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Monday, 23 March 2015

What's new for 'birdRS' in PubMed March 2015, Week 2

This message contains My NCBI what's new results from the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM).

PubMed Results



1. Acta Virol. 2015;59(1):3-13.

Next generation sequencing technologies: Tool to study avian virus diversity.

Kapgate SS, Barbuddhe SB, Kumanan K.

Abstract

Increased globalisation, climatic changes and wildlife-livestock interface led to emergence of novel viral pathogens or zoonoses that have become serious concern to avian, animal and human health. High biodiversity and bird migration facilitate spread of the pathogen and provide reservoirs for emerging infectious diseases. Current classical diagnostic methods designed to be virus-specific or aim to be limited to group of viral agents, hinder identifying of novel viruses or viral variants. Recently developed approaches of next-generation sequencing (NGS) provide culture-independent methods that are useful for understanding viral diversity and discovery of novel virus, thereby enabling a better diagnosis and disease control. This review discusses the different possible steps of a NGS study utilizing sequence-independent amplification, high-throughput sequencing and bioinformatics approaches to identify novel avian viruses and their diversity. NGS lead to the identification of a wide range of new viruses such as picobirnavirus, picornavirus, orthoreovirus and avian gamma coronavirus associated with fulminating disease in guinea fowl and is also used in describing viral diversity among avian species. The review also briefly discusses areas of viral-host interaction and disease associated causalities with newly identified avian viruses.
PMID: 25790045 [PubMed - in process]
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2. Proc Biol Sci. 2015 Apr 22;282(1805). pii: 20150032. doi: 10.1098/rspb.2015.0032.

Rapidly increasing methyl mercury in endangered ivory gull (Pagophila eburnea) feathers over a 130 year record.

Bond AL1, Hobson KA2, Branfireun BA3.
Author information:
Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, Saskatchewan, Canada S7N 5E2 Environment Canada, 11 Innovation Boulevard, Saskatoon, Saskatchewan, Canada S7N 3H5 alex.bond@rspb.org.uk.
Environment Canada, 11 Innovation Boulevard, Saskatoon, Saskatchewan, Canada S7N 3H5.
Department of Biology and Centre for Environment and Sustainability, Western University, Biological and Geological Sciences Building, London, Ontario, Canada N6A 5B7.

Abstract

Mercury (Hg) is increasing in marine food webs, especially at high latitudes. The bioaccumulation and biomagnification of methyl mercury (MeHg) has serious effects on wildlife, and is most evident in apex predators. The MeHg body burden in birds is the balance of ingestion and excretion, and MeHg in feathers is an effective indicator of overall MeHg burden. Ivory gulls (Pagophila eburnea), which consume ice-associated prey and scavenge marine mammal carcasses, have the highest egg Hg concentrations of any Arctic bird, and the species has declined by more than 80% since the 1980s in Canada. We used feathers from museum specimens from the Canadian Arctic and western Greenland to assess whether exposure to MeHg by ivory gulls increased from 1877 to 2007. Based on constant feather stable-isotope (δ(13)C, δ(15)N) values, there was no significant change in ivory gulls' diet over this period, but feather MeHg concentrations increased 45× (from 0.09 to 4.11 µg g(-1) in adults). This dramatic change in the absence of a dietary shift is clear evidence of the impact of anthropogenic Hg on this high-latitude threatened species. Bioavailable Hg is expected to increase in the Arctic, raising concern for continued population declines in high-latitude species that are far from sources of environmental contaminants.
© 2015 The Author(s) Published by the Royal Society. All rights reserved.
PMID: 25788594 [PubMed - in process]
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3. J Acoust Soc Am. 2015 Mar;137(3):1069. doi: 10.1121/1.4906168.

Dynamic time warping and sparse representation classification for birdsong phrase classification using limited training data.

Tan LN1, Alwan A1, Kossan G2, Cody ML2, Taylor CE2.
Author information:
Department of Electrical Engineering, University of California, Los Angeles 56-125B Engineering IV Building, Box 951594, Los Angeles, California 90095.
Department of Ecology and Evolutionary Biology, University of California, Los Angeles 621 Charles Young Drive South, Los Angeles, California 90095.

Abstract

Annotation of phrases in birdsongs can be helpful to behavioral and population studies. To reduce the need for manual annotation, an automated birdsong phrase classification algorithm for limited data is developed. Limited data occur because of limited recordings or the existence of rare phrases. In this paper, classification of up to 81 phrase classes of Cassin's Vireo is performed using one to five training samples per class. The algorithm involves dynamic time warping (DTW) and two passes of sparse representation (SR) classification. DTW improves the similarity between training and test phrases from the same class in the presence of individual bird differences and phrase segmentation inconsistencies. The SR classifier works by finding a sparse linear combination of training feature vectors from all classes that best approximates the test feature vector. When the class decisions from DTW and the first pass SR classification are different, SR classification is repeated using training samples from these two conflicting classes. Compared to DTW, support vector machines, and an SR classifier without DTW, the proposed classifier achieves the highest classification accuracies of 94% and 89% on manually segmented and automatically segmented phrases, respectively, from unseen Cassin's Vireo individuals, using five training samples per class.
PMID: 25786922 [PubMed - in process]
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4. Parasitol Res. 2015 Mar 20. [Epub ahead of print]

Acanthocephalans of the genus Centrorhynchus (Palaeacanthocephala: Centrorhynchidae) of birds of prey (Falconiformes) and owls (Strigiformes) in Slovakia.

Komorová P1, Špakulová M, Hurníková Z, Uhrín M .
Author information:
Department of Epizootology and Parasitology, Institute of Parasitology, The University of Veterinary Medicine and Pharmacy in Košice, Komenského 73, 041 81, Košice, Slovakia, petronela.komorova@gmail.com.

Abstract

Three species of thorny-headed worms of the genus Centrorhynchus were found to parasitize birds of prey and owls in the territory of the Slovakia during the years 2012-2014. Out of 286 examined bird individuals belonging to 23 species, only Buteo buteo, Buteo rufinus, Falco tinnunculus (Falconiformes), Asio otus, Strix aluco, Strix uralensis and Tyto alba (Strigiformes) were infected by acanthocephalans. All the bird species except for S. aluco represent new host records for Slovakia. The most prevalent acanthocephalan Centrorhynchus aluconis was detected in all 15 examined birds of non-migratory Ural owl S. uralensis (P = 100 %); however, it was found occasionally also in two individuals of the tawny owl S. aluco (P = 20 %), one long-eared owl A. otus (P = 7.7 %), one barn owl T. alba (P = 33.3 %) and the common buzzard B. buteo (P = 0.8 %). Two other thorny-headed worms occurred exclusively in Falconiformes in raw or mixed infections: Centrorhynchus buteonis was found in 11 individuals of B. buteo (P = 9.2 %), and two birds (B. buteo and B. rufinus) were parasitized simultaneously by C. buteonis and the species Centrorhynchus globocaudatus. Moreover, the latest, relatively rare acanthocephalan was found alone in two common kestrels F. tinnunculus (P = 2.7 %). Regarding intensity of infection, it ranged from a single female of C. buteonis, C. globocaudatus or C. aluconis per host (four cases) to a maximum of 82 C. aluconis per an Ural owl. The difference in acanthocephalan species spectrum between birds of prey and owls in Slovakia was apparent.
PMID: 25786606 [PubMed - as supplied by publisher]
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5. Zh Obshch Biol. 2014 Jul-Aug;75(4):287-301.

[Population dynamics of thrushes and seasonal resource partition].

[Article in Russian]
[No authors listed]

Abstract

We studied seasonal population dynamics in birds using four thrush species from the Yenisei middle taiga region as an example. Long-term data on bird route censuses, capture-mark-recapture, and nest observations were incorporated in the analysis. Particularly, methodological problems that complicate a direct comparison between assessed numbers at different phases of the annual cycle are considered. The integrated analysis of the results allowed comparing changes in numbers, energy expenditure, age structure, migrating status, and density distribution of selected populations during the snowless period and relating them to seasonal changes in food resource abundance. Thrush population numbers within the breeding range, and their energy consumption in the Yenisei middle taiga proportionately reflect the seasonal change in abundance of food resources. The compliance between resource intake and carrying capacity of the environment is attained by: timing of arrival and departure regarding to the species' range of tolerance; change in numbers as a result of reproduction and mortality; change in numbers due to habitat changes and long-distance movements; increasing energetic expenditures during reproduction and molt; timing, intensity and replication of nesting attempts; timing of molt and proportion of molting individuals in a population; individual variations of the annual cycle. Reproductive growth of local bird populations is not fast enough to catch up with seasonal growth of ecosystems productivity. Superabundance of invertebrates at the peak of the season offers a temporal niche which, on the one hand, is suitable for species capable of diet switching, while, on the other hand, may be used by specialized consumers, namely tropical migrants for whom, at high resource level, a shortened breeding period suffices.
PMID: 25786310 [PubMed - in process]




6. Foodborne Pathog Dis. 2015 Mar 18. [Epub ahead of print]

Characterization of Antimicrobial Resistance and Extended-Spectrum β-Lactamase Genes in Escherichia coli Isolated from Chickens.

Tong P1, Sun Y, Ji X, Du X, Guo X, Liu J, Zhu L, Zhou B, Zhou W, Liu G, Feng S.
Author information:
1 College of Veterinary Medicine, Jilin University , Changchun, China .

Abstract

Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli have been frequently isolated from food-producing animals and pose a serious threat to human health. This study collected 195 ESBL-producing E. coli isolates from 20 chicken farms and 3 live-bird markets located in Northeast China (Heilongjiang, Liaoning, Jilin) and Jiangsu province from February 2011 to October 2013. ESBL genes, including blaCTX-M, blaTEM, and blaSHV, were detected and characterized, and the susceptibilities of these strains to various antimicrobial agents were determined. One hundred ninety-one of these isolates carried 1 or more bla genes. blaCTX-M, blaTEM-1, and blaSHV-5 were identified in 183, 121, and 2 isolates, respectively. The most common blaCTX-M genes were blaCTX-M-15 (68 strains), blaCTX-M-65 (41 strains), blaCTX-M-55 (35 strains), blaCTX-M-14 (32 strains), followed by blaCTX-M-3, blaCTX-M-13, blaCTX-M-79, and blaCTX-M-101, as well as the chimeric genes blaCTX-M-64, blaCTX-M-123, and blaCTX-M-132. Fifteen strains (7.7%) co-harboring CTX-M-1 group and CTX-M-9 group genes were detected in 195 ESBL-producing strains. Pulsed-field gel electrophoresis of 45 strains showed that these CTX-M-producing isolates belonged to 34 different types. To our knowledge, this is the first study to report the blaSHV-5 gene in E. coli isolated from chickens in China. Conjugation experiments demonstrated that the bla CTX-M and blaTEM genes could be transferred to E. coli strain J53, while conjugative transfer of the blaSHV-5 gene from two isolates was not detectable. blaCTX-M genes are carried by many kinds of transferable and untypable plasmids. Our findings demonstrate that the CTX-M enzymes are predominant in both type and quantity.
PMID: 25785885 [PubMed - as supplied by publisher]

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7. BMC Infect Dis. 2015 Dec;15(1):826. doi: 10.1186/s12879-015-0826-y. Epub 2015 Feb 19.

A retrospective study of contributing factors for prognosis and survival length of cryptococcal meningoencephalitis in Southern part of China (1998-2013).

Zheng H1, Li M, Luo Y, Wang D, Yang J, Chen Q, Lao J, Chen N, Yang M, Wang Q.
Author information:
Department of Neurology, Nanfang Hospital, Southern Medical University, No.1838 North Guangzhou Avenue, Guangzhou City, Guangdong Province, People's republic of China, gzzhenghui0527@gmail.com.

Abstract

BACKGROUND:

Cryptococcal meningoencephalitis (CM) is the most common opportunistic infection of the central nervous system (CNS). Despite this observation, there have only been a few studies analyzing clinical characteristics as well as cerebrospinal fluid (CSF), electroencephalograph (EEG), and magnetic resonance imaging (MRI) features in CM patients of all ages.

METHODS:

We reviewed the medical records of all patients diagnosed with cryptococcal meningoencephalitis from 1998 to 2013 in the Nanfang Hospital in China and gathered data on the underlying diseases, bird exposure history, and clinical features, including those from CSF, EEG and MRI.

RESULTS:

CM is more likely to infect adults younger than 60 years old. 71.3% of CM patients were male. Unlike data from other countries, we found that chronic use of corticosteroids or other immunosuppressants (17.59%) was the most frequent risk factor in CM patients rather than HIV infection (1.85%). Clear exposure with bird/ bird droppings before CM onset is obvious in a previous study in CM children. However, our study found that 4.63% CM patients had such an exposure. More importantly, patients with brain tissue damage (p = 0.021) and decreased CSF/blood glucose ratio (p = 0.008) were significantly associated with death, but only the decreased CSF/blood glucose ratio was the contributing factor of prognosis (odds ratio, 0.047; p = 0.025). Decreased CSF/blood glucose ratio was significantly related to the survival length of CM (odds ratio, 0.134; p = 0.033).

CONCLUSIONS:

Our study shows that CM has predilection for young male adults. The chronic use of corticosteroids or other immunosuppressants, rather than HIV infection or bird/bird droppings exposure, was the most frequent risk factor in CM patients in our study. Decreased CSF/blood glucose ratio was both an independent contributing factor to death and was significantly related to the survival length of CM patients. The more decreased the CSF/blood glucose ratio was, the worse prognosis and shorter survival length CM patients had.
PMCID: PMC4349236 Free Article
PMID: 25783104 [PubMed - in process]

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8. Malar J. 2015 Dec;14(1):617. doi: 10.1186/s12936-015-0617-3. Epub 2015 Mar 3.

Prevalence of new and known species of haemoparasites in feral pigeons in northwest Italy.

Scaglione FE1, Pregel P, Cannizzo FT, Pérez-Rodríguez AD, Ferroglio E, Bollo E.
Author information:
Dipartimento di Scienze Veterinarie, Università degli Studi di Torino, Via L. da Vinci 44, 10095, Grugliasco, Italy, frineeleonora.scaglione@unito.it.

Abstract

BACKGROUND:

Haemoparasites in feral pigeons have been studied in several countries but no data are available from Italy. The aim of this work was to evaluate the prevalence and diversity of Haemoproteus spp./Plasmodium spp. and Leucocytozoon spp. in feral pigeons from northwest Italy, as well as the association between infection and host age or sex.

METHODS:

Feral pigeons were collected during a regional culling programme from the Piedmont region (northwest Italy) and subjected to necropsy. Infections were detected from DNA extracted from the spleen following a nested PCR protocol. The association between sex or age and infection status was evaluated using the chi-squared test for independence or Fisher's exact test.

RESULTS:

Out of 51 animals, 15 were positive for Haemoproteus/Plasmodium spp. and eight for Leucocytozoon spp., with a significant difference between haemoparasites prevalence. There was no significant association between age or sex and infection status. The coinfection with different haemoparasites was very significant (p < 0.01), showing a greater relative risk to be infected by a second haemoparasite in birds already infected, in particular in male and in adult pigeons. DNA sequencing of Leucocytozoon spp. showed six different lineages in pigeons, and one of Haemoproteus and Plasmodium, respectively.

CONCLUSIONS:

Blood parasites are continuously circulating around the world, and the results presented in the paper suggest that cross infection of feral pigeons with haemoparasites typical of other migratory or nonmigratory bird species is possible. Moreover, the geographical location of Italy along the main migratory routes is a crucial factor to be considered for migratory birds, because they can be affected by blood parasites detected in feral pigeons, and vice versa.
PMCID: PMC4350268 Free Article
PMID: 25782830 [PubMed - in process]

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9. Zootaxa. 2015 Mar 9;3926(1):480-98. doi: 10.11646/zootaxa.3926.4.2.

A new genus and two new species of feather lice (Phthiraptera: Ischnocera: Philopteridae) from New Zealand endemic passerines (Aves: Passeriformes).

Valim MP1, Palma RL2.
Author information:
Museu de Zoologia da USP, Av. Nazaré, 481, Ipiranga, São Paulo, SP 04263-000, Brazil.; Email: mpvalim@gmail.com.
Museum of New Zealand Te Papa Tongarewa, P.O. Box 467, Wellington, New Zealand.; Email: ricardop@tepapa.govt.nz.

Abstract

The first descriptions of New Zealand endemic feather lice belonging to the Brueelia-complex (Phthiraptera: Ischnocera: Philopteridae) are given. The new genus Melibrueelia and new species M. novaeseelandiae are described, illustrated and compared with morphologically close taxa within the complex. The type host of M. novaeseelandiae is the tui, Prosthemadera novaeseelandiae (Gmelin, 1788), and an additional host is the bellbird, Anthornis melanura (Sparrman, 1786) (Passeriformes: Meliphagidae), both endemic to New Zealand. Also, the new species Brueelia callaeincola is described and illustrated from four endemic bird species belonging to two endemic genera and an endemic family: Philesturnus carunculatus (Gmelin, 1789) (the type host), Ph. rufusater (Lesson, 1828), Callaeas cinerea (Gmelin, 1788) and C. wilsoni (Bonaparte, 1851) (Passeriformes: Callaeidae). Brief discussions on possible evolutionary histories of the new taxa are included.
PMID: 25781798 [PubMed - in process]





10. Mol Ecol. 2015 Mar 17. doi: 10.1111/mec.13159. [Epub ahead of print]

Polymorphism at the Clock gene predicts phenology of long-distance migration in birds.

Saino N1, Bazzi G, Gatti E, Caprioli M, Cecere JG, Possenti CD, Galimberti A, Orioli V, Bani L, Rubolini D, Gianfranceschi L, Spina F.
Author information:
Department of Biosciences, University of Milan, via Celoria 26, I-20133, Milan, Italy.

Abstract

Dissecting phenotypic variance in life-history traits into its genetic and environmental components is at the focus of evolutionary studies and of pivotal importance to identify the mechanisms and predict the consequences of human-driven environmental change. The timing of recurrent life-history events (phenology) is under strong selection but the study of the genes that control potential environmental canalization in phenological traits is at its infancy. Candidate genes for circadian behavior entrained by photoperiod have been screened as potential controllers of phenological variation of breeding and molt in birds, with inconsistent results. Despite photoperiodic control of migration is well-established, no study has reported on migration phenology in relation to polymorphism at candidate genes in birds. We analyzed variation in spring migration dates within four trans-Saharan migratory species (Luscinia megarhynchos; Ficedula hypoleuca; Anthus trivialis; Saxicola rubetra) at a Mediterranean island in relation to Clock and Adcyap1 polymorphism. Individuals with larger number of glutamine residues in the poly-Q region of Clock gene migrated significantly later in one or, respectively, two species depending on sex and whether the within-individual mean length or the length of the longer Clock allele were considered. The results hinted at dominance of the longer Clock allele. No significant evidence for migration date to covary with Adcyap1 polymorphism emerged. This is the first evidence that migration phenology is associated with Clock in birds. This finding is important for evolutionary studies of migration and sheds light on the mechanisms that drive bird phenological changes and population trends in response to climate change. This article is protected by copyright. All rights reserved.
This article is protected by copyright. All rights reserved.
PMID: 25780812 [PubMed - as supplied by publisher]

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11. Philos Trans R Soc Lond B Biol Sci. 2015 May 5;370(1667). pii: 20140128. doi: 10.1098/rstb.2014.0128.

Effects of nocturnal illumination on life-history decisions and fitness in two wild songbird species.

de Jong M1, Ouyang JQ2, Da Silva A3, van Grunsven RH 4, Kempenaers B3, Visser ME2, Spoelstra K2.
Author information:
Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, 6700 AB Wageningen, The Netherlands m.dejong@nioo.knaw.nl.
Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, 6700 AB Wageningen, The Netherlands.
Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, Eberhard-Gwinner-Strasse, 82319 Seewiesen, Germany.
Nature Conservation and Plant Ecology Group, Wageningen University, PO Box 47, 6700 AA Wageningen, The Netherlands.

Abstract

The effects of artificial night lighting on animal behaviour and fitness are largely unknown. Most studies report short-term consequences in locations that are also exposed to other anthropogenic disturbance. We know little about how the effects of nocturnal illumination vary with different light colour compositions. This is increasingly relevant as the use of LED lights becomes more common, and LED light colour composition can be easily adjusted. We experimentally illuminated previously dark natural habitat with white, green and red light, and measured the effects on life-history decisions and fitness in two free-living songbird species, the great tit (Parus major) and pied flycatcher (Ficedula hypoleuca) in two consecutive years. In 2013, but not in 2014, we found an effect of light treatment on lay date, and of the interaction of treatment and distance to the nearest lamp post on chick mass in great tits but not in pied flycatchers. We did not find an effect in either species of light treatment on breeding densities, clutch size, probability of brood failure, number of fledglings and adult survival. The finding that light colour may have differential effects opens up the possibility to mitigate negative ecological effects of nocturnal illumination by using different light spectra.
© 2015 The Author(s) Published by the Royal Society. All rights reserved.
PMID: 25780240 [PubMed - in process]

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12. Philos Trans R Soc Lond B Biol Sci. 2015 May 5;370(1667). pii: 20140126. doi: 10.1098/rstb.2014.0126.

Light pollution alters the phenology of dawn and dusk singing in common European songbirds.

Da Silva A1, Valcu M1, Kempenaers B2.
Author information:
Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, Eberhard-Gwinner-Strasse, 82319 Seewiesen, Germany.
Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, Eberhard-Gwinner-Strasse, 82319 Seewiesen, Germany b.kempenaers@orn.mpg.de.

Abstract

Artificial night lighting is expanding globally, but its ecological consequences remain little understood. Animals often use changes in day length as a cue to time seasonal behaviour. Artificial night lighting may influence the perception of day length, and may thus affect both circadian and circannual rhythms. Over a 3.5 month period, from winter to breeding, we recorded daily singing activity of six common songbird species in 12 woodland sites, half of which were affected by street lighting. We previously reported on analyses suggesting that artificial night lighting affects the daily timing of singing in five species. The main aim of this study was to investigate whether the presence of artificial night lighting is also associated with the seasonal occurrence of dawn and dusk singing. We found that in four species dawn and dusk singing developed earlier in the year at sites exposed to light pollution. We also examined the effects of weather conditions and found that rain and low temperatures negatively affected the occurrence of dawn and dusk singing. Our results support the hypothesis that artificial night lighting alters natural seasonal rhythms, independently of other effects of urbanization. The fitness consequences of the observed changes in seasonal timing of behaviour remain unknown.
Free Article
PMID: 25780238 [PubMed - in process]

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13. BMC Vet Res. 2015 Dec;11(1):329. doi: 10.1186/s12917-015-0329-5. Epub 2015 Feb 7.

Mortality associated with avian reovirus infection in a free-living magpie (Pica pica) in Great Britain.

Lawson B1, Dastjerdi A, Shah S, Everest D, Núñez A, Pocknell A, Hicks D, Horton DL, Cunningham AA, Irvine RM.
Author information:
Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK, becki.lawson@ioz.ac.uk.

Abstract

BACKGROUND:

Avian reoviruses (ARVs) cause a range of disease presentations in domestic, captive and free-living bird species. ARVs have been reported as a cause of significant disease and mortality in free-living corvid species in North America and continental Europe. Until this report, there have been no confirmed cases of ARV-associated disease in British wild birds.

CASE PRESENTATION:

Sporadic individual magpie (Pica pica) mortality was detected at a single site in Buckinghamshire, England, April-September 2013. An adult female magpie was found moribund and subsequently died. Post-mortem examination identified hepatomegaly and splenomegaly as the most severe macroscopic abnormalities. Histopathological examination revealed extensive hepatic and splenic necrosis. Transmission electron microscopy (TEM) identified virions of a size (circa 78 nm diameter) and morphology consistent with ARV in both the liver and the small intestinal (SI) contents. Nucleic acid extracted from pooled liver and spleen was positive on both a pan-reovirus nested PCR targeting the RNA-dependent RNA polymerase gene and a PCR using primers specific to the ARV sigma C protein gene. Virus isolated from the liver and the SI contents was characterised by a syncytial-type cytopathic effect, a reovirus-like appearance on TEM and sequence identical to that from PCR of tissues. In situ hybridisation confirmed co-localisation of ARV with lesions in the liver and spleen, implicating ARV as the causative agent. Splenic lymphoid atrophy and necrotic stomatitis associated with Aspergillus fumigatus infection were consistent with generalised immunosuppression and resultant opportunistic infection.

CONCLUSIONS:

The pathology and comprehensive virus investigations in this case indicate ARV as the primary pathogen in this magpie, with concurrent secondary infection subsequent to immunosuppression, as has been observed with reoviral infections in other bird species. ARV should be considered as a differential diagnosis for magpie, and potentially other corvid, disease and mortality incidents. This is the first demonstration of ARV-associated mortality in a wild bird in Britain. The prevalence and significance of ARV infection in British wild birds, and its implications for poultry and captive bird health, are currently unknown.
PMCID: PMC4336486 Free PMC Article
PMID: 25779781 [PubMed - in process]

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14. Parasit Vectors. 2015 Dec;8(1):646. doi: 10.1186/s13071-015-0646-3. Epub 2015 Feb 8.

Intermediate hosts of the trematode Collyriclum faba (Plagiochiida: Collyriclidae) identified by an integrated morphological and genetic approach.

Heneberg P1, Faltýnková A, Bizos J, Malá M, Žiak J, Literák I.
Author information:
Third Faculty of Medicine, Charles University in Prague, Ruská 87, CZ-100 00, Prague, Czech Republic, petr.heneberg@lf3.cuni.cz.

Abstract

BACKGROUND:

The cutaneous monostome trematode Collyriclum faba (Bremser in Schmalz, 1831) is a bird parasite with a hitherto unknown life cycle and highly focal occurrence across the Holarctic and Neotropic ecozones.

METHODS:

Representative specimens of benthic organisms were sampled at multiple sites and dates within the known foci of C. faba occurrence in Slovakia. A combined approach involving detailed morphological examination and sequencing of two independent DNA loci was used for their analysis.

RESULTS:

We elucidated the complete life cycle of C. faba, which we determined to include the aquatic gastropod mollusk Bythinella austriaca (Frauenfeld, 1857) as the first intermediate host, the mayflies of the family Heptageniidae, Ecdyonurus venosus (Fabricius, 1775) and Rhithrogena picteti Sowa, 1971 x iridina (Kolenati, 1839), as the second intermediate hosts, and birds (primarily but not exclusively passeriform birds) as the definitive hosts. Bythinella austriaca occurs focally in the springs of tributaries of the Danube in the Alpine-Carpathian region. The restricted distribution of B. austriaca explains the highly focal distribution of C. faba noticed previously in spite of the broad distribution of its second intermediate and definitive host species. Utilization of both larval and adult Ephemeroptera spp. as the second intermediate hosts explains the known spectrum of the definitive host species, with the highest prevalence in species feeding on larvae of Ephemeroptera, such as Cinclus cinclus (Linnaeus, 1758) and Motacilla cinerea Tunstall, 1771, or adults of Ephemeroptera, such as Sylvia atricapilla (Linnaeus, 1758) and Regulus regulus (Linnaeus, 1758). In this study, we also determine the prevalence and DNA sequences of other immature trematode specimens found in the examined benthic organisms (particularly the families Microphallidae, Troglotrematidae and Nanophyetidae and Euryhelmis zelleri Grabda-Kazubska, 1980, Heterophyidae), and describe cercariae of C. faba.

CONCLUSIONS:

We determined the full life cycle of the Central European populations of C. faba. We speculate that other species of Bythinella and the closely related genus Amnicola may serve as first intermediate hosts in other parts of the distribution range of C. faba. Similarly, other Ephemeroptera of the family Heptageniidae may serve as the second intermediate hosts of C. faba in the Americas.
PMCID: PMC4332736 Free PMC Article
PMID: 25779229 [PubMed - in process]

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15. BMC Microbiol. 2015 Dec;15(1):388. doi: 10.1186/s12866-015-0388-6. Epub 2015 Feb 27.

Comparison of fecal and cecal microbiotas reveals qualitative similarities but quantitative differences.

Stanley D1, Geier MS, Chen H, Hughes RJ, Moore RJ.
Author information:
Central Queensland University, School of Medical and Applied Sciences, Bruce Highway, Rockhampton, QLD, 4702, Australia, d.stanley@cqu.edu.au.

Abstract

BACKGROUND:

The majority of chicken microbiota studies have used the ceca as a sampling site due to the specific role of ceca in chicken productivity, health and wellbeing. However, sampling from ceca and other gastrointestinal tract sections requires the bird to be sacrificed. In contrast, fecal sampling does not require sacrifice and thus allows the same bird to be sampled repeatedly over time. This is a more meaningful and preferred way of sampling as the same animals can be monitored and tracked for temporal studies. The commonly used practice of selecting a subset of birds at each time-point for sacrifice and sampling introduces added variability due to the known animal to animal variation in microbiota.

RESULTS:

Cecal samples and fecal samples via cloacal swab were collected from 163 birds across 3 replicate trials. DNA was extracted and 16S rRNA gene sequences amplified and pyrosequenced to determine and compare the phylogenetic profile of the microbiota within each sample. The fecal and cecal samples were investigated to determine to what extent the microbiota found in fecal samples represented the microbiota of the ceca. It was found that 88.55% of all operational taxonomic units (OTUs), containing 99.25% of all sequences, were shared between the two sample types, with OTUs unique for each sample type found to be very rare. There was a positive correlation between cecal and fecal abundance in the shared sequences, however the two communities differed significantly in community structure, represented as either alpha or beta diversity. The microbial populations present within the paired ceca of individual birds were also compared and shown to be similar.

CONCLUSIONS:

Fecal sample analysis captures a large percentage of the microbial diversity present in the ceca. However, the qualitative similarities in OTU presence are not a good representation of the proportions of OTUs within the microbiota from each sampling site. The fecal microbiota is qualitatively similar to cecal microbiota but quantitatively different. Fecal samples can be effectively used to detect some shifts and responses of cecal microbiota.
Free Article
PMID: 25777030 [PubMed - in process]

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16. J Plant Res. 2015 Mar 15. [Epub ahead of print]

Persistent history of the bird-dispersed arctic-alpine plant Vaccinium vitis-idaea L. (Ericaceae) in Japan.

Ikeda H1, Yoneta Y, Higashi H, Eidesen PB, Barkalov V, Yakubov V, Brochmann C, Setoguchi H.
Author information:
Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan, ike@okayama-u.ac.jp.

Abstract

Arctic-alpine plants have expanded and contracted their ranges in response to the Pleistocene climate oscillations. Today, many arctic-alpine plants have vast distributions in the circumarctic region as well as marginal, isolated occurrences in high mountains at lower latitudes. These marginal populations may represent relict, long-standing populations that have persisted for several cycles of cold and warm climate during the Pleistocene, or recent occurrences that either result from southward step-wise migration during the last glacial period or from recent long-distance dispersal. In light of these hypotheses, we investigated the biogeographic history of the marginal Japanese populations of the widespread arctic-alpine plant Vaccinium vitis-idaea (Ericaceae), which is bird-dispersed, potentially over long distances. We sequenced three nuclear loci and one plastid DNA region in 130 individuals from 65 localities covering its entire geographic range, with a focus on its marginal populations in Japan. We found a homogenous genetic pattern across its enormous range based on the loci analysed, in contrast to the geographically structured variation found in a previous study of amplified fragment length polymorphisms in this species. However, we found several unique haplotypes in the Japanese populations, excluding the possibility that these marginal populations result from recent southward migration. Thus, even though V. vitis-idaea is efficiently dispersed via berries, our study suggests that its isolated populations in Japan have persisted during several cycles of cold and warm climate during the Pleistocene.
PMID: 25773306 [PubMed - as supplied by publisher]
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17. Mol Reprod Dev. 2015 Mar 12. doi: 10.1002/mrd.22476. [Epub ahead of print]

Sexual dimorphism in the early embryogenesis of the chicken (Gallus Gallus domesticus).

Tagirov M1, Golovan S.
Author information:
Poultry Research Institute, Ukrainian Academy of Agrarian Sciences, Borky, Zmiiv District, Kharkiv Region, Ukraine.

Abstract

Studies of dioecious animals suggest that sex-specific development occurs from the onset of embryogenesis. This must be accounted for when addressing issues involving sex-ratio regulation in domestic animals and conservation biology. We investigated the occurrence of growth-rate sexual dimorphism in 84 chicken embryos incubated for 30 hr and nucleic-acid abundance in 99 embryos incubated for 4 hr. Comparative expression of the genes engaged in cell-cycle regulation (16 genes), embryo growth (10 genes), metabolic activity (2 genes), and epigenetic regulation (4 genes) in 4-hr male and female embryos were further analyzed by reverse-trancriptase quantitative PCR. At the stage when somite structure commences, males are growing faster than females. DNA and RNA yields at 4 hr are elevated in males compared to females, and most cell-proliferation-promoting genes are overexpressed in males. Expression of key metabolic genes (G6PD and HPRT) and the principal genes responsible for DNA methylation (DNMTs), however, does not differ between the sexes. These data suggest that the faster growth of early male embryos is conserved among mammalian and bird phyla, and may have an evolutionary importance. Mol. Reprod. Dev. 2015. © 2015 Wiley Periodicals, Inc.
© 2015 Wiley Periodicals, Inc.
PMID: 25772689 [PubMed - as supplied by publisher]
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18. J Helminthol. 2015 Mar 16:1-4. [Epub ahead of print]

The occurrence and pathogenicity of Serratospiculum tendo (Nematoda: Diplotriaenoidea) in birds of prey from southern Italy.

Santoro M1, D'Alessio N2, Di Prisco F2, Kinsella JM3, Barca L2, Degli Uberti B2, Restucci B4, Martano M4, Troisi S5, Galiero G2, Veneziano V4.
Author information:
Department of Public Health and Infectious Diseases,Section of Parasitology, 'Sapienza - University of Rome',P. le Aldo Moro n. 5,00185Rome,Italy.
Istituto Zooprofilattico Sperimentale del Mezzogiorno,Via Salute n. 2,Portici,Italy.
Helm West Laboratory,2108 Hilda Avenue,Missoula, Montana59801,USA.
Department of Veterinary Medicine and Animal Production,University of Naples Federico II,Naples,Italy.
Istituto Di Gestione Della Fauna - Onlus (IGF),Via Mezzocannone n. 8,80134 Naples,Italy.

Abstract

The air sacs of free-ranging birds of prey (n= 652) from southern Italy, including 11 species of Accipitriformes and six of Falconiforms, were examined for infections with Serratospiculum tendo (Nematoda: Diplotriaenoidea). Of the 17 species of birds examined, 25 of 31 (80.6%) peregrine falcons (Falco peregrinus) from Calabria Region and a single northern goshawk (Accipiter gentilis) from Campania Region were infected with S. tendo, suggesting a strong host specificity for the peregrine falcon. The northern goshawk and 18 of 25 infected peregrine falcons showed cachexia and all infected birds had bone fractures. At gross examination, air sacculitis and pneumonia were the most common lesions in infected birds. Microscopically, the air-sac walls showed thickening of the smooth muscle cells, resulting in a papillary appearance, along with hyperplasia of the mesothelium and epithelium, and foci of plasma cell infiltration and macrophages associated with several embryonated eggs and adult parasites. Extensive areas of inflammation were found in the lungs, characterized by lymphocytes, macrophages and fibroblasts surrounding embryonated eggs. The northern goshawk also had detachment of the dextral lung with several necrotic foci. In this case, the death of the bird was directly attributed to S. tendo infection. Lesions and pathological changes observed here suggest that S. tendo can cause disease.
PMID: 25772632 [PubMed - as supplied by publisher]
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20. Antonie Van Leeuwenhoek. 2015 Mar 14. [Epub ahead of print]

Prevalence, diversity and characterization of enterococci from three coraciiform birds.

Splichalova P1, Svec P, Ghosh A, Zurek L, Oravcova V, Radimersky T, Bohus M, Literak I.
Author information:
Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences Brno, Palackeho 1-3, 612 42, Brno, Czech Republic, p.frolkova@seznam.cz.

Abstract

Coraciiform birds hoopoe (Upupa epops), common kingfisher (Alcedo atthis) and European roller (Coracius garrulus) were examined for enterococci in their cloacae and uropygial glands. The enterococcal isolates were identified at the species level using several genomic and proteomic methods, screened for antibiotic susceptibility and genotyped by pulsed-field gel electrophoresis (PFGE). Clonality of isolates from the common kingfisher was also assessed by multi-locus sequence typing (MLST). Using selective media, putative enterococcal isolates (n = 117) were recovered from 74 % (32 out of a total of 43) of the bird samples and 114 isolates were confirmed as enterococci. Overall, among the total of 6 different species detected, Enterococcus faecalis was dominant (59 %) in all three bird species. The second most frequently isolated species was Enterococcus casseliflavus (32 %). PFGE revealed great diversity of strains from different bird species and anatomic location. Closely related strains were found only from nestlings from the same nest. No genes conferring resistance to vancomycin (vanA, vanB, vanC1 and van C2/C3) or erythromycin (erm A, ermB and mefA/E) were detected. MLST analysis and eBURST clustering revealed that sequence types of E. faecalis from the common kingfisher were identical to those of isolates found previously in water, chickens, and humans.
PMID: 25772302 [PubMed - as supplied by publisher]
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