Discretized and aggregated: modeling dive depth of harbor seals from ordered categorical data with temporal autocorrelation

Summary Ordered categorical data are pervasive in environmental and ecological data, and often arise from constraints that require discretizing a continuous variable into ordered categories. A great deal of data have been collected toward the study of marine mammal dive behavior using satellite depth recorders (SDRs), which often discretize a continuous variable such as depth. Additionally, data storage or transmission constraints may also necessitate the aggregation of data over time intervals of a specified length. The categorization and aggregation create a time series of ordered multicategory counts for each animal, which present challenges in terms of statistical modeling and practical interpretation. We describe an intuitive strategy for modeling such aggregated, ordered categorical data allowing for inference regarding the category probabilities and a measure of central tendency on the original scale of the data (e.g., meters), along with incorporation of temporal correlation and overdispersion. The strategy extends covariate-specific cutpoint models for ordinal data. We demonstrate the method in an analysis of SDR dive-depth data collected on harbor seals in Alaska. The primary goal of the analysis is to assess the relationship of covariates, such as time of day, with number of dives and maximum depth of dives. We also predict missing values and introduce novel graphical summaries of the data and results.     

A method for reconstructing three-dimensional dive profiles of marine mammals using geomagnetic intensity data: results from two lactating Weddell seals

The under-ice behavior of two free-ranging female Weddell seals (Leptonychotes weddellii) was studied using geomagnetic, acceleration and velocity sensors at Big Razorback Island in McMurdo Sound, Antarctica. The seals' body angle and posture were calculated from the acceleration data and the heading from the geomagnetic intensity data. Together with swim speed, the seals' three-dimensional underwater dive path, heading and even posture were reconstructed for each dive. Each instrument was deployed for 2 days, during which time these females made multiple, deep (₞ m) dives, with average maximum depths of 236ᆯ m (n=4) and 244끁 m (n=40). Each seal appeared to choose a particular heading on which to descend. These headings were significantly different between seals and bouts (Watson's U² test, P<0.05). These new instruments and methodologies are shown to provide valuable information on the fine-scale and complex movements of diving animals.     

Palmitate interaction with physiological states of myoglobin

Background

Previous studies have shown that palmitate (PA) can bind specifically and non-specifically to Fe(III) MbCN. The present study has observed PA interaction with physiological states of Fe(II) Mb, and the observations support the hypothesis that Mb may have a potential role in facilitating intracellular fatty acid transport.

Methods

¹H NMR spectra measurements of the Mb signal during PA titration show signal changes consistent with specific and non-specific binding.

Results

Palmitate (PA) interacts differently with physiological states of Mb. Deoxy Mb does not interact specifically or non-specifically with PA, while the carbonmonoxy myoglobin (MbCO) interaction with PA decreases the intensity of selective signals and produces a 0.15 ppm upfield shift of the PA methylene peak. The selective signal change upon PA titration provides a basis to determine an apparent PA binding constant, which serves to create a model comparing the competitive PA binding and facilitated fatty acid transport of Mb and fatty acid binding protein (FABP).

Conclusions

Given contrasting PA interaction of ligated vs. unligated Mb, the cellular fatty acid binding protein (FABP) and Mb concentration in the cell, the reported cellular diffusion coefficients, the PA dissociation constants from ligated Mb and FABP, a fatty acid flux model suggests that Mb can compete with FABP transporting cellular fatty acid.

General significance

Under oxygenated conditions and continuous energy demand, Mb dependent fatty acid transport could influence the cell's preference for carbohydrate or fatty acid as a fuel source and regulate fatty acid metabolism.     

Body size and skeletal muscle myoglobin of cetaceans: adaptations for maximizing dive duration

Cetaceans exhibit an exceptionally wide range of body mass that influence both the capacities for oxygen storage and utilization; the balance of these factors is important for defining dive limits. Furthermore, myoglobin content is a key oxygen store in the muscle as it is many times higher in marine mammals than terrestrial mammals. Yet little consideration has been given to the effects of myoglobin content or body mass on cetacean dive capacity. To determine the importance of myoglobin content and body mass on cetacean diving performance, we measured myoglobin content of the longissimus dorsi for ten odontocete (toothed whales) and one mysticete (baleen whales) species ranging in body mass from 70 to 80000 kg. The results showed that myoglobin content in cetaceans ranged from 1.81 to 5.78 g (100 g wet muscle)(-1). Myoglobin content and body mass were both positively and significantly correlated to maximum dive duration in odontocetes; this differed from the relationship for mysticetes. Overall, the combined effects of body mass and myoglobin content accounts for 50% of the variation in cetacean diving performance. While independent analysis of the odontocetes showed that body mass and myoglobin content accounts for 83% of the variation in odontocete dive capacity.     

Foraging a new trail with northern fur seals (Callorhinus ursinus): Lactating seals from islands with contrasting population dynamics have different foraging strategies,and forage at scales previously unrecognized by GPS interpolated dive data

We reconstructed the foraging tracks of lactating northern fur seals (Callorhinus ursinus) from two eastern Bering Sea islands (St. Paul Island and Bogoslof Island) using linear interpolation between GPS locations recorded at a maximum of four times per hour and compared it to tri‐axial accelerometer and magnetometer data collected at 16 Hz to reconstruct pseudotracks between the GPS fixes. The high‐resolution data revealed distances swum per foraging trip were much greater than the distances calculated using linearly interpolated GPS tracks (1.5 times further for St. Paul fur seals and 1.9 times further for Bogoslof fur seals). First passage time metrics calculated from the high resolution data revealed that the optimal scale at which the seals searched for prey was 500 m (radius of circle searched) for fur seals from St. Paul Island that went off‐shelf, and 50 m for fur seals from Bogoslof Island and surprisingly, 50 m for fur seals from St. Paul that foraged on‐shelf. These area‐restricted search scales were significantly smaller than those calculated from GPS data alone (12 km for St. Paul and 6 km for Bogoslof) indicating that higher resolution movement data can reveal novel information about foraging behaviors that have important ecological implications.     

Aerobic and anaerobic enzyme assays in Southern California Rockfish: Proxies for physiological and ecological data

Rockfish are commercially and recreationally important, yet due to the depths they inhabit (3-500 m), little is known about their ecology. The present study examined 19 different species of Sebastes from the Southern California Bight over four seasons (late summer, fall, early winter, and spring) using metabolic enzyme assays. Enzymes used were lactate dehydrogenase (LDH), malate dehydrogenase (MDH), pyruvate kinase (PK), and citrate synthase (CS). Muscle proximate composition data (protein, water and lipid content) were also used to help interpret the enzyme data. Enzyme activity was lowest in the summer when expressed as activity per gram wet weight but when it was expressed per gram protein the trend was reversed. The rockfish have the highest protein as a percentage of wet mass (P%WM) in the spring, right before the upwelling period begins and the lowest P%WM in late summer after the peak of upwelling. Lipid content also showed a seasonal change with the highest lipid content in the late summer and the lowest in winter. The enzyme profiles have been broken into three groups which fit with their locomotory habit and their prey selection. These findings show that enzymes and muscle proximate composition can be used along with limited observational data on related species to deduce condition, seasonal impacts and ecologically important life habits in species that are difficult to observe and monitor.     

Development of the aerobic dive limit and muscular efficiency in northern fur seals (Callorhinus ursinus)

Northern fur seal (Callorhinus ursinus; NFS) populations have been declining, perhaps due to limited foraging ability of pups. Because a marine mammal’s proficiency at exploiting underwater prey resources is based on the ability to store large amounts of oxygen (O₂) and to utilize these reserves efficiently, this study was designed to determine if NFS pups had lower blood, muscle, and total body O₂ stores than adults. Pups (<1-month old) had a calculated aerobic dive limit only ~40% of adult females due to lower blood and, to a much greater extent, muscle O₂ stores. Development of the Pectoralis (Pec) and Longissimus dorsi (LD) skeletal muscles was further examined by determining their myosin heavy chain (MHC) composition and enzyme activities. In all animals, the slow MHC I and fast-twitch IIA proteins typical of oxidative fiber types were dominant, but adult muscles contained more (Pec ~50%; LD ~250% higher) fast-twitch MHC IID/X protein characteristic of glycolytic muscle fibers, than pup muscles. This suggests that adults have greater ability to generate muscle power rapidly and/or under anaerobic conditions. Pup muscles also had lower aerobic and anaerobic ATP production potential, as indicated by lower metabolically scaled citrate synthase, β-hydroxyacyl CoA dehydrogenase, and lactate dehydrogenase activities (all P values ≤0.001). In combination, these findings indicate that pups are biochemically and physiologically limited in their diving capabilities relative to adults. This may contribute to lower NFS first year survival.     

Characterization of postdive recovery using sound recordings and its relationship to dive duration,exertion, and foraging effort of southern elephant seals (Mirounga leonina)

It is notoriously difficult to measure physiological parameters in cryptic free‐ranging marine mammals. However, it is critical to understand how marine mammals manage their energy expenditure and their diving behavior in environments where the predation risks are low and where survival is mainly linked to capacities to maintain physiological homeostasis and energy budget balance. Elephant seals are top marine predators that dive deeply and continuously when at sea. Using acoustic recorders deployed on two postbreeding southern elephant seals (SES) females, we developed methods to automatically estimate breathing frequency at the surface. Using this method, we found that seals took successive identical breaths at high frequency (0.29 Hz) when recovering at the surface and that breath count was strongly related to postdive surfacing time. In addition, dive depth was the main factor explaining surfacing time through the effects of dive duration and total underwater swimming effort exerted. Finally, we found that recovery does not only occur over one dive timescale, but over a multidive time scale for one individual. The way these predators manage their recovery will determine how they respond to the change in oceanic water column structure in the future.     

Structural dynamics of myoglobin: spectroscopic and structural characterization of ligand docking sites in myoglobin mutant L29W

We have studied CO binding to the heme and CO migration among protein internal cavities after photodissociation in sperm whale carbonmonoxy myoglobin (MbCO) mutant L29W using Fourier transform infrared (FTIR) spectroscopy combined with temperature derivative spectroscopy (TDS) and kinetic experiments at cryogenic temperatures. Photoproduct intermediates, characterized by CO at particular locations in the protein, were selectively enhanced by applying special laser illumination protocols. These studies were performed on the L29W mutant protein and a series of double mutants constructed so that bulky amino acid side chains block passageways between cavities or fill these sites. Binding of xenon was also employed as an alternative means of occluding cavities. All mutants exhibit two conformations, A(I) and A(II), with distinctly different photoproduct states and ligand binding properties. These differences arise mainly from different positions of the W29 and H64 side chains in the distal heme pocket [Ostermann, A., et al. (2000) Nature 404, 205-208]. The detailed knowledge of the interplay between protein structure, protein dynamics, and ligand migration at cryogenic temperatures allowed us to develop a dynamic model that explains the slow CO and O(2) bimolecular association observed after flash photolysis at ambient temperature.     

Assessing the distribution of the Argentine ant using physiological data

To address the lack of physiological approaches in current models assessing the potential distribution of the Argentine ant, we used data on brood development from distinct sources to evaluate a series of degree-day models for Catalonia (NE Iberian Peninsula), and data on the brood survival and oviposition rates to develop a worker production model. The degree-day model generated using data from Newell and Barber (1913) and Benois (1973) indicated that the number of degree-days required for the complete development from egg to adult worker was 445.4 degree-days above a threshold of 15.9 °C, while the model calibrated using data from Abril et al. (2008, in press) suggested 599.5 degree-days above 18.4 °C. Comparisons between the degree-day model predictions and the currently known distribution of the Argentine ant suggested that the one generated using data from Newell and Barber (1913) and Benois (1973) overestimated the presence of the species, while the one calibrated using data from Abril et al. (2008; in press) underestimated it. On the other hand, the predicted daily net production of Argentine ant workers generated by the worker production model predicted more accurately the distribution of the Argentine ant than the degree-day models. Our results show the utility of incorporating physiological data in models to assess the distribution limits of the Argentine ant, which up to date have taken little account of the physiological needs of the species in terms of its establishment and dispersion in its introduced ranges.     

Morphological and physiological characteristics of transgenic cherry tomato mutant with HBsAg gene

HBsAg gene was previously introduced into cherry tomato (Lycopersicum esculentum var. cerasiforme) by Agrobacterium-mediated transformation. To investigate the side effect of HBsAg gene in cherry tomato, we analyzed morphological and physiological characteristics of the transgenic mutant N244. The process was performed under field conditions. The results suggested that the mutant N244 exhibited morphological, cytological and physiological variation. First of all, compared with the wild plants NK, N244 had fleshy and dark green leaves, the fewer notches of leaf edge, more adventitious roots and barren seeds. Moreover, the chromosome of N244 were found to be triploid (n = 36) by flow cytometric analysis. Furthermore, N244 has obvious physiological alterations, as compared to NK. It was speculated that transformation of the genes probably led to ploidy variation, and further caused phenotype and physiological changes of plants. Our study will reveal side effects of the mutants, and promote cultivation of transgenic plants in the field.     

Thermal responses of mutant enzymes and temperature limits to growth

Summary The half-lives of fifty-two mutant forms of -galactosidase, in which serine had been substituted for the original amino-acid, were measured at 57°C. Sixty percent of the mutant enzymes had less than half the stability of the normal enzyme at high temperature but none had greater sensitivity to low temperature. A sample of these thermolabile enzymes showed unaltered activation energy. Enzymes with altered substrate affinity generally had reduced apparent heats of activation, decreased heats and entropies of association, and were thus relatively less sensitive to temperature change.The intracellular behaviour of thermolabile enzymes was examined by showing that substrate hydrolysis is the limiting step in lactose utilization, that the enzyme-substrate complex is more stable than the free enzyme and that binding of the enzyme to structures within the cell increases stability and lowers affinity. Amongst enzymes having half-lives less than about seven minutes at 47.75°C, there is a close relationship between enzyme lability and diminished growth rate on lactose at 44°C. The effect of mutation on the thermal behaviour of multi-enzyme systems and the relation of enzyme thermolability to temperature-induced growth deficiencies and temperature-dependent heterosis are discussed.     

Seasonal changes in the oxygen storage capacity and aerobic dive limits of the muskrat (Ondatra zibethicus)

Summary The oxygen storage capacity and partitioning of body oxygen reserves were compared in summer-and winter-acclimatized muskrats (Ondatra zibethicus). Blood volume, blood oxygen capacity, and skeletal muscle myoglobin content were higher in December than in July (P<0.02). Total lung capacity increased only slightly in winter (P>0.05). The oxygen storage capacity of a diving muskrat was calculated at 25.2 ml O₂ STPD · kg^-1 in July, compared to 35.7 ml O₂ STPD · kg^-1 in December. Blood comprised the major storage compartment in both seasons, accounting for 57% and 65% of the total oxygen stores in summer and winter, respectively. Based on available oxygen stores and previous estimates of the cost of diving, the aerobic dive limit (ADL) increased from 40.9 s in July to 57.9 s in December. Concurrent behavioral studies suggested that most voluntary diving by muskrats is aerobic. However, the proportion of dives exceeding the calculated ADL of these animals was shown to vary with the context of the dive. Only 3.5% of all dives initiated by muskrats floating in the water exceeded their estimated ADL. Provision of a dry resting site and access to a submerged food source increased this proportion to 18–61%, depending on the underwater distance that foraging muskrats were required to swim. Serial dives exceeding the estimated ADL were not accompanied by extended postdive recovery periods.Abbreviations ADL acrobic dive limit - Hb hemoglobin - Hct hematocrit - Mb myoglobin - PaO₂ arterial O₂ tension - STPD standard temperature and pressure, dry     

Characterization of an alpine tree line using airborne LiDAR data and physiological modeling

Understanding what environmental drivers control the position of the alpine tree line is important for refining our understanding of plant stress and tree development, as well as for climate change studies. However, monitoring the location of the tree line position and potential movement is difficult due to cost and technical challenges, as well as a lack of a clear boundary. Advanced remote sensing technologies such as Light Detection and Ranging (LiDAR) offer significant potential to map short individual tree crowns within the transition zone despite the lack of predictive capacity. Process‐based forest growth models offer a complementary approach by quantifying the environmental stresses trees experience at the tree line, allowing transition zones to be defined and ultimately mapped. In this study, we investigate the role remote sensing and physiological, ecosystem‐based modeling can play in the delineation of the alpine tree line. To do so, we utilize airborne LiDAR data to map tree height and stand density across a series of altitudinal gradients from below to above the tree line within the Swiss National Park (SNP), Switzerland. We then utilize a simple process‐based model to assess the importance of seasonal variations on four climatically related variables that impose non‐linear constraints on photosynthesis. Our results indicate that all methods predict the tree line to within a 50 m altitudinal zone and indicate that aspect is not a driver of significant variations in tree line position in the region. Tree cover, rather than tree height is the main discriminator of the tree line at higher elevations. Temperatures in fall and spring are responsible for the major differences along altitudinal zones, however, changes in evaporative demand also control plant growth at lower altitudes. Our results indicate that the two methods provide complementary information on tree line location and, when combined, provide additional insights into potentially endangered forest/grassland transition zones.