Simultaneous estimation of the temporal and spatial extent of animal migration using step lengths and turning angles.

BACKGROUND: Animals of many different species, trophic levels, and life history strategies migrate, and the improvement of animal tracking technology allows ecologists to collect increasing amounts of detailed data on these movements. Understanding when animals migrate is important for managing their populations, but is still difficult despite modelling advancements. METHODS: We designed a model that parametrically estimates the timing of migration from animal tracking data. Our model identifies the beginning and end of migratory movements as signaled by change-points in step length and turning angle distributions. To this end, we can also use the model to estimate how an animal's movement changes when it begins migrating. In addition to a thorough simulation analysis, we tested our model on three datasets: migratory ferruginous hawks (Buteo regalis) in the Great Plains, barren-ground caribou (Rangifer tarandus groenlandicus) in northern Canada, and non-migratory brown bears (Ursus arctos) from the Canadian Arctic. RESULTS: Our simulation analysis suggests that our model is most useful for datasets where an increase in movement speed or directional autocorrelation is clearly detectable. We estimated the beginning and end of migration in caribou and hawks to the nearest day, while confirming a lack of migratory behaviour in the brown bears. In addition to estimating when caribou and ferruginous hawks migrated, our model also identified differences in how they migrated; ferruginous hawks achieved efficient migrations by drastically increasing their movement rates while caribou migration was achieved through significant increases in directional persistence. CONCLUSIONS: Our approach is applicable to many animal movement studies and includes parameters that can facilitate comparison between different species or datasets. We hope that rigorous assessment of migration metrics will aid understanding of both how and why animals move.

Separation of protactinium from uranium-niobium alloys for 231Pa-235U radiochronometry in nuclear forensic investigations.

The isolation and purification of protactinium from uranium materials is essential for 231Pa-235U radiochronometry, but separating Pa from uranium-niobium alloys, a common material in the nuclear fuel cycle, is challenging due to the chemical similarity of Pa and Nb. Here we present three resin chromatography separation techniques for isolating Pa from U and Nb which were independently developed by three different laboratories through ad hoc adaptations of standard operating procedures. Our results underscore the need for and value of purification methods suitable for a diversity of uranium-based materials to ensure the operational readiness of nuclear forensics laboratories. Supplementary Information: The online version contains supplementary material available at 10.1007/s10967-023-08928-y.

Time-dependent memory and individual variation in Arctic brown bears (Ursus arctos).

BACKGROUND: Animal movement modelling provides unique insight about how animals perceive their landscape and how this perception may influence space use. When coupled with data describing an animal's environment, ecologists can fit statistical models to location data to describe how spatial memory informs movement. METHODS: We performed such an analysis on a population of brown bears (Ursus arctos) in the Canadian Arctic using a model incorporating time-dependent spatial memory patterns. Brown bear populations in the Arctic lie on the periphery of the species' range, and as a result endure harsh environmental conditions. In this kind of environment, effective use of memory to inform movement strategies could spell the difference between survival and mortality. RESULTS: The model we fit tests four alternate hypotheses (some incorporating memory; some not) against each other, and we found a high degree of individual variation in how brown bears used memory. We found that 71% (15 of 21) of the bears used complex, time-dependent spatial memory to inform their movement decisions. CONCLUSIONS: These results, coupled with existing knowledge on individual variation in the population, highlight the diversity of foraging strategies for Arctic brown bears while also displaying the inference that can be drawn from this innovative movement model.

Assessing the nutritional consequences of switching foraging behavior in wood bison.

Diet is one of the most common traits used to organize species of animals into niches. For ruminant herbivores, the breadth and uniqueness of their dietary niche are placed on a spectrum from browsers that consume woody (i.e., browse) and herbaceous (i.e., forbs) plants, to grazers with graminoid-rich diets. However, seasonal changes in plant availability and quality can lead to switching of their dietary niche, even within species. In this study, we examined whether a population of wood bison (Bison bison athabascae) in northeast Alberta, Canada, seasonally switched their foraging behavior, and if so, whether this was associated with changes in nutrient acquisition. We hypothesized that bison should switch foraging behaviors from grazing in the winter when standing, dead graminoids are the only foliar plants readily available to browsing during spring and summer as nutritious and digestible foliar parts of browse and forbs become available. If bison are switching foraging strategy to maximize protein consumption, then there should be a corresponding shift in the nutritional niche. Alternatively, if bison are eating different plants, but consuming similar amounts of nutrients, then bison are switching their dietary niche to maintain a particular nutrient composition. We found wood bison were grazers in the winter and spring, but switch to a browsing during summer. However, only winter nutrient consumption of consumed plants differed significantly among seasons. Between spring and summer, bison maintained a specific nutritional composition in their diet despite compositional differences in the consumed plants. Our evidence suggests that bison are selecting plants to maintain a target macronutrient composition. We posit that herbivore's can and will switch their dietary niche to maintain a target nutrient composition.

Automated algorithm for CBCT-based dose calculations of prostate radiotherapy with bilateral hip prostheses.

OBJECTIVE: Cone beam CT (CBCT) images contain more scatter than a conventional CT image and therefore provide inaccurate Hounsfield units (HUs). Consequently, CBCT images cannot be used directly for radiotherapy dose calculation. The aim of this study is to enable dose calculations to be performed with the use of CBCT images taken during radiotherapy and evaluate the necessity of replanning. METHODS: A patient with prostate cancer with bilateral metallic prosthetic hip replacements was imaged using both CT and CBCT. The multilevel threshold (MLT) algorithm was used to categorize pixel values in the CBCT images into segments of homogeneous HU. The variation in HU with position in the CBCT images was taken into consideration. This segmentation method relies on the operator dividing the CBCT data into a set of volumes where the variation in the relationship between pixel values and HUs is small. An automated MLT algorithm was developed to reduce the operator time associated with the process. An intensity-modulated radiation therapy plan was generated from CT images of the patient. The plan was then copied to the segmented CBCT (sCBCT) data sets with identical settings, and the doses were recalculated and compared. RESULTS: Gamma evaluation showed that the percentage of points in the rectum with γ < 1 (3%/3 mm) were 98.7% and 97.7% in the sCBCT using MLT and the automated MLT algorithms, respectively. Compared with the planning CT (pCT) plan, the MLT algorithm showed -0.46% dose difference with 8 h operator time while the automated MLT algorithm showed -1.3%, which are both considered to be clinically acceptable, when using collapsed cone algorithm. CONCLUSION: The segmentation of CBCT images using the method in this study can be used for dose calculation. For a patient with prostate cancer with bilateral hip prostheses and the associated issues with CT imaging, the MLT algorithms achieved a sufficient dose calculation accuracy that is clinically acceptable. The automated MLT algorithm reduced the operator time associated with implementing the MLT algorithm to achieve clinically acceptable accuracy. This saved time makes the automated MLT algorithm superior and easier to implement in the clinical setting. ADVANCES IN KNOWLEDGE: The MLT algorithm has been extended to the complex example of a patient with bilateral hip prostheses, which with the introduction of automation is feasible for use in adaptive radiotherapy, as an alternative to obtaining a new pCT and reoutlining the structures.

Poor health is associated with use of anthropogenic resources in an urban carnivore.

Rates of encounters between humans and wildlife are increasing in cities around the world, especially when wildlife overlap with people in time, space and resources. Coyotes (Canis latrans) can make use of anthropogenic resources and reported rates of conflict have increased in cities across North America. This increase may be linked to individual differences in the use of human food and developed areas. We compared the relationships between coyote age, sex or health and the use of anthropogenic resources, which we defined as using developed areas over large home ranges, being active during the day, and consuming anthropogenic food. To do so, we applied GPS collars to 19 coyotes and sampled hair for stable isotope analysis. Eleven coyotes appeared to be healthy and eight were visibly infested with sarcoptic mange (Sarcoptes scabiei), a mite that causes hair loss. Diseased coyotes used more developed areas, had larger monthly home ranges, were more active during the day, and assimilated less protein than coyotes that appeared to be healthy. We speculate that anthropogenic food provides a low-quality but easily accessible food source for diseased coyotes, which in turn may increase reliance on it and other anthropogenic resources to promote encounters with people.

Mating-related behaviour of grizzly bears inhabiting marginal habitat at the periphery of their North American range.

In comparison to core populations, peripheral populations have low density and recruitment, and are subject to different selective pressures, such as environmental conditions, food type and availability, predation, disease, etc., which may result in behavioural modifications to mating. We test the roam-to-mate hypothesis for a peripheral population of grizzly bears (Ursus arctos) at the northern extent of their North American range, in Canada's Arctic. If bears are roaming-to-mate, we predicted greater range size and daily displacement, and more linear movements for receptive animals during the mating period compared to post-mating. In contrast to our predictions, we found that in general range size and displacement increased from mating to post-mating regardless of reproductive status. When considered across both periods, females with cubs-of-the-year had smaller range use metrics than other reproductive groups, which we attribute to a counter-strategy against sexually selected infanticide and the reduced mobility of cubs. Linearity of movements remained near zero during both periods across all groups, suggesting tortuous movements more characteristic of foraging than of mate-searching. We suggest that for this population, finding quality habitat takes precedence over mate-searching in this marginal Arctic landscape. Alternatively, a more monogamous mating system and sequestering behaviour may have obscured movement differences between the two periods. The behavioural differences in mating that we observed from what is typical of core populations may reflect local adaptation to marginal conditions and could benefit the species in the face of ongoing environmental change.

Home range size variation in female arctic grizzly bears relative to reproductive status and resource availability.

The area traversed in pursuit of resources defines the size of an animal's home range. For females, the home range is presumed to be a function of forage availability. However, the presence of offspring may also influence home range size due to reduced mobility, increased nutritional need, and behavioral adaptations of mothers to increase offspring survival. Here, we examine the relationship between resource use and variation in home range size for female barren-ground grizzly bears (Ursus arctos) of the Mackenzie Delta region in Arctic Canada. We develop methods to test hypotheses of home range size that address selection of cover where cover heterogeneity is low, using generalized linear mixed-effects models and an information-theoretic approach. We found that the reproductive status of female grizzlies affected home range size but individually-based spatial availability of highly selected cover in spring and early summer was a stronger correlate. If these preferred covers in spring and early summer, a period of low resource availability for grizzly bears following den-emergence, were patchy and highly dispersed, females travelled farther regardless of the presence or absence of offspring. Increased movement to preferred covers, however, may result in greater risk to the individual or family.

Capturing chloroplast variation for molecular ecology studies: a simple next generation sequencing approach applied to a rainforest tree.

BACKGROUND: With high quantity and quality data production and low cost, next generation sequencing has the potential to provide new opportunities for plant phylogeographic studies on single and multiple species. Here we present an approach for in silicio chloroplast DNA assembly and single nucleotide polymorphism detection from short-read shotgun sequencing. The approach is simple and effective and can be implemented using standard bioinformatic tools. RESULTS: The chloroplast genome of Toona ciliata (Meliaceae), 159,514 base pairs long, was assembled from shotgun sequencing on the Illumina platform using de novo assembly of contigs. To evaluate its practicality, value and quality, we compared the short read assembly with an assembly completed using 454 data obtained after chloroplast DNA isolation. Sanger sequence verifications indicated that the Illumina dataset outperformed the longer read 454 data. Pooling of several individuals during preparation of the shotgun library enabled detection of informative chloroplast SNP markers. Following validation, we used the identified SNPs for a preliminary phylogeographic study of T. ciliata in Australia and to confirm low diversity across the distribution. CONCLUSIONS: Our approach provides a simple method for construction of whole chloroplast genomes from shotgun sequencing of whole genomic DNA using short-read data and no available closely related reference genome (e.g. from the same species or genus). The high coverage of Illumina sequence data also renders this method appropriate for multiplexing and SNP discovery and therefore a useful approach for landscape level studies of evolutionary ecology.

Chloroplast genome sequences from total DNA for plant identification.

Chloroplast DNA sequence data are a versatile tool for plant identification or barcoding and establishing genetic relationships among plant species. Different chloroplast loci have been utilized for use at close and distant evolutionary distances in plants, and no single locus has been identified that can distinguish between all plant species. Advances in DNA sequencing technology are providing new cost-effective options for genome comparisons on a much larger scale. Universal PCR amplification of chloroplast sequences or isolation of pure chloroplast fractions, however, are non-trivial. We now propose the analysis of chloroplast genome sequences from massively parallel sequencing (MPS) of total DNA as a simple and cost-effective option for plant barcoding, and analysis of plant relationships to guide gene discovery for biotechnology. We present chloroplast genome sequences of five grass species derived from MPS of total DNA. These data accurately established the phylogenetic relationships between the species, correcting an apparent error in the published rice sequence. The chloroplast genome may be the elusive single-locus DNA barcode for plants.

Fast carnivores and slow herbivores: differential foraging strategies among grizzly bears in the Canadian Arctic.

Categorizing animal populations by diet can mask important intrapopulation variation, which is crucial to understanding a species' trophic niche width. To test hypotheses related to intrapopulation variation in foraging or the presence of diet specialization, we conducted stable isotope analysis (δ(13)C, δ(15)N) on hair and claw samples from 51 grizzly bears (Ursus arctos) collected from 2003 to 2006 in the Mackenzie Delta region of the Canadian Arctic. We examined within-population differences in the foraging patterns of males and females and the relationship between trophic position (derived from δ(15)N measurements) and individual movement. The range of δ(15)N values in hair and claw (2.0-11.0‰) suggested a wide niche width and cluster analyses indicated the presence of three foraging groups within the population, ranging from near-complete herbivory to near-complete carnivory. We found no linear relationship between home range size and trophic position when the data were continuous or when grouped by foraging behavior. However, the movement rate of females increased linearly with trophic position. We used multisource dual-isotope mixing models to determine the relative contributions of seven prey sources within each foraging group for both males and females. The mean bear dietary endpoint across all foraging groups for each sex fell toward the center of the mixing polygon, which suggested relatively well-mixed diets. The primary dietary difference across foraging groups was the proportional contribution of herbaceous foods, which decreased for both males and females from 42-76 to 0-27% and 62-81 to 0-44%, respectively. Grizzlies of the Mackenzie Delta live in extremely harsh conditions and identifying within-population diet specialization has improved our understanding of varying habitat requirements within the population.

Lack of functional expression of NMDA receptors in PC12 cells.

PC12 cells are an established model for studying the role of N-methyl-d-aspartate (NMDA) receptors in excitotoxicity and function as multimeric assemblies of NR1 with at least one NR2(A-D) subunit. We examined NR1 splice variant and NR2 subunit expression in four PC12 cell-lines (ATCC, WEHI, Ordway and Flinders), correlated mRNA expression with protein expression, and used patch-clamp recordings to test functionality. PCR indicated strong expression of the NR1 splice variants NR1-2a and NR1-4a in all cell-lines, with the remainder weakly detected or absent. Real-time PCR showed variable levels of NR1 mRNA expression (all splice variants) between cell-lines and a significant increase in response to nerve growth factor in the WEHI and Ordway lines (NGF: 50ng/ml, 2.1- and 13.4-fold increases, respectively, P< or =0.05). mRNA for NR2A or NR2B was not detected in any PC12 cell-line. NR2C mRNA expression varied between lines and increased after NGF treatment (approximately 4-fold increase in WEHI and Ordway lines, P< or =0.05). In the Ordway line, NR2D mRNA was seen only after NGF treatment. Immunohistochemistry confirmed protein expression for NR1, NR2C and NR2D, and while fluorescence intensity changes in response to NGF paralleled mRNA responses, the degree of increase was of reduced magnitude. Whole-cell patch-clamping of NGF treated cells failed to detect functional NMDA receptors in any of the cell-lines. Our study demonstrates that in contrast to neurons from the CNS, PC12 cells do not express a normal complement of NMDA receptor-subunits, and this may be one factor limiting functional responses to NMDA/glutamate and consequently the use of PC12 cells as a neuronal model.

Unique levels of expression of N-methyl-D-aspartate receptor subunits and neuronal nitric oxide synthase in the rostral ventrolateral medulla of the spontaneously hypertensive rat.

The rostral ventrolateral medulla (RVLM) is the major brainstem region contributing to sympathetic control of blood pressure. We have compared the expression of N-methyl-d-aspartate (NMDA) receptor subunits (NR1, NR2A-D), NR1 splice variants (NR1-1a/1b, -2a/2b, -3a/3b, -4a/4b), and the neuronal and inducible isoforms of NO synthase (nNOS and iNOS) in the RVLM of Wistar Kyoto (WKY) and spontaneously hypertensive rats (SHR), based on the hypothesis that altered NMDA receptor make-up or altered expression of endogenous NO may be associated with the increase in sympathetic output described from this site in hypertension. Total RNA was extracted and reverse transcribed from the RVLM of mature male WKY and SHR (16-23 weeks). Conventional polymerase chain reaction (PCR) indicated that only the NR1 splice variants NR1-2a, NR1-2b, NR1-4a and NR1-4b were expressed in the RVLM of either species. Quantitative real-time PCR indicated that for both strains of rat, mRNA for the NR1 subunit (all splice variants) was the most abundant (16.5-fold greater, P< or =0.05, relative to the NR2A subunit). Amongst the NR2A-D subunits, NR2C was the most abundant (7- and 1.7-fold greater relative to the NR2A subunit, P< or =0.05, WKY and SHR, respectively). Relative to WKY, mRNA levels for the NR2C and NR2D subunits in the SHR RVLM were significantly lower (0.3- and 0.25-fold less, P< or =0.05), while nNOS was significantly higher (1.76-fold greater, P< or =0.05). This was confirmed immunohistochemically for nNOS expression. These results demonstrate differential expression levels of NMDA receptor subunits and NOS isoforms in the RVLM region of SHR when compared to WKY rats.