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Most cited protocols related to «Foxes»

1
Estimating Canine Leishmania Infectiousness
The date of patent infection for dogs and foxes was estimated as the first date at which animals were positive by any serological or parasitological assay; all samples thereafter were considered as infected based on previous analyses demonstrating a very low incidence of serological reversal [31] (link), [35] (link), [36] (link). At each bimonthly examination, dogs were classified according to their total clinical score as asymptomatic (scores 0–2), oligosymptomatic (3–6) and symptomatic (>6). Dogs with >8 months post infection follow-up and all bimonthly clinical scores <3 were considered long-term asymptomatic. Infectiousness was assessed as either positive (≥1 sandfly infected) or negative, or as the proportion of sandflies infected at any single time point (point xenodiagnosis). Dogs were also classified previously [22] (link), [35] (link) as “highly infectious” (>20% of total flies infected), “mildly infectious” (>0% and <20% flies infected), and “non-infectious” (no flies infected) by serial xenodiagnoses (n = 6,002 flies dissected from 173 independent trials): the highly infectious group were shown to be responsible for >80% of all transmission events [22] (link). All foxes were non-infectious (n = 1,469 flies from 44 trials) [35] (link).
Courtenay O., Carson C., Calvo-Bado L., Garcez L.M, & Quinnell R.J. (2014). Heterogeneities in Leishmania infantum Infection: Using Skin Parasite Burdens to Identify Highly Infectious Dogs. PLoS Neglected Tropical Diseases, 8(1), e2583.
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Publication 2014
Animals Biological Assay Canis familiaris Diptera Foxes Infection Phlebotominae Phlebotomus Transmission, Communicable Disease Xenodiagnosis
2
Comprehensive rodent sample analysis
Four types of samples were selected in this study. Firstly, 265 high quality tissue samples preserved in ethanol were used as references. They had been collected in Asia, Africa and Europe from rodents that were unambiguously identified at the species level by specialists, based on either morphological characters or molecular data (www.ceropath.org; www.bdrss.ird.fr/bdrsspub_form.php; [55] ). Specimens were selected in order to maximize the number of species and various geographic locations. The total reference sample comprised 103 species, 38 genera and 8 families. In addition, this reference set included closely related species and cryptic species that were only recently described (e.g. species of the Rattus rattus complex, Microtus complex, Gerbillus complex, etc.).
Secondly, 555 samples preserved in ethanol but with uncertain taxonomic status were selected. Feces found in the traps were collected at the same time in order to compare results obtained using high quality DNA (from tissue) or poor quality DNA (from non-invasive samples). Tissue and fecal samples were obtained for 11 and 38 rodents from Mali and Thailand respectively.
Thirdly, 54 DNAs were extracted from museum specimens (skins) and kindly provided by the MNHN of Paris.
And finally, feces from predators that were likely to have ingested rodents were collected. Feces thought to have originated from four foxes (Vulpes vulpes), four martens (Martes martes) and four wild cats (Felis silvestris), as well as 11 owl pellets were analyzed to determine their rodent diets. Sample information is detailed in Table S1.
Galan M., Pagès M, & Cosson J.F. (2012). Next-Generation Sequencing for Rodent Barcoding: Species Identification from Fresh, Degraded and Environmental Samples. PLoS ONE, 7(11), e48374.
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Publication 2012
CFC1 protein, human Character Diet DNA Ethanol Feces Felis Felis catus Martes Microtus Pellets, Drug Rattus Rodent Specialists Tissues Vulpes vulpes
3
Comprehensive Echinococcus multilocularis Surveillance
The study was designed to collect five individual worms per fox intestine and 20 foxes per geographical area investigated (for geographical areas, refer to Table 1). The final panel obtained was composed of 571 worms originating from 123 autopsied red foxes, allocated into nine subregions based on topographical and ecological criteria (Figure 1). Collections were performed by nine research units dealing with diagnostic and epidemiological aspects of E. multilocularis in Europe (see author list and respective information). Collection and worm isolation procedures were carried out identically in all laboratories according to a standard protocol [16] using the intestinal scraping technique (IST) as described by Deplazes and Eckert [17] (link). Worm specimens were individually preserved in 70% (v/v) ethanol until use. Thus, the subregion of Ardennes demarcated with polygons clustered 79 individual adult stage E. multilocularis samples (derived from 16 foxes), Switzerland 84 (19 foxes), Jura Swabe 39 (8 foxes), Bavaria 48 (10 foxes), west Czech Republic 61 (13 foxes), north Austria 103 (23 foxes), central Slovakia 30 (7 foxes), Tatra Mountains (east Slovakia and south Poland) 81 (17 foxes), and north Poland 46 (10 foxes). Among these subregions, Switzerland, Jura Swabe, Bavaria, west Czech Republic, and north Austria were gathered into a set of the historical endemic area, whereas the others were considered as western (Ardennes) and eastern (central Slovakia, Tatra Mountains, and north Poland) European subregions. Parasites were collected between 2001 and 2005.
Knapp J., Bart J.M., Giraudoux P., Glowatzki M.L., Breyer I., Raoul F., Deplazes P., Duscher G., Martinek K., Dubinsky P., Guislain M.H., Cliquet F., Romig T., Malczewski A., Gottstein B, & Piarroux R. (2009). Genetic Diversity of the Cestode Echinococcus multilocularis in Red Foxes at a Continental Scale in Europe. PLoS Neglected Tropical Diseases, 3(6), e452.
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Publication 2009
Adult Diagnosis Europeans Foxes Helminths Intestinal helminthiasis Intestines isolation Parasites Vulpes vulpes
4
Phylogenetic Analysis of Aleutian Mink Disease Virus
The dataset of sequences obtained for this study included 174 partial NS1 sequences from viruses detected between 2004 and 2014 in Newfoundland, other parts of North America (Nova Scotia, Ontario and Wisconsin), and Europe (Denmark). Sequences from Newfoundland originated from both wild mink and from ten different farms. A subset of 131 sequences was selected by excluding sequences that presented observable double peaks on chromatograms, recombinant sequences (identified using RDP software, see below), and all identical sequences derived from the same year and the same geographical area (same farm for Newfoundland) and used for phylogenetic inference. For each sample collected in 2014, only one representative clonal sequence for every strain was included. Reference sequences included only viruses for which the complete coding sequence of one or both ORFs were available and AMDV-like viruses (RFAV and GFADV) identified in foxes and raccoon dogs (Bloom et al. 1988 (link); Gottschalck et al. 1991 (link), 1994 (link); Oie et al. 1996 (link); Schuierer et al. 1997 (link); Li et al. 2011 (link), 2012 (link); Huang et al. 2012 (link); Shao et al. 2014 (link)).
Other sequence datasets were built with sequences downloaded from GenBank (www.ncbi.nlm.nih.gov/genbank) by mapping all available AMDV sequences (N = 456) to a reference complete genome to identify the genomic regions most frequently used for molecular epidemiological studies (Olofsson et al. 1999 (link); Dyer, Ching, and Bloom 2000 (link); Mañas et al. 2001 (link); Knuuttila et al. 2009 (link), 2015 (link); Jahns et al. 2010 (link); Christensen et al. 2011 (link); Jensen et al. 2012 (link); Leimann et al. 2015 (link)). Genomic areas represented by the majority of the sequences were selected, and sequences that mapped to these areas were extracted and used to perform phylogenetic analyses.
Sequences were aligned with ClustalX 2.1 (Larkin et al. 2007 (link)), alignments were manually edited when needed with BioEdit 7.0.5.3 (Hall 1999 ) and then used for phylogenetic inference. A model selection was performed for each alignment to identify the best model for distance estimation, and phylogenetic trees were constructed with MEGA 6.06 (Tamura et al. 2013 (link)) using the maximum-likelihood method (Felsenstein 1981 (link)). Information about numbers of sequences, the genomic regions investigated, and models used are provided in the figure legends. Bootstrap analyses (Felsenstein 1985 ) with 1,000 replicates were performed to test the robustness of the analyses, and only clusters supported by ≥ 70 per cent were considered valid.
Accession numbers of all sequences used in this study are available in the Supplementary Sequence Details File.
Canuti M., O’Leary K.E., Hunter B.D., Spearman G., Ojkic D., Whitney H.G, & Lang A.S. (2016). Driving forces behind the evolution of the Aleutian mink disease parvovirus in the context of intensive farming. Virus Evolution, 2(1), vew004.
Publication 2016
Clone Cells Foxes Genome Mink Open Reading Frames Raccoon Dogs Strains Virus
5
Phylogenetic Analysis of Gray Foxes
To examine phylogenetic relationships between island, California and eastern gray foxes, additional publically available mammal mitogenomes were obtained from GenBank and aligned to the fox dataset. The alignment was run through JModelTest v.2.1 and the GTR+I+ Γ model was used to run 1000 pseudobootstrap replicates of the maximium likelihood tree program Garli as implemented on the Lattice grid computing system [52 (link),53 ].
To date the divergence between island and mainland foxes, Bayesian phylogenetic analysis was conducted in BEAST v.1.7.5. Each gene, as well as the entire alignment, were run through JModelTest v2.1 and PartitionFinder v1.1.1. Based on this analysis, no codon partitioning and empirical base frequencies were used with each gene fitting the HKY or the TN93 model. Both a lognormal relaxed and strict clock were tested with a coalescent of constant size. The earliest calibrated radiocarbon date was used as a prior estimate of the time to the most recent common ancestor for all island fox samples. An eastern gray fox sample was used as an outgroup as indicated by the maximum likelihood analysis. The eastern gray fox is deeply diverged from California foxes but this split must be younger than the oldest fossil date for Urocyon so we set the root length to the early Pliocene Urocyon fossil dating to 5.332–2.558 MYA [54 ].
All other priors were left to default settings and the MCMC was run in two independent runs of 100 million chains each, logging every 10,000 chains. An empty alignment was tested to sample for effects of the prior and the resulting poor posterior and prior ESS with values below 200 indicated that the priors were not strongly influencing the tree. Substitution rates were compared to other canids and mammals (see S1 Text) to examine how the radiocarbon date prior influenced divergence dates.
Hofman C.A., Rick T.C., Hawkins M.T., Funk W.C., Ralls K., Boser C.L., Collins P.W., Coonan T., King J.L., Morrison S.A., Newsome S.D., Sillett T.S., Fleischer R.C, & Maldonado J.E. (2015). Mitochondrial Genomes Suggest Rapid Evolution of Dwarf California Channel Islands Foxes (Urocyon littoralis). PLoS ONE, 10(2), e0118240.
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Publication 2015
Canidae Codon Genes Mammals Plant Roots Trees Urocyon Youth

Most recents protocols related to «Foxes»

1
Echinococcus multilocularis Specimen Collection
Echinococcus multilocularis specimens were collected from gastrointestinal (GI) tracts of red foxes and coyotes of either road-killed or trap-harvested animals (trapped for purposes independent of this study), collected between 2012 and 2017 in Western Canada. Trapped animals were obtained from licensed trappers with the collaboration of the Alberta Trappers Association. GI tracts were screened using a modification of the scraping, filtration and counting technique, to identify and collect Echinococcus spp. worms [35 (link),36 (link)]. We analysed Em worms from 70 coyotes and 13 foxes from northern, central and southern Alberta (AB); four coyotes from north-west British Columbia (BC); and 10 coyotes from southeast Saskatchewan (SK). Extraction of DNA was performed on up to five individual worms per host using the Nucleospin 96 Tissue Kit (Macherey-Nagel, Germany) for samples processed in France (Anses Nancy Laboratory for Rabies and Wildlife) and the E.Z.N.A. MicroElute Genomic DNA Kit (Omega Bio-tek, US) for samples processed in Canada (University of Calgary, Faculty of Veterinary Medicine). Extraction was performed following the manufacturer's instructions, and DNA was stored at −20°C until processed.
Santa M.A., Umhang G., Klein C., Grant D.M., Ruckstuhl K.E., Musiani M., Gilleard J.S, & Massolo A. (2023). It's a small world for parasites: evidence supporting the North American invasion of European Echinococcus multilocularis. Proceedings of the Royal Society B: Biological Sciences, 290(1994), 20230128.
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Publication 2023
Animals Coyotes Echinococcus Echinococcus multilocularis Faculty Filtration Foxes Gastrointestinal Tract Genome Helminths Hydrophobia Tissues Vulpes vulpes
2
Livestock Guardian Dogs Protect Pastured Chickens
Fieldwork was conducted from 8 July to 23 August 2019 at Blue Tractor Farm in Glen Mervyn, Western Australia. The farm had been working as a commercial egg farm for about 2 yr at the time of this study, keeping pastured Isa Brown chicken (Gallus gallus domesticus) layers. The owner had experienced substantial losses to predators in the year before acquiring the LGDs: on one night, 35 chickens were killed by foxes, another 15 on a separate occasion, and foxes were regularly seen both day and night. In addition, an estimated ~15 chickens were seen killed by raptors. Furthermore, uncounted numbers of chickens that flew out of the fenced paddocks (and could not be re-captured) were also likely predated, as they did not remain present for many days. In the subsequent year of operation, after getting two alpacas and then two LGDs, there were no reported losses to either foxes or raptors, and fewer foxes had been noticed on the property (a distinction in timing between the alpacas and LGDs was not made).
The property had three separate 50 × 50 m chicken paddocks (Figure 1) surrounded by solar-powered electric poultry fences and each containing a “chicken caravan” for egg laying and night-time roosting (Figure 2a). Paddock “M,” the focus of our work, contained two Maremma LGDs and 450 ~9-month-old chickens (Figure 2b). The 2-yr-old sibling LGDs (male: Hiro and female: Coco) had been acquired 1 yr previously from another open pasture chicken farm, where they had been raised amongst chickens. Paddock “A” contained two alpacas (which always remained within the confines of their paddock) and 500 ~6-month-old chickens (Figure 2c). There has been some reported success in protecting flocks of sheep by llamas (Lama glama) (Meadows and Knowlton, 2000 ) and the smaller alpacas (Mahoney and Charry, 2007 ); however, we are not aware of any test of the guardian value for poultry and we also did not have sufficient data to carry out a robust experimental design on this property. Both Paddock M and Paddock A were moved every 2 to 3 wk to an adjacent 50 × 50 m area for fresh green pick and foraging opportunities. Paddock “N” contained no guardian animal and the oldest chickens at ~18-months-old. Paddock N was not moved during the study as the chickens were being sold off; there were 68 chickens for the first 12 d of monitoring, 47 for the next day and then 25 chickens for the last 2 d of monitoring for this paddock.
McKellar R.A., Kreplins T.L, & Fleming P.A. (2023). Chicken’s best friend? Livestock guardian dog bonding with free-ranging chickens. Translational Animal Science, 7(1), txad014.
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Publication 2023
Animals Cacao Chickens Diptera Domestic Sheep Electricity Fowls, Domestic Foxes Legal Guardians Llamas Males Raptors SELL protein, human Vicugna pacos Vision Woman
3
Modeling Mange Epidemics in Kit Foxes
From the simulated epidemic histories we gathered and analysed the following outputs: mean epidemic time, mean kit fox population persistence time, maximum and median number of E + I, and minimum and median N (adult female kit fox population size). Local extinction of kit foxes and disease occurs when N = 0 and E + I = 0, respectively. After confirming normality, we used paired t-tests to compare mean epidemic times that occurred using the actual, heterogeneous landscape versus a flat landscape in which K was constant across all quads. Given that an influx of juvenile S individuals could impact epidemic duration and magnitude, we also examined model outputs with varying birthrates. Because mange transmission among foxes has been reported to be frequency-dependent [39 (link)], we also compared model output for frequency (by dividing the transmission function by N) and DDT. Default parameters remained static across model runs except where noted to implement the analysis; each analysis was done by running the model for at least 10 trials and 4000 days.
Foley P., Foley J., Rudd J., Clifford D., Westall T, & Cypher B. (2023). Spatio-temporal and transmission dynamics of sarcoptic mange in an endangered New World kit fox. PLOS ONE, 18(2), e0280283.
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Publication 2023
Epidemics Extinction, Psychological Foxes Genetic Heterogeneity Mange Transmission, Communicable Disease Woman
4
Modeling San Joaquin Kit Fox Populations
The population size in Bakersfield was initiated at 400 San Joaquin kit foxes, i.e. 200 females (Table 2). Seasonal birth rate was calculated as ln(3.8/2 * the probability of an adult female birthing pups)/45 day window in which pups could be born, where 3.8 is mean llitter size and it is divided by 2 to estimate number of female pups born. We calculated the daily average natural death rate as -ln(total annual mortality) and dividing by 365 days.
Epidemiological parameters were also estimated from our data, other available data for the species, and where necessary, the most closely related species for which data were available (Table 3). We assumed that once exposed, kit foxes entered and then exited the E state such that the mean incubation time is 1⁄σ. Values of αβ were informed by observations of dispersal distance described in the section “Kit fox movement”, i.e. 1/αβ ~ mean dispersal distance. The reciprocal of αβ (i.e. αβ-1) gives the mean transmission distance, since the decay over distance is assumed exponential. Thus αβ of 0.6 corresponds to a mean transmission distance of 1.67 kilometers, the distance from the center to the edge of one of our patches. The disease projection β/αβ is a transmission measure that takes into account local transmission and the geographic impact beyond local transmission. Values of β were derived: once there was an estimate of αβ, we calculated the value of β that produced output models that fit the observed epidemic history. Of note, concurrent to this study and data collection, we had applied a long-acting acaricide (flumethrin) to 17 kit foxes, which may have acted as a temporary form of “immunity”, essentially putting these kit foxes into an R class in the SEIR model [45 (link)].
Foley P., Foley J., Rudd J., Clifford D., Westall T, & Cypher B. (2023). Spatio-temporal and transmission dynamics of sarcoptic mange in an endangered New World kit fox. PLOS ONE, 18(2), e0280283.
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Publication 2023
Acaricides Childbirth Epidemics Females flumethrin Foxes Movement Response, Immune Transmission, Communicable Disease Woman
5
Phylogenetic Analysis of H5N1 Genomes
In addition to the virus sequences obtained from foxes and wild birds in the Netherlands in this study, the top five BLAST results for related sequences in Eurasia were included in the phylogenetic analysis. These H5N1 genome sequences were downloaded from the GISAID database (26 (link)). A phylogenetic analysis of the complete genome sequences was performed for each genome segment separately, aligning the virus sequences using MAFFT v7.475 (27 (link)) and reconstructing the phylogeny using a maximum likelihood (ML) analysis with IQ-TREE software v2.0.3 and 1,000 bootstrap replicates (28 (link)). The ML tree was visualized using the R package ggtree (29 (link)). The GISAID sequences used in the phylogenetic analysis are listed in Table S5, in which we acknowledge all of the contributors to the GISAID database.
Bordes L., Vreman S., Heutink R., Roose M., Venema S., Pritz-Verschuren S.B., Rijks J.M., Gonzales J.L., Germeraad E.A., Engelsma M, & Beerens N. (2023). Highly Pathogenic Avian Influenza H5N1 Virus Infections in Wild Red Foxes (Vulpes vulpes) Show Neurotropism and Adaptive Virus Mutations. Microbiology Spectrum, 11(1), e02867-22.
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Publication 2023
Aves Genome Influenza in Birds Trees Virus

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More about "Foxes"

Foxes are fascinating members of the Canidae family, known for their distinctive features, behaviors, and ecological roles.
These cunning carnivores can be found in a variety of habitats, from urban environments to remote wilderness areas.
Understanding the biology and conservation of foxes is crucial, as they play important roles in their ecosystems.
Genetic research on foxes often utilizes advanced tools and techniques, such as the MEGA software for phylogenetic analysis, the ABI BigDye Terminator v3.1 Cycle Sequencing Kit for DNA sequencing, and the QIAamp DNA Stool Mini Kit for extracting DNA from fecal samples.
Researchers may also employ statistical analysis software like SPSS to study fox population dynamics and behavior.
In the field, scientists may collect blood samples using Vacutainer® Heparin Blood Collection Tubes and purify DNA using the MEGAquick-spin Total Fragment DNA Purification Kit.
High-throughput sequencing platforms like the HiSeq 2000 can be leveraged to generate genomic data for foxes, while the Sherlock AX kit and ID Screen® Toxoplasmosis Indirect Multi-Species kit can be used to detect pathogens and diseases in these animals.
By combining these advanced tools and techniques, researchers can gain valuable insights into the evolutionary history, population genetics, and ecological interactions of foxes, ultimately supporting their conservation and management.