feedr and animalnexus.ca: A paired R package and user‐friendly Web application for transforming and visualizing animal movement data from static stations

Radio frequency identification (RFID) provides a simple and inexpensive approach for examining the movements of tagged animals, which can provide information on species behavior and ecology, such as habitat/resource use and social interactions. In addition, tracking animal movements is appealing to naturalists, citizen scientists, and the general public and thus represents a tool for public engagement in science and science education. Although a useful tool, the large amount of data collected using RFID may quickly become overwhelming. Here, we present an R package (feedr) we have developed for loading, transforming, and visualizing time‐stamped, georeferenced data, such as RFID data collected from static logger stations. Using our package, data can be transformed from raw RFID data to visits, presence (regular detections by a logger over time), movements between loggers, displacements, and activity patterns. In addition, we provide several conversion functions to allow users to format data for use in functions from other complementary R packages. Data can also be visualized through static or interactive maps or as animations over time. To increase accessibility, data can be transformed and visualized either through R directly, or through the companion site: http://animalnexus.ca , an online, user‐friendly, R‐based Shiny Web application. This system can be used by professional and citizen scientists alike to view and study animal movements. We have designed this package to be flexible and to be able to handle data collected from other stationary sources (e.g., hair traps, static very high frequency (VHF) telemetry loggers, observations of marked individuals in colonies or staging sites), and we hope this framework will become a meeting point for science, education, and community awareness of the movements of animals. We aim to inspire citizen engagement while simultaneously enabling robust scientific analysis.     

Phylogenomics using formalin‐fixed and 100+ year‐old intractable natural history specimens

Museum specimens provide a wealth of information to biologists, but obtaining genetic data from formalin‐fixed and fluid‐preserved specimens remains challenging. While DNA sequences have been recovered from such specimens, most approaches are time‐consuming and produce low data quality and quantity. Here, we use a modified DNA extraction protocol combined with high‐throughput sequencing to recover DNA from formalin‐fixed and fluid‐preserved snakes that were collected over a century ago and for which little or no modern genetic materials exist in public collections. We successfully extracted DNA and sequenced ultraconserved elements ( = 2318 loci) from 10 fluid‐preserved snakes and included them in a phylogeny with modern samples. This phylogeny demonstrates the general use of such specimens in phylogenomic studies and provides evidence for the placement of enigmatic snakes, such as the rare and never‐before sequenced Indian Xylophis stenorhynchus. Our study emphasizes the relevance of museum collections in modern research and simultaneously provides a protocol that may prove useful for specimens that have been previously intractable for DNA sequencing.     

IgG Fc variant cross-reactivity between human and rhesus macaque FcγRs

Non-human primate (NHP) studies are often an essential component of antibody development efforts before human trials. Because the efficacy or toxicity of candidate antibodies may depend on their interactions with Fcγ receptors (FcγR) and their resulting ability to induce FcγR-mediated effector functions such as antibody-dependent cell-meditated cytotoxicity and phagocytosis (ADCP), the evaluation of human IgG variants with modulated affinity toward human FcγR is becoming more prevalent in both infectious disease and oncology studies in NHP. Reliable translation of these results necessitates analysis of the cross-reactivity of these human Fc variants with NHP FcγR. We report evaluation of the binding affinities of a panel of human IgG subclasses, Fc amino acid point mutants and Fc glycosylation variants against the common allotypes of human and rhesus macaque FcγR by applying a high-throughput array-based surface plasmon resonance platform. The resulting data indicate that amino acid variation present in rhesus FcγRs can result in disrupted, matched, or even increased affinity of IgG Fc variants compared with human FcγR orthologs. These observations emphasize the importance of evaluating species cross-reactivity and developing an understanding of the potential limitations or suitability of representative in vitro and in vivo models before human clinical studies when either efficacy or toxicity may be associated with FcγR engagement.     

Reduced expression of PMCA1 is associated with increased blood pressure with age which is preceded by remodelling of resistance arteries

Hypertension is a well‐established risk factor for adverse cardiovascular events, and older age is a risk factor for the development of hypertension. Genomewide association studies have linked ATP2B1, the gene for the plasma membrane calcium ATPase 1 (PMCA1), to blood pressure (BP) and hypertension. Here, we present the effects of reduction in the expression of PMCA1 on BP and small artery structure and function when combined with advancing age. Heterozygous PMCA1 null mice (PMCA1^Ht) were generated and conscious BP was measured at 6 to 18 months of age. Passive and active properties of isolated small mesenteric arteries were examined by pressure myography. PMCA1^Ht mice exhibited normal BP at 6 and 9 months of age but developed significantly elevated BP when compared to age‐matched wild‐type controls at ≥12 months of age. Decreased lumen diameter, increased wall thickness and increased wall:lumen ratio were observed in small mesenteric arteries from animals 9 months of age and older, indicative of eutrophic remodelling. Increases in mesenteric artery intrinsic tone and global intracellular calcium were evident in animals at both 6 and 18 months of age. Thus, decreased expression of PMCA1 is associated with increased BP when combined with advancing age. Changes in arterial structure precede the elevation of BP. Pathways involving PMCA1 may be a novel target for BP regulation in the elderly.     

Meal Pattern Analysis of Diet‐Induced Obesity in Susceptible and Resistant Rats

Objective: To characterize the meal patterns of free feeding Sprague‐Dawley rats that become obese or resist obesity when chronically fed a high‐fat diet. Research Methods and Procedures: Male Sprague‐Dawley rats (N = 120) were weaned onto a high‐fat diet, and body weight was monitored for 19 weeks. Rats from the upper [diet‐induced obese (DIO)] and lower [diet‐resistant (DR)] deciles for body‐weight gain were selected for study. A cohort of chow‐fed (CF) rats weight‐matched to the DR group was also studied. Food intake was continuously monitored for 7 consecutive days using a BioDAQ food intake monitoring system. Results: DIO rats were obese, hyperphagic, hyperleptinemic, hyperinsulinemic, hyperglycemic, and hypertriglyceridemic relative to the DR and CF rats. The hyperphagia of DIOs was caused by an increase in meal size, not number. CF rats ate more calories than DR rats; however, this was because of an increase in meal number, not size. When expressed as a function of lean mass, CF and DR rats consumed the same amount of calories. The intermeal intervals of DIO and DR rats were similar; both were longer than CF rats. The nocturnal satiety ratio of DIO rats was significantly lower than DR and CF rats. The proportion of calories eaten during the nocturnal period did not differ among groups. Discussion: The hyperphagia of a Sprague‐Dawley rat model of chronic diet‐induced obesity is caused by an increase in meal size, not number. These results are an important step toward understanding the mechanisms underlying differences in feeding behavior of DIO and DR rats.     

Regional vegetation mapping in Australia: a case study in the practical use of statistical modelling

Conservation evaluation of large areas ( > 10 000 km²) in Australia requires detailed mapping of vegetation types. Predicting the original vegetation cover of extensive cleared areas in an explicit, consistent and repeatable manner necessitates the use of statistical modelling. This paper describes an integrated approach to vegetation mapping in a region of New South Wales, Australia. The approach uses separate statistical models for each tree and shrub species to predict the vegetation composition in each grid cell in a geographic information system (GIS). Allocation of these grid cells to communities allows communities that no longer exist in the remaining remnants of woodland to be defined. Examples of use of this information for management are presented. This paper addresses the practical considerations which constrain the way statistical modelling can be used for vegetation mapping in an applied project. Constraints include: (1) data availability (use of sampling to fill gaps in existing data), (2) the effects of cover abundance values, (3) availability of GIS predictors, (4) data management, (5) current generalised additive model methods and (6) prediction methods. Careful attention to the practicality of all components of a vegetation mapping study is essential if modern methods are to be applied in regional studies which must provide functional products for land managers with limited resources, skills and finances at their disposal.     

Xylene monooxygenase, a membrane-spanning non-heme diiron enzyme that hydroxylates hydrocarbons via a substrate radical intermediate

The non-heme diiron enzyme xylene monooxygenase (XylM) has been shown to hydroxylate hydrocarbons via a hydrogen abstraction-carbon radical recombination mechanism (oxygen rebound). Using the radical clock bicyclo[4.1.0]heptane (norcarane) in a whole-cell assay, and observing the ratio of rearranged 3-(hydroxymethyl)cyclohexene and unrearranged 2-norcaranol products, the lifetime of the substrate radical was determined to be approximately 0.2 ns. The wild-type organism Pseudomonas putida mt-2 and two separate Escherichia coli clones expressing xylMA genes gave similar results. One clone produced the Pseudomonas putida mt-2 XylMA hydroxylase and the other produced Sphingomonas yanoikuyae B1 XylMA hydroxylase. Clones were constructed by inserting genes for xylene monooxygenase and xylene monooxygenase reductase downstream from an IPTG-inducible T7 promoter. Mechanistic investigations using whole-cell assays will facilitate more rapid screening of structure-function relationships and the identification of novel oxygenases. This approach should enable the construction of a picture of the key metalloenzymes and the mechanisms they use in selected parts of the global carbon cycle without requiring the isolation of every protein involved.