Eastern Canada Flocks: images and manually annotated bird positions.

The Eastern Canada (ECA) Flocks data set consists of manually annotated images from the Common Eider (COEI, Somateria mollissima) Winter Survey and the Greater Snow Geese (GSGO, Anser caerulescens atlanticus) Spring Survey. The images were taken in eastern Canada using fixed-wing aircraft and manually annotated with ImageJ's Cell counter plugins. We selected and annotated the ECA Flocks images in order to test the precision of the CountEm flock size estimation method. ECA Flocks includes 179 COEI and 99 GSGO single flock images. We cut each image manually to a rectangle that excluded large parts of the image with no birds. Both versions (original and cut) of each image are available in the data set. We manually annotated 637,555 (124,309 COEI and 514,235 GSGO) bird positions in the cut images from both surveys. Each bird has an associated "Type," which refers to species and/or sex. Sex identification was only possible for adult common eiders, because females and immature males are brown birds, whereas adult males have mainly white plumage. In the COEI images 64,484 males and 58,029 females, as well as 1,796 birds of other species, were identified. In the GSGO images 504,891 Snow Geese and 9,344 birds of other species were labeled. A .csv file including all annotated bird positions and types is available for each image. The COEI and GSGO photos of the ECA Flocks data set were taken in the years 2006 and 2018 and 2016-2018, respectively. We selected these photos in order to include images with different quality and resolution. COEI and GSGO flock sizes range from 6 to 4,154 and from 43 to 36,241 respectively. There is high variability in light conditions, backgrounds, and number and spatial arrangement of birds across the images. The data set is therefore potentially useful to test the precision of methods for analyzing imagery to estimate the abundance of animals by directly detecting, identifying, and counting individuals. We release these data into the public domain under a Creative Commons Zero license waiver. When you use the data in your publication, cite this data paper. Should ECA Flocks be a major part of the data analyzed in your study, you should consider inviting the ECA Flocks originators as collaborators. If you plan to use the ECA Flocks data set, we request that you contact the ECA Flocks core team to learn whether updates are available, and whether similar analyses are already ongoing.

Spatially explicit network analysis reveals multi-species annual cycle movement patterns of sea ducks.

Conservation of long-distance migratory species poses unique challenges. Migratory connectivity, that is, the extent to which groupings of individuals at breeding sites are maintained in wintering areas, is frequently used to evaluate population structure and assess use of key habitat areas. However, for species with complex or variable annual cycle movements, this traditional bimodal framework of migratory connectivity may be overly simplistic. Like many other waterfowl, sea ducks often travel to specific pre- and post-breeding sites outside their nesting and wintering areas to prepare for migration by feeding extensively and, in some cases, molting their flight feathers. These additional migrations may play a key role in population structure, but are not included in traditional models of migratory connectivity. Network analysis, which applies graph theory to assess linkages between discrete locations or entities, offers a powerful tool for quantitatively assessing the contributions of different sites used throughout the annual cycle to complex spatial networks. We collected satellite telemetry data on annual cycle movements of 672 individual sea ducks of five species from throughout eastern North America and the Great Lakes. From these data, we constructed a multi-species network model of migratory patterns and site use over the course of breeding, molting, wintering, and migratory staging. Our results highlight inter- and intra-specific differences in the patterns and complexity of annual cycle movement patterns, including the central importance of staging and molting sites in James Bay, the St. Lawrence River, and southern New England to multi-species annual cycle habitat linkages, and highlight the value of Long-tailed Ducks (Calengula haemalis) as an umbrella species to represent the movement patterns of multiple sea duck species. We also discuss potential applications of network migration models to conservation prioritization, identification of population units, and integrating different data streams.

INTRANASAL ADMINISTRATION OF MIDAZOLAM HYDROCHLORIDE IMPROVES SURVIVAL IN FEMALE SURF SCOTERS (MELANITTA PERSPICILLATA) SURGICALLY IMPLANTED WITH INTRACOELOMIC TRANSMITTERS.

The intracoelomic implantation of satellite transmitters is associated with lower survival in surf scoters (Melanitta perspicillata) compared with other species of diving ducks, potentially due to physiologic alterations following physical exertion and stress caused by handling and confinement. The effect of intranasal administration of midazolam hydrochloride on survival of surf scoters surgically implanted with intracelomic transmitters was evaluated. Shortly after their capture in Forestville (QC, Canada) in the fall of 2013, 26 randomly selected adult female surf scoters were administered midazolam hydrochloride (4.6-5.9 mg/kg) intranasally. The same volume of saline (1 mL) was given to another 26 adult female surf scoters as a control group. All birds were surgically implanted with an intracoelomic transmitter equipped with a percutaneous antenna. Transmitters were programmed to transmit 2 hr each day for 30 days after implantation, and mortality was estimated for each group using the telemetry data. The association between the administration of midazolam and survival was assessed while controlling for other factors such as body mass, transmitter-mass-to-body-mass ratio, hematocrit, total solids, and duration of surgery, anesthesia, and confinement. The odds of presumed death in the saline group were 5.3 times higher than in the midazolam group (95% confidence interval: 1.7, 19.0; P = 0.004). The presumed mortality at 30 days for the midazolam group (23%) was lower than for the saline group (61%). No other variable was significantly associated with survival. These results suggest that sedation with midazolam shortly after capture increased the postsurgical survival of female surf scoters surgically implanted with intracoelomic transmitters.

Selection of Salmonella enterica serovar Typhi genes involved during interaction with human macrophages by screening of a transposon mutant library.

The human-adapted Salmonella enterica serovar Typhi (S. Typhi) causes a systemic infection known as typhoid fever. This disease relies on the ability of the bacterium to survive within macrophages. In order to identify genes involved during interaction with macrophages, a pool of approximately 10(5) transposon mutants of S. Typhi was subjected to three serial passages of 24 hours through human macrophages. Mutants recovered from infected macrophages (output) were compared to the initial pool (input) and those significantly underrepresented resulted in the identification of 130 genes encoding for cell membrane components, fimbriae, flagella, regulatory processes, pathogenesis, and many genes of unknown function. Defined deletions in 28 genes or gene clusters were created and mutants were evaluated in competitive and individual infection assays for uptake and intracellular survival during interaction with human macrophages. Overall, 26 mutants had defects in the competitive assay and 14 mutants had defects in the individual assay. Twelve mutants had defects in both assays, including acrA, exbDB, flhCD, fliC, gppA, mlc, pgtE, typA, waaQGP, SPI-4, STY1867-68, and STY2346. The complementation of several mutants by expression of plasmid-borne wild-type genes or gene clusters reversed defects, confirming that the phenotypic impairments within macrophages were gene-specific. In this study, 35 novel phenotypes of either uptake or intracellular survival in macrophages were associated with Salmonella genes. Moreover, these results reveal several genes encoding molecular mechanisms not previously known to be involved in systemic infection by human-adapted typhoidal Salmonella that will need to be elucidated.

So similar, yet so different: uncovering distinctive features in the genomes of Salmonella enterica serovars Typhimurium and Typhi.

Salmonella enterica represents a major human and animal pathogen. Many S. enterica genomes have been completed and many more genome sequencing projects are underway, constituting an excellent resource for comparative genome analysis studies leading to a better understanding of bacterial evolution and pathogenesis. Salmonella enterica serovar Typhimurium and Typhi are the best-characterized serovars, with the first being involved in localized gastroenteritis in many hosts and the latter causing a systemic human-specific disease. Here, we summarize the major genetic differences between the two different serovars. We detail the divergent repertoires of the virulence factors responsible for the pathogenesis of the organisms and that ultimately result in the distinct clinical outcomes of infection. This comparative genomic overview highlights hypotheses for future investigations on S. enterica pathogenesis and the basis of host specificity.

An outer membrane protease of the omptin family prevents activation of the Citrobacter rodentium PhoPQ two-component system by antimicrobial peptides.

The PhoPQ two-component system of the intracellular pathogen Salmonella enterica senses and controls resistance to alpha-helical antimicrobial peptides (AMPs) by regulating covalent modifications of lipid A. A homologue of the phoPQ operon was found in the genome of the murine enteric extracellular pathogen, Citrobacter rodentium. Here we report that C. rodentium PhoPQ was apparently unable to mediate activation of target genes in the presence of alpha-helical AMPs. However, these AMPs activated C. rodentium PhoPQ expressed in a S. entericaDeltaphoPQ mutant. Analysis of the outer membrane (OM) fractions of the C. rodentium wild-type and DeltaphoPQ strains led to the identification of an omptin family protease (CroP) that was absent in DeltaphoPQ. Deletion of croP in C. rodentium resulted in higher susceptibility to alpha-helical AMPs, indicating a direct role of CroP in AMP resistance. CroP greatly contributed to the protection of the OM from AMP damage by actively degrading alpha-helical AMPs before they reach the periplasmic space. Accordingly, transcriptional activation of PhoP-regulated genes by alpha-helical AMPs was restored in the DeltacroP mutant. This study shows that resistance to alpha-helical AMPs by the extracellular pathogen C. rodentium relies primarily on the CroP OM protease.