Center for Zoo and Wild Animal Health

Copenhagen, Denmark

Center for Zoo and Wild Animal Health

Copenhagen, Denmark
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Nilsson M.A.,Biodiversity and Climate Research Center | Nilsson M.A.,Lund University | Klassert D.,Biodiversity and Climate Research Center | Bertelsen M.F.,Center for Zoo and Wild Animal Health | And 3 more authors.
Molecular Biology and Evolution | Year: 2012

In the genome of Artiodactyla (cow, sheep, pigs, camels, and whales), a major retroposon group originated from a presumable horizontal transfer of BovB, a retrotransposon-like element retroposon, between 52 and 70 million years ago. Since then, BovB retroposons have proliferated and today occupy a quarter of the cow's genome sequence. The BovB-related short interspersed elements (SINEs) were used for resolving the phylogeny of Bovinae (cows, spiral-horned antelopes, and nilgais) and their relatives. In silico screening of 55,000 intronic retroposon insertions in the cow genome and experimental validation of 126 introns resulted in 29 informative retroposon markers for resolving bovine evolutionary relationships. A transposition-in-transposition analysis identifies three different phases of SINE activity and show how BovB elements have expanded in the cattle genome. © 2012 The Author.


Villar D.,University of Cambridge | Berthelot C.,European Bioinformatics Institute | Aldridge S.,University of Cambridge | Aldridge S.,Astrazeneca | And 14 more authors.
Cell | Year: 2015

The mammalian radiation has corresponded with rapid changes in noncoding regions of the genome, but we lack a comprehensive understanding of regulatory evolution in mammals. Here, we track the evolution of promoters and enhancers active in liver across 20 mammalian species from six diverse orders by profiling genomic enrichment of H3K27 acetylation and H3K4 trimethylation. We report that rapid evolution of enhancers is a universal feature of mammalian genomes. Most of the recently evolved enhancers arise from ancestral DNA exaptation, rather than lineage-specific expansions of repeat elements. In contrast, almost all liver promoters are partially or fully conserved across these species. Our data further reveal that recently evolved enhancers can be associated with genes under positive selection, demonstrating the power of this approach for annotating regulatory adaptations in genomic sequences. These results provide important insight into the functional genetics underpinning mammalian regulatory evolution. © 2015 The Authors.


Patzke N.,University of Witwatersrand | Bertelsen M.F.,Center for Zoo and Wild Animal Health | Fuxe K.,Karolinska Institutet | Manger P.R.,University of Witwatersrand
Journal of Chemical Neuroanatomy | Year: 2014

This study investigated the nuclear organization of four immunohistochemically identifiable neural systems (cholinergic, catecholaminergic, serotonergic and orexinergic) within the brains of three male Tasmanian devils (. Sarcophilus harrisii), which had a mean brain mass of 11.6. g. We found that the nuclei generally observed for these systems in other mammalian brains were present in the brain of the Tasmanian devil. Despite this, specific differences in the nuclear organization of the cholinergic, catecholaminergic and serotonergic systems appear to carry a phylogenetic signal. In the cholinergic system, only the dorsal hypothalamic cholinergic nucleus could be observed, while an extra dorsal subdivision of the laterodorsal tegmental nucleus and cholinergic neurons within the gelatinous layer of the caudal spinal trigeminal nucleus were observed. Within the catecholaminergic system the A4 nucleus of the locus coeruleus complex was absent, as was the caudal ventrolateral serotonergic group of the serotonergic system. The organization of the orexinergic system was similar to that seen in many mammals previously studied. Overall, while showing strong similarities to the organization of these systems in other mammals, the specific differences observed in the Tasmanian devil reveal either order specific, or class specific, features of these systems. Further studies will reveal the extent of change in the nuclear organization of these systems in marsupials and how these potential changes may affect functionality. © 2014 Elsevier B.V.


Stevens H.,Rega Institute for Medical Research | Bertelsen M.F.,Center for Zoo and Wild Animal Health | Sijmons S.,Rega Institute for Medical Research | Van Ranst M.,Rega Institute for Medical Research | Maes P.,Rega Institute for Medical Research
PLoS ONE | Year: 2013

Viruses of the family Polyomaviridae infect a wide variety of avian and mammalian hosts with a broad spectrum of outcomes including asymptomatic infection, acute systemic disease, and tumor induction. In this study a novel polyomavirus, the African elephant polyomavirus 1 (AelPyV-1) found in a protruding hyperplastic fibrous lesion on the trunk of an African elephant (Loxodonta africana) was characterized. The AelPyV-1 genome is 5722 bp in size and is one of the largest polyomaviruses characterized to date. Analysis of the AelPyV-1 genome reveals five putative open-reading frames coding for the classic small and large T antigens in the early region, and the VP1, VP2 and VP3 capsid proteins in the late region. In the area preceding the VP2 start codon three putative open-reading frames, possibly coding for an agnoprotein, could be localized. A regulatory, non-coding region separates the 2 coding regions. Unique for polyomaviruses is the presence of a second 854 bp long non-coding region between the end of the early region and the end of the late region. Based on maximum likelihood phylogenetic analyses of the large T antigen of the AelPyV-1 and 61 other polyomavirus sequences, AelPyV-1 clusters within a heterogeneous group of polyomaviruses that have been isolated from bats, new world primates and rodents. © 2013 Stevens et al.


Sigler L.,University of Alberta | Gibas C.F.C.,University of Alberta | Kokotovic B.,Technical University of Denmark | Bertelsen M.F.,Center for Zoo and Wild Animal Health
Journal of Clinical Microbiology | Year: 2010

An outbreak of disseminated granulomatous disease occurred in a group of veiled chameleons (Chamaeleo calyptratus) in a zoo collection. An adult female and six offspring developed large granulomas in multiple organs and were euthanized. At necropsy, roughly spherical yellow-to-white nodules 1 to 3 mm in diameter were grossly visible in the liver and other organs. Histopathology revealed fungal elements that were spherical to ovoid in shape, fragments of slender to irregularly swollen hyphae, and occasional conidia produced on phialides. Fungal isolates were initially suspected on the basis of morphology results to represent Paecilomyces viridis, a species known only from one outbreak of fatal mycosis in carpet chameleons (Furcifer lateralis). Data obtained from morphological studies and from phylogenetic analyses of nuclear ribosomal rRNA (rDNA) sequence data revealed the Danish chameleon isolates to be a related undescribed anamorphic species within the family Clavicipitaceae that includes many insect pathogens. Chamaeleomyces granulomatis gen. et sp. nov. is given as the name for the newly described fungus, and P. viridis is transferred to the new genus as Chamaeleomyces viridis comb. nov. Chamaeleomyces species are distinguished by having basally swollen phialides tapering to a narrow neck, conidia in fragile chains, and pale green to greenish-gray colonies. Both species are dimorphic, producing a transitory yeast stage characterized by ovoid-to-subglobose or subcylindrical yeast-like cells. Chamaeleomyces species appear to be rare but aggressive pathogens of chameleons. Copyright © 2010, American Society for Microbiology. All Rights Reserved.


Madsen J.,Copenhagen University | Bertelsen M.F.,Center for Zoo and Wild Animal Health
Journal of Animal Science | Year: 2012

The claimed low production of CH4 by kangaroos and marsupials in general has been questioned because of a lack of data. The extent of their CH4 production is of interest both from the point of view of discussing meat production of marsupials and as a basis for developing methods to reduce CH4 production from ruminants. In the present experiment, the CH4 production of 8 red-necked wallabies (Macropus rufogriseus) was measured of which 4 were fed 2 different diets in an open-circuit respiration chamber. These results were compared with a newly developed, inexpensive, and simple method that does not influence the behavior of the animal, and where the ratio between CH4 and CO2 is measured and used together with the calculated CO2 to quantify the CH4 production. The experiment demonstrated that the wallabies produce CH4. However, the amount of CH4 produced by these wallabies was between 1.6 and 2.5 L/d equivalent to 1.6 and 2.5% of GE or 2.2% and 3.5% of DE intake and 0.22 L/BW, kg0.75. This is between 25 and 33% of what can be expected from ruminants fed the same diet. Based on the uneven release of CH4 with time, it is most likely that the CH4 is excreted through flatulence and not through breathing as is seen in ruminants. The experiments also showed that a reasonably accurate determination of the CH4 production of a group of animals can be obtained by simply measuring the CH4/ CO2 ratio over a limited time span. This may represent the situation in a natural setting better than measurements in a respiration chamber. It was found that the CH4/CO2 ratio in itself represents a reasonable prediction of the proportion of feed GE that is lost as CH4, and that this method offers new opportunities for CH4 measurements on a large number of animals. © 2012 American Society of Animal Science. All rights reserved.


Schnell I.B.,Copenhagen University | Schnell I.B.,Center for Zoo and Wild Animal Health | Bohmann K.,Copenhagen University | Bohmann K.,University of Bristol | And 2 more authors.
Molecular Ecology Resources | Year: 2015

Metabarcoding of environmental samples on second-generation sequencing platforms has rapidly become a valuable tool for ecological studies. A fundamental assumption of this approach is the reliance on being able to track tagged amplicons back to the samples from which they originated. In this study, we address the problem of sequences in metabarcoding sequencing outputs with false combinations of used tags (tag jumps). Unless these sequences can be identified and excluded from downstream analyses, tag jumps creating sequences with false, but already used tag combinations, can cause incorrect assignment of sequences to samples and artificially inflate diversity. In this study, we document and investigate tag jumping in metabarcoding studies on Illumina sequencing platforms by amplifying mixed-template extracts obtained from bat droppings and leech gut contents with tagged generic arthropod and mammal primers, respectively. We found that an average of 2.6% and 2.1% of sequences had tag combinations, which could be explained by tag jumping in the leech and bat diet study, respectively. We suggest that tag jumping can happen during blunt-ending of pools of tagged amplicons during library build and as a consequence of chimera formation during bulk amplification of tagged amplicons during library index PCR. We argue that tag jumping and contamination between libraries represents a considerable challenge for Illumina-based metabarcoding studies, and suggest measures to avoid false assignment of tag jumping-derived sequences to samples. © 2015 John Wiley & Sons Ltd.


Jewgenow K.,Leibniz Institute for Zoo and Wildlife Research | Wiedemann C.,Leibniz Institute for Zoo and Wildlife Research | Bertelsen M.F.,Center for Zoo and Wild Animal Health | Ringleb J.,Leibniz Institute for Zoo and Wildlife Research
International Zoo Yearbook | Year: 2011

The ability to freeze unfertilized oocytes and the ovarian cortex is valuable for genetic resource banking, especially in the case of genetically important individuals that undergo castration or euthanasia for medical reasons. Although offspring have been produced from frozen-thawed oocytes in mice, humans, cattle and rabbits, the results have been variable and not sufficiently successful for routine use. This review provides an overview on the recent knowledge of female germ cell cryopreservation, with a focus on wildlife species, and introduces the Felid Gametes Rescue Project within European Association of Zoos and Aquaria zoos. © 2010 The Authors. International Zoo Yearbook © 2010 The Zoological Society of London.


Hansen L.L.,Center for Zoo and Wild Animal Health | Bertelsen M.F.,Center for Zoo and Wild Animal Health
Veterinary Anaesthesia and Analgesia | Year: 2013

Objective: To characterise four different intramuscular (IM) anaesthetic protocols, two with alfaxalone and two with alfaxalone in combination with medetomidine in terrestrial tortoises. Study design: Blinded, randomized, cross-over experimental study. Animals: Nine healthy adult male Horsfield's tortoises (Agrionemys horsfieldii). Methods: Each tortoise was randomly assigned to one of four different protocols: 1) 10 mg kg-1 alfaxalone; 2) 10 mg kg-1 alfaxalone + 0.10 mg kg-1 medetomidine; 3) 20 mg kg-1 alfaxalone; and 4) 20 mg kg-1 alfaxalone + 0.05 mg kg-1 medetomidine. During the experiment, the following variables were recorded: heart rate; respiratory rate; peripheral nociceptive responses; muscle strength; ability to intubate; palpebral, corneal and tap reflexes; and cloacal temperature. Results: Protocols 1 and 2 resulted in moderate sedation with no analgesia, and moderate to deep sedation with minimal analgesia, respectively. Protocols 3 and 4 resulted in deep sedation or anaesthesia with variable analgesic effect; these two protocols had the longest total anaesthetic time and allowed intubation in 6/9 and 8/9 tortoises respectively. The total anaesthesia/sedation time produced by alfaxalone was significantly increased (p < 0.05) by the addition of medetomidine. There were no significant differences regarding time to plateau phase and duration of plateau phase. Baseline heart rate of 53 ± 6 beats minute-1 decreased significantly (p < 0.05) with all protocols, and was lower (p < 0.05) in protocols 3 and 4. Heart rate increased after atipamezole administration, but the increase was transient. In two tortoises, extreme bradycardia with no cardiac activity for 10 minutes was observed with protocols 3 and 4. Conclusion and clinical relevance: Alfaxalone 10 and 20 mg kg-1 IM can be used for sedation for non-painful procedures. Alfaxalone in combination with medetomidine can be used for deeper sedation or anaesthesia, but the observed respiratory and cardiovascular depression may limit its use. © 2013 Association of Veterinary Anaesthetists and the American College of Veterinary Anesthesia and Analgesia.


Christensen H.,Copenhagen University | Bertelsen M.F.,Copenhagen University | Bertelsen M.F.,Center for Zoo and Wild Animal Health | Bojesen A.M.,Copenhagen University | Bisgaard M.,Copenhagen University
International Journal of Systematic and Evolutionary Microbiology | Year: 2012

Pasteurella species B has so far only been reported from the oral cavity of dogs, cats and a ferret. In the present study, information from 15 recent isolates from different sources, including African hedgehogs (Atelerix albiventris), banded mongoose (Mungos mungo), Moholi bushbabies (Galago moholi) and pneumonia of a cat, were compared to five strains investigated previously from bite wounds in humans inflicted by a cat and dog and from gingiva of a cat. rpoB gene sequence comparison showed that 17 isolates, including the reference strain (CCUG 19794T), had identical sequences, whereas two were closely related and demonstrated 97.9 and 99.6 % similarity to strain CCUG 19794T, respectively; the type strain of Pasteurella stomatis was the most closely related strain, with 92.3 % similarity. This is within the mean range (76-100 %) of rpoB gene sequence similarity between species of the same genus within the family Pasteurellaceae. 16S rRNA gene sequencing of four strains selected based on rpoB sequence comparison showed at least 99.7 % similarity between strains of Pasteurella species B, with 96.2 % similarity to the type strain of the closest related species (Pasteurella canis), indicating that Pasteurella species B should have separate species status. Separate species status was also documented when recN sequence comparisons were converted to a genome similarity of 93.7 % within Pasteurella species B and 59.0 % to the type strain of the closest related species (P. canis). Based on analysis of the phylogenetic and phenotypic data, and since most isolates originate from the oral cavities of a diverse group of animals, it is suggested that these bacteria be classified as Pasteurella oralis sp. nov.; the type strain is P683T (= CCUG 19794T = CCM 7950T = strain 23193T = MCCM 00102T), obtained from a cat. Previous reports of the type strain have shown ubiquinone-8, demethylmenaquinone-8 and menaquinone-8 as the major quinones. Polyamines in the type strain were reported as diaminopropane, putrescine, cadaverine, sym-norspermidine, spermidine and spermine in a previous investigation, and the major fatty acids of the type strain were reported to be C16: 0, C16: 1ω7c and C14: 0, with minor amounts of C18: 0 and C18: 1ω9c. The DNA G+C content of the type strain has been reported to be 40.0 mol%. © 2012 IUMS.

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