Amyloid-like fibrils from a domain-swapping protein feature a parallel, in-register conformation without native-like interactions

The formation of amyloid-like fibrils is characteristic of various diseases, but the underlying mechanism and the factors that determine whether, when, and how proteins form amyloid, remain uncertain. Certain mechanisms have been proposed based on the three-dimensional or runaway domain swapping, inspired by the fact that some proteins show an apparent correlation between the ability to form domain-swapped dimers and a tendency to form fibrillar aggregates. Intramolecular β-sheet contacts present in the monomeric state could constitute intermolecular β-sheets in the dimeric and fibrillar states. One example is an amyloid-forming mutant of the immunoglobulin binding domain B1 of streptococcal protein G, which in its native conformation consists of a four-stranded β-sheet and one α-helix. Under native conditions this mutant adopts a domainswapped dimer, and it also forms amyloid-like fibrils, seemingly in correlation to its domain-swapping ability. We employ magic angle spinning solid-state NMR and other methods to examine key structural features of these fibrils. Our results reveal a highly rigid fibril structure that lacks mobile domains and indicate a parallel in-register β-sheet structure and a general loss of native conformation within the mature fibrils. This observation contrasts with predictions that native structure, and in particular intermolecular β-strand interactions seen in the dimeric state, may be preserved in "domain-swapping" fibrils. We discuss these observations in light of recent work on related amyloidforming proteins that have been argued to follow similar mechanisms and how this may have implications for the role of domain-swapping propensities for amyloid formation. © 2011 by The American Society for Biochemistry and Molecular Biology, Inc

Swimming kinematics and efficiency of entangled North Atlantic right whales

© The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Endangered Species Research 32 (2017): 1-17, doi:10.3354/esr00781.Marine mammals are streamlined for efficient movement in their relatively viscous fluid environment and are able to alter their kinematics (i.e. fluke stroke frequency, amplitude, or both) in response to changes in force balance. Entanglement in fishing gear adds significant drag and buoyant forces that can impact swimming behaviors across a range of timescales. We deployed biologging tags during the disentanglement of 2 North Atlantic right whales Eubalaena glacialis to (1) examine how their kinematics changed in response to drag and buoyancy from entanglement in fishing gear, and (2) calculate resultant changes in swimming efficiency for one individual. We observed variable responses in dive behavior, but neither whale appeared to exploit added buoyancy to reduce energy expenditure. While some of the observed changes in behavior were individually specific, some swimming kinematics were consistently modulated in response to high drag and buoyancy associated with entangling gear, affecting thrust production. In high drag and buoyancy conditions, fluke strokes were significantly shorter and more variable in shape, and gliding was less frequent. Thrust and efficiency significantly differed among dive phases. Disentanglement reduced thrust coefficients ~4-fold, leading to 1.2 to 1.8-fold lower power (W). Ideal propulsive efficiency was significantly lower when entangled, though we detected no difference in observed propulsive efficiency between the conditions. Similar to carrying heavy objects or changing shoes, we present another condition where animals perceive unique movement constraints over seconds to minutes and develop compensatory strategies, altering their movement accordingly.J.M.v.d.H was supported by a postgraduate scholarship from the Natural Sciences and Engineering Research Council of Canada, the MIT Martin Family for Sustainability Fellowship, the Herrington Fitch Family Foundation, a NOAA Award #NA14OAR4320158 to The Cooperative Institute for the North Atlantic Region, and a WHOI-Duke Fellowship through the WHOI Marine Mammal Center

Estimating energetics in cetaceans from respiratory frequency : why we need to understand physiology

© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Biology Open 5 (2016): 436-442, doi:10.1242/bio.017251.The accurate estimation of field metabolic rates (FMR) in wild animals is a key component of bioenergetic models, and is important for understanding the routine limitations for survival as well as individual responses to disturbances or environmental changes. Several methods have been used to estimate FMR, including accelerometer-derived activity budgets, isotope dilution techniques, and proxies from heart rate. Counting the number of breaths is another method used to assess FMR in cetaceans, which is attractive in its simplicity and the ability to measure respiration frequency from visual cues or data loggers. This method hinges on the assumption that over time a constant tidal volume (VT) and O2 exchange fraction (ΔO2) can be used to predict FMR. To test whether this method of estimating FMR is valid, we measured breath-by-breath tidal volumes and expired O2 levels of bottlenose dolphins, and computed the O2 consumption rate (V̇O2) before and after a pre-determined duration of exercise. The measured V̇O2 was compared with three methods to estimate FMR. Each method to estimate V̇O2 included variable VT and/or ΔO2. Two assumption-based methods overestimated V̇O2 by 216-501%. Once the temporal changes in cardio-respiratory physiology, such as variation in VT and ΔO2, were taken into account, pre-exercise resting V̇O2 was predicted to within 2%, and post-exercise V̇O2 was overestimated by 12%. Our data show that a better understanding of cardiorespiratory physiology significantly improves the ability to estimate metabolic rate from respiratory frequency, and further emphasizes the importance of eco-physiology for conservation management efforts.Funding for this project was provided by the Office of Naval Research [ONR YIP Award # N000141410563]. M.J.M. received funding from National Oceanographic Partnership Program [9N00014-11-1-0113]

Response to ‘On the importance of understanding physiology when estimating energetics in cetaceans’

© The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Biology Open 6 (2017): 307-308, doi:10.1242/bio.023143.We are grateful for the interest in our paper by two eminent physiologists and hope this response to their comments will clarify the objectives of our paper. The analysis in Fahlman et al. (2016) was not intended to provide an accurate method to estimate field metabolic rate (FMR) in large mysticetes; the objective was to measure the dynamic changes in physiology associated with recovery from exercise and show that they are important to consider when estimating FMR. While static averages can provide useful estimates of FMR for a variety of situations, these need to be appropriately selected. For example, we illustrate that it is not possible to use selected average values chosen from excised tissues or resting animals (as in Blix and Folkow, 1995) to provide meaningful estimates of FMR for animals at different activities (i.e. the dolphins in our study). Our study highlights the importance of temporal variation in physiological models: the Blix and Folkow (1995) estimates rely on the assumption that only breathing frequency (fR) changes with activity, while we argue that both the tidal volume (VT) and mixed lung O2 content also vary with activity and recovery from a dive (Ridgway et al., 1969). Including this variation in all three parameters reduces temporal uncertainty in the same conceptual model (see Eqn. 1 in Fahlman et al., 2016)

Anthropogenic Threats to Wild Cetacean Welfare and a Tool to Inform Policy in This Area

Human activities and anthropogenic environmental changes are having a profound effect on biodiversity and the sustainability and health of many populations and species of wild mammals. There has been less attention devoted to the impact of human activities on the welfare of individual wild mammals, although ethical reasoning suggests that the welfare of an individual is important regardless of species abundance or population health. There is growing interest in developing methodologies and frameworks that could be used to obtain an overview of anthropogenic threats to animal welfare. This paper shows the steps taken to develop a functional welfare assessment tool for wild cetaceans (WATWC) via an iterative process involving input from a wide range of experts and stakeholders. Animal welfare is a multidimensional concept, and the WATWC presented made use of the Five Domains model of animal welfare to ensure that all areas of potential welfare impact were considered. A pilot version of the tool was tested and then refined to improve functionality. We demonstrated that the refined version of the WATWC was useful to assess real-world impacts of human activity on Southern Resident killer whales. There was close within-scenario agreement between assessors as well as between-scenario differentiation of overall welfare impact. The current article discusses the challenges raised by assessing welfare in scenarios where objective data on cetacean behavioral and physiological responses are sparse and proposes that the WATWC approach has value in identifying important information gaps and in contributing to policy decisions relating to human impacts on whales, dolphins, and porpoises

Swimming Energy Economy in Bottlenose Dolphins Under Variable Drag Loading

Instrumenting animals with tags contributes additional resistive forces (weight, buoyancy, lift, and drag) that may result in increased energetic costs; however, additional metabolic expense can be moderated by adjusting behavior to maintain power output. We sought to increase hydrodynamic drag for near-surface swimming bottlenose dolphins, to investigate the metabolic effect of instrumentation. In this experiment, we investigate whether (1) metabolic rate increases systematically with hydrodynamic drag loading from tags of different sizes or (2) whether tagged individuals modulate speed, swimming distance, and/or fluking motions under increased drag loading. We detected no significant difference in oxygen consumption rates when four male dolphins performed a repeated swimming task, but measured swimming speeds that were 34% (>1 m s-1) slower in the highest drag condition. To further investigate this observed response, we incrementally decreased and then increased drag in six loading conditions. When drag was reduced, dolphins increased swimming speed (+1.4 m s-1; +45%) and fluking frequency (+0.28 Hz; +16%). As drag was increased, swimming speed (-0.96 m s-1; -23%) and fluking frequency (-14 Hz; 7%) decreased again. Results from computational fluid dynamics simulations indicate that the experimentally observed changes in swimming speed would have maintained the level of external drag forces experienced by the animals. Together, these results indicate that dolphins may adjust swimming speed to modulate the drag force opposing their motion during swimming, adapting their behavior to maintain a level of energy economy during locomotion.Summary Statement: Biologging and tracking tags add drag to study subjects. When wearing tags of different sizes, dolphins changed their swimming paths, speed, and movements to modulate power output and energy consumption

Bottlenose dolphins modify behavior to reduce metabolic effect of tag attachment

Author Posting. © The Author(s), 2014. This is the author's version of the work. It is posted here by permission of The Company of Biologists for personal use, not for redistribution. The definitive version was published in Journal of Experimental Biology 217 (2014): 4229-4236, doi:10.1242/​jeb.108225.Attaching bio-telemetry or -logging devices (‘tags’) to marine animals for research and monitoring adds drag to streamlined bodies, thus affecting posture, swimming gaits and energy balance. These costs have never been measured in free-swimming cetaceans. To examine the effect of drag from a tag on metabolic rate, cost of transport and swimming behavior, four captive male dolphins (Tursiops truncatus) were trained to swim a set course, either non-tagged (n=7) or fitted with a tag (DTAG2; n=12), and surface exclusively in a flow-through respirometer in which oxygen consumption (Graphic) and carbon dioxide production (Graphic; ml kg−1 min−1) rates were measured and respiratory exchange ratio (Graphic/Graphic) was calculated. Tags did not significantly affect individual mass-specific oxygen consumption, physical activity ratios (exercise Graphic/resting Graphic), total or net cost of transport (COT; J m−1 kg−1) or locomotor costs during swimming or two-minute recovery phases. However, individuals swam significantly slower when tagged (by ~11%; mean ± s.d., 3.31±0.35 m s−1) than when non-tagged (3.73±0.41 m s−1). A combined theoretical and computational fluid dynamics model estimating drag forces and power exertion during swimming suggests that drag loading and energy consumption are reduced at lower swimming speeds. Bottlenose dolphins in the specific swimming task in this experiment slowed to the point where the tag yielded no increases in drag or power, while showing no difference in metabolic parameters when instrumented with a DTAG2. These results, and our observations, suggest that animals modify their behavior to maintain metabolic output and energy expenditure when faced with tag-induced drag.This project was funded by the National Oceanographic Partnership Program [National Science Foundation via the Office of Naval Research, N00014-11-1-0113]. J.v.d.H. was supported by a Postgraduate Scholarship from the Natural Sciences and Engineering Research Council of Canada.2015-10-1