muscle degeneration

Oxadiazole-Based Cell Permeable Macrocyclic Transition State Inhibitors of Norovirus 2CL Protease

Human noroviruses are the primary causative agents of acute gastroenteritis and a pressing public health burden worldwide. There are currently no vaccines or small molecule therapeutics available for the treatment or prophylaxis of norovirus infections. Norovirus 3CL protease plays a vital role in viral replication by generating structural and nonstructural proteins via the cleavage of the viral polyprotein. Thus, molecules that inhibit the viral protease may have potential therapeutic value. We describe herein the structure-based design, synthesis, and in vitro and cell-based evaluation of the first class of oxadiazole-based, permeable macrocyclic inhibitors of norovirus 3CL protease