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Thursday, 24 March 2016

What's new for 'birdRS' in PubMed. March Week 3, 2016

birdRS.net Latest Research News

PubMed Results

1. FEBS J. 2016 Mar 14. doi: 10.1111/febs.13710. [Epub ahead of print] 


Calcium channels in chicken sperm regulate motility and the acrosome reaction. 
Nguyen TM(1,)(2,)(3,)(4), Duittoz A(1,)(2,)(3), Praud C(5), Combarnous Y(1,)(2,)(3), Blesbois E(1,)(2,)(3). Author information: (1)INRA, UMR85 Physiologie de la Reproduction et des Comportements, F-37380, Nouzilly, France. (2)CNRS, UMR7247, F-37380, Nouzilly, France. (3)Université François Rabelais de Tours, F-37000, Tours, France. (4)Quy Nhon University, VietNam. (5)INRA, UR083 Recherches Avicoles, F-37380, Nouzilly, France. 

Abstract
Intracellular cytoplasmic calcium ([Ca(2+) ]i ) has an important regulatory role in gamete functions. The involved biochemical actors, however, are still unknown in birds, an animal class that has lost functional sperm-specific CatSper channels. In this report, we provide evidence for the presence and expression of different Ca(2+) channels in chicken sperm, including high voltage-activated channels (L and R-type), the Store Operated Ca(2+) channel (SOC) complex component Orai1, transient receptor potential channel (TRPC1) and inositol 1,4,5-trisphosphate receptors (IP3 R1). L and R-types channels were mainly localized in the acrosome and the midpiece, whereas T-type channels were not detected in chicken sperm. Orai1 was found in all compartments but with a weak, diffuse signal in the flagellum. TRCP1 was mainly localized in the acrosome and the midpiece, but was also identified with a weak, diffuse signal in the nucleus and the flagellum. IP3 R1 was mainly detected in the nucleus. The Ca(2+) channel inhibitors Nifedipine (L-type), SNX-482 (R-type), MRS-1845, 2-APB and YM-58483 (SOCs) decreased [Ca(2+) ]i sperm motility and acrosome reaction (AR) capability, with the SOC inhibitors most efficiently inhibiting these functions. Furthermore, we showed that Ca(2+) -mediated induction of AMPK phosphorylation was blocked by SOC inhibition. Our identification of important regulators of Ca(2+) signaling in bird sperm suggests that SOCs have a predominant role in gamete function, whereas T-type channels might not be involved. In addition, Ca(2+) entry via SOCs appears to be the most likely pathway for AMPK activation and consequent energy-requiring sperm functions such as motility and the AR. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved. PMID: 26990886 [PubMed - as supplied by publisher] 


2. Rev Med Virol. 2016 Mar 15. doi: 10.1002/rmv.1876. [Epub ahead of print] 

Sindbis virus as a human pathogen-epidemiology, clinical picture and pathogenesis. 
Adouchief S(1), Smura T(1), Sane J(2), Vapalahti O(1,)(3,)(4), Kurkela S(1,)(3). Author information: (1)Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland. (2)National institute for Health and Welfare (THL), Helsinki, Finland. (3)Department of Virology and Immunology, HUSLAB, Helsinki University Central Hospital, Helsinki, Finland. (4)Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland. 

Abstract
Sindbis virus (SINV; family Togaviridae, genus Alphavirus) is an enveloped RNA virus widely distributed in Eurasia, Africa, Oceania and Australia. SINV is transmitted among its natural bird hosts via mosquitoes. Human disease caused by SINV infection has been reported mainly in South Africa and in Northern Europe. Vector mosquito abundance affects the annual incidence of SINV infections with occasional outbreaks of up to 1500 patients. Symptoms include fever, malaise, rash and musculoskeletal pain. In a significant portion of patients the debilitating musculoskeletal symptoms persist for years. Chronic disease after SINV infection shares many features with autoimmune diseases. Currently there is no specific treatment available. Recently SINV infections have been detected outside the previously known distribution range. In this article we will summarize the current knowledge on epidemiology, clinical disease and pathogenesis of SINV infection in man. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd. PMID: 26990827 [PubMed - as supplied by publisher] 


3. Glob Chang Biol. 2016 Mar 17. doi: 10.1111/gcb.13283. [Epub ahead of print] 

Estimating indices of range shifts in birds using dynamic models when detection is imperfect. 
Clement MJ(1), Hines JE(1), Nichols JD(1), Pardieck KL(1), Ziolkowski DJ Jr(1). Author information: (1)United States Geological Survey, Patuxent Wildlife Research Center, Laurel, MD, 20770. 

Abstract
There is intense interest in basic and applied ecology about the effect of global change on current and future species distributions. Projections based on widely used static modeling methods implicitly assume that species are in equilibrium with the environment and that detection during surveys is perfect. We used multi-season correlated detection occupancy models, which avoid these assumptions, to relate climate data to distributional shifts of Louisiana Waterthrush in the North American Breeding Bird Survey (BBS) data. We summarized these shifts with indices of range size and position and compared them to the same indices obtained using more basic modeling approaches. Detection rates during point counts in BBS surveys were low, and models that ignored imperfect detection severely underestimated the proportion of area occupied and slightly overestimated mean latitude. Static models indicated Louisiana Waterthrush distribution was most closely associated with moderate temperatures, while dynamic occupancy models indicated that initial occupancy was associated with diurnal temperature ranges and colonization of sites was associated with moderate precipitation. Overall, the proportion of area occupied and mean latitude changed little during the 1997 to 2013 study period. Near-term forecasts of species distribution generated by dynamic models were more similar to subsequently observed distributions than forecasts from static-models. Occupancy models incorporating a finite mixture model on detection - a new extension to correlated detection occupancy models - were better supported and may reduce bias associated with detection heterogeneity. We argue that replacing phenomenological static models with more mechanistic dynamic models can improve projections of future species distributions. In turn, better projections can improve biodiversity forecasts, management decisions, and understanding of global change biology This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved. PMID: 26990459 [PubMed - as supplied by publisher] 


4. PLoS One. 2016 Mar 18;11(3):e0151099. doi: 10.1371/journal.pone.0151099. 

Ultra-Rapid Vision in Birds. 
Boström JE(1), Dimitrova M(1,)(2), Canton C(1), Håstad O(3), Qvarnström A(1), Ödeen A(1,)(3). Author information: (1)Department of Animal Ecology, Uppsala University, Norbyvägen 18D, S-752 36, Uppsala, Sweden. (2)Department of Zoology, Stockholm University, S-106 91, Stockholm, Sweden. (3)Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Box 7011, S-750 07, Uppsala, Sweden. 

Abstract
Flying animals need to accurately detect, identify and track fast-moving objects and these behavioral requirements are likely to strongly select for abilities to resolve visual detail in time. However, evidence of highly elevated temporal acuity relative to non-flying animals has so far been confined to insects while it has been missing in birds. With behavioral experiments on three wild passerine species, blue tits, collared and pied flycatchers, we demonstrate temporal acuities of vision far exceeding predictions based on the sizes and metabolic rates of these birds. This implies a history of strong natural selection on temporal resolution. These birds can resolve alternating light-dark cycles at up to 145 Hz (average: 129, 127 and 137, respectively), which is ca. 50 Hz over the highest frequency shown in any other vertebrate. We argue that rapid vision should confer a selective advantage in many bird species that are ecologically similar to the three species examined in our study. Thus, rapid vision may be a more typical avian trait than the famously sharp vision found in birds of prey. PMID: 26990087 [PubMed - as supplied by publisher] 


5. Sci Rep. 2016 Mar 18;6:23380. doi: 10.1038/srep23380. 

Pathobiological Characterization of a Novel Reassortant Highly Pathogenic H5N1 Virus Isolated in British Columbia, Canada, 2015. 
Berhane Y(1,)(2), Kobasa D(3,)(4), Embury-Hyatt C(1), Pickering B(1), Babiuk S(1,)(5), Joseph T(6), Bowes V(6), Suderman M(1), Leung A(3), Cottam-Birt C(1), Hisanaga T(1), Pasick J(1). Author information: (1)Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, Manitoba, Canada R3E 3M4. (2)Department of Animal Science, University of Manitoba, Winnipeg, Canada. (3)Public Health Agency of Canada, National Microbiology Laboratory, 1015 Arlington Street, Winnipeg, Manitoba, Canada. (4)Department of Medical Microbiology, University of Manitoba, Winnipeg, Canada. (5)Department of Immunology, University of Manitoba, Winnipeg, Canada. (6)Animal Health Centre, Ministry of Agriculture, Abbotsford, British Columbia, Canada V3G 2M3. 

Abstract
In the current study, we describe the pathobiologic characteristics of a novel reassortant virus - A/chicken/BC/FAV-002/2015 (H5N1) belonging to clade 2.3.4.4 that was isolated from backyard chickens in British Columbia, Canada. Sequence analyses demonstrate PB1, PA, NA and NS gene segments were of North American lineage while PB2, HA, NP and M were derived from a Eurasian lineage H5N8 virus. This novel virus had a 19 amino acid deletion in the neuraminidase stalk. We evaluated the pathogenic potential of this isolate in various animal models. The virus was highly pathogenic to mice with a LD50 of 10 plaque forming units (PFU), but had limited tissue tropism. It caused only subclinical infection in pigs which did result in seroconversion. This virus was highly pathogenic to chickens, turkeys, juvenile Muscovy ducks (Cairnia moschata foma domestica) and adult Chinese geese (Anser cynoides domesticus) causing a systemic infection in all species. The virus was also efficiently transmitted and resulted in mortality in naïve contact ducks, geese and chickens. Our findings indicate that this novel H5N1 virus has a wide host range and enhanced surveillance of migratory waterfowl may be necessary in order to determine its potential to establish itself in the wild bird reservoir. PMID: 26988892 [PubMed - in process] 


6. Parasitol Res. 2016 Mar 17. [Epub ahead of print] 

Occurrence of Mesocestoides canislagopodis (Rudolphi, 1810) (Krabbe, 1865) in mammals and birds in Iceland and its molecular discrimination within the Mesocestoides species complex. 
Skirnisson K(1), Jouet D(2), Ferté H(2), Nielsen ÓK(3). Author information: (1)Laboratory of Parasitology, Institute for Experimental Pathology, University of Iceland, Keldur, IS-112, Reykjavík, Iceland. karlsk@hi.is. (2)EA4688 « Vecpar », UFR de Pharmacie, Université de Reims Champagne-Ardenne, 51 rue Cognacq-Jay, 51096, Reims Cedex, France. (3)Icelandic Institute of Natural History, Urriðaholtsstræti 6-8, 210, Garðabær, Iceland. 

Abstract
The life cycle of Mesocestoides tapeworms (Cestoda: Cyclophyllidea: Mesocestoididae) requires three hosts. The first intermediate host is unknown but believed to be an arthropod. The second intermediate host is a vertebrate. The primary definitive host is a carnivore mammal, or a bird of prey, that eats the tetrathyridium-infected second intermediate host. One representative of the genus, Mesocestoides canislagopodis, has been reported from Iceland. It is common in the arctic fox (Vulpes lagopus) and has also been detected in domestic dogs (Canis familiaris) and cats (Felis domestica). Recently, scolices of a non-maturing Mesocestoides sp. have also been detected in gyrfalcon (Falco rusticolus) intestines, and tetrathyridia in the body cavity of rock ptarmigan (Lagopus muta). We examined the taxonomic relationship of Mesocestoides from arctic fox, gyrfalcon, and rock ptarmigan using molecular methods, both at the generic level (D1 domain LSU ribosomal DNA) and at the specific level (cytochrome c oxidase subunit I (COI) and 12S mitochondrial DNA). All stages belonged to Mesocestoides canislagopodis. Phylogenetic analysis of the combined 12S-COI at the specific level confirmed that M. canislagopodis forms a distinct clade, well separated from three other recognized representatives of the genus, M. litteratus, M. lineatus, and M. corti/vogae. This is the first molecular description of this species. The rock ptarmigan is a new second intermediate host record, and the gyrfalcon a new primary definitive host record. However, the adult stage seemed not to be able to mature in the gyrfalcon, and successful development is probably restricted to mammalian hosts. PMID: 26984208 [PubMed - as supplied by publisher] 


7. Avian Pathol. 2016 Mar 16:1-17. [Epub ahead of print] 

Efficacy of Avilamycin for the Prevention of Necrotic Enteritis Caused by a Pathogenic Strain of Clostridium perfringens in Broiler Chickens. 
Paradis MA(1), McMillan E(2), Bagg R(1), Vessie G(1), Zocche A(3), Thompson M(4). Author information: (1)a Elanco Animal Health , Division of Eli Lilly Canada Inc ., 150 Research Lane, Suite 120, Guelph , Ontario , Canada N1G 4T2. (2)b Nutreco Canada Agresearch , RR#3 473, Sixth Concession Road, Burford , Ontario , Canada N0E 1A0. (3)c Elanco Animal Health , 2500 Innovation Way, Greenfield , Indiana , United States 46140. (4)d Novometrix Research Inc ., 4564 Nassagaweya-Puslinch Townline, Moffat , Ontario , Canada L0P 1J0. 

Abstract
The efficacy of avilamycin for the prevention of necrotic enteritis (NE) was investigated in a 35-day floor pen study of 2,200 broiler cockerels using a Clostridium perfringens (Cp) feed inoculum challenge model. Treatments consisted of 1) nonmedicated, nonchallenged; 2) nonmedicated, challenged; 3) avilamycin at 15 ppm, challenged; 4) avilamycin at 30 ppm, challenged. Avilamycin was administered in the feed from day 7 to day 30 of the study. Challenge inoculum was administered on day 14 and delivered approximately 10(9) CFU Cp/bird. Necrotic enteritis mortality rates from day 14-35 were significantly (P<0.0001) lower in birds treated with avilamycin at 15 and 30 ppm when compared to nonmedicated, challenged birds. Treatment with avilamycin also resulted in a significant reduction in ileal Cp count on day 21 (P<0.0001) and NE lesion scores on day 17 (P<0.006) when compared to nonmedicated, challenged birds. The performance of birds treated with avilamycin was also improved when compared to nonmedicated, challenged birds. Cockerels that received either 15 or 30 ppm avilamycin had a significantly (P<0.0001) increased body weight on day 35 and average daily gain from days 0-35 than nonmedicated, challenged birds. Furthermore, birds treated with avilamycin had an improved feed conversion rate from days 0-35 than both nonmedicated, nonchallenged birds and nonmedicated, challenged birds. This study confirms that avilamycin is effective at controlling mortality related to NE in growing broiler chickens. PMID: 26981841 [PubMed - as supplied by publisher] 


8. J Wildl Dis. 2016 Mar 16. [Epub ahead of print] 

SURVEY FOR WEST NILE VIRUS ANTIBODIES IN WILD DUCKS, 2004-06, USA. 
Hofmeister EK(1), Jankowski MD(1), Goldberg D(1), Franson JC(1). Author information: (1)1   U.S. Geological Survey, National Wildlife Health Center, 6006 Schroeder Road, Madison, Wisconsin 53711, USA. 

Abstract
Detection of West Nile virus (WNV) in ducks has been reported in North America in isolated cases of mortality in wild waterbirds and following outbreaks in farmed ducks. Although the virus has been noted as an apparent incidental finding in several species of ducks, little is known about the prevalence of exposure or the outcome of infection with WNV in wild ducks in North America. From 2004-06, we collected sera from 1,406 wild-caught American Wigeon ( Anas americana ), Mallard ( Anas platyrhynchos ), and Northern Pintail ( Anas acuta ) ducks at national wildlife refuges (NWRs) in North Dakota and Wood Ducks ( Aix sponsa ) at NWRs in South Carolina and Tennessee. We measured the prevalence of previous exposure to WNV in these ducks by measuring WNV antibodies and evaluated variation in exposure among species, age, and year. Additionally, we evaluated the performance of a commercial antibody to wild bird immunoglobulin in duck species that varied in their phylogenetic relatedness to the bird species the antibody was directed against. As determined by a screening immunoassay and a confirmatory plaque reduction neutralization assay, the prevalence of WNV antibody was 10%. In light of experimental studies that show ducks to be relatively resistant to mortality caused by WNV, the antibody prevalence we detected suggests that wild ducks may be less-frequently exposed to WNV than expected for birds inhabiting wetlands where they may acquire infection from mosquitoes. PMID: 26981693 [PubMed - as supplied by publisher] 


9. J Wildl Dis. 2016 Mar 16. [Epub ahead of print] 

SUSCEPTIBILITY AND ANTIBODY RESPONSE OF VESPER SPARROWS (POOECETES GRAMINEUS) TO WEST NILE VIRUS: A POTENTIAL AMPLIFICATION HOST IN SAGEBRUSH-GRASSLAND HABITAT. 
Hofmeister EK(1), Dusek RJ(1), Fassbinder-Orth C(2,)(3), Owen B(3), Franson JC(1). Author information: (1)1   US Geological Survey, National Wildlife Health Center, 6006 Schroeder Road, Madison, Wisconsin 53711, USA. (2)2   University of Wisconsin, Madison, Wisconsin 53706, USA. (3)3   Creighton University, Omaha, Nebraska 68178, USA. West Nile virus (WNV) spread to the US western plains states in 2003, when a significant mortality event attributed to WNV occurred in Greater Sage-grouse ( Centrocercus urophasianus ). 

Abstract
The role of avian species inhabiting sagebrush in the amplification of WNV in arid and semiarid regions of the North America is unknown. We conducted an experimental WNV challenge study in Vesper Sparrows ( Pooecetes gramineus ), a species common to sagebrush and grassland habitats found throughout much of North America. We found Vesper Sparrows to be moderately susceptible to WNV, developing viremia considered sufficient to transmit WNV to feeding mosquitoes, but the majority of birds were capable of surviving infection and developing a humoral immune response to the WNV nonstructural 1 and envelope proteins. Despite clearance of viremia, after 6 mo, WNV was detected molecularly in three birds and cultured from one bird. Surviving Vesper Sparrows were resistant to reinfection 6 mo after the initial challenge. Vesper sparrows could play a role in the amplification of WNV in sagebrush habitat and other areas of their range, but rapid clearance of WNV may limit their importance as competent amplification hosts of WNV. PMID: 26981692 [PubMed - as supplied by publisher] 


10. J Appl Ecol. 2016 Apr 1;53(2):511-518. Epub 2015 Dec 18. 

An introduced parasitic fly may lead to local extinction of Darwin's finch populations. 
Koop JA(1), Kim PS(2), Knutie SA(1), Adler F(3), Clayton DH(1). Author information: (1)Department of Biology, University of Utah, Salt Lake City, UT, USA. (2)Mathematics Department, University of Utah, Salt Lake City, UT, USA. (3)Department of Biology, University of Utah, Salt Lake City, UT, USA; Mathematics Department, University of Utah, Salt Lake City, UT, USA. 

Abstract
Introduced pathogens and other parasites are often implicated in host population level declines and extinctions. However, such claims are rarely supported by rigorous real-time data. Indeed, the threat of introduced parasites often goes unnoticed until after host populations have declined severely. The recent introduction of the parasitic nest fly, Philornis downsi, to the Galápagos Islands provides an opportunity to monitor the current impact of an invasive parasite on endemic land bird populations, including Darwin's finches.In this paper we present a population viability model to explore the potential long-term effect of P. downsi on Darwin's finch populations. The goal of our study was to determine whether P. downsi has the potential to drive host populations to extinction and whether management efforts are likely to be effective.Our model is based on data from five years of experimental field work documenting the effect of P. downsi on the reproductive success of medium ground finch Geospiza fortis populations on Santa Cruz Island. Under two of the three scenarios tested, the model predicted medium ground finches are at risk of extinction within the next century.However, sensitivity analyses reveal that even a modest reduction in the prevalence of the parasite could improve the stability of finch populations. We discuss the practicality of several management options aimed at achieving this goal.Synthesis and applications. Our study demonstrates the predicted high risk of local extinction of an abundant host species, the medium ground finch Geospiza fortis due to an introduced parasite, Philornis downsi. However, our study further suggests that careful management practices aimed at reducing parasite prevalence have the potential to significantly lower the risk of host species extinction. PMCID: PMC4788638 [Available on 2017-04-01] PMID: 26980922 [PubMed] 


11. Genome Biol Evol. 2016 Mar 14. pii: evw041. [Epub ahead of print] 

Whole genome identification, phylogeny and evolution of the cytochrome P450 family 2 (CYP2) sub-families in birds. 
Almeida D(1), Maldonado E(2), Khan I(1), Silva L(1), Gilbert MT(3), Zhang G(4), Jarvis ED(5), O'Brien SJ(6), Johnson WE(7), Antunes A(8). Author information: (1)CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas 177, 4050-123 Porto, Portugal Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal. (2)CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas 177, 4050-123 Porto, Portugal. (3)Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Volgade 5-7, 1350 Copenhagen, Denmark. (4)BGI-Shenzhen, Main Building 2#, Beishan Industrial Zoon, Yantian District, Shenzhen, China. (5)Howard Hughes Medical Institute, Department of Neurobiology, Box 3209, Duke University Medical Center Durham, North Carolina 27710, USA. (6)Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004. Oceanographic Center, 8000 N. Ocean Drive, USA; Nova Southeastern University, Ft Lauderdale, Florida 33004. (7)Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA 22630, USA. (8)CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas 177, 4050-123 Porto, Portugal Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal aantunes@ciimar.up.pt. 

Abstract
The cytochrome P450 (CYP) superfamily defends organisms from endogenous and noxious environmental compounds, and thus is crucial for survival. However, beyond mammals the molecular evolution of CYP2 subfamilies is poorly understood. Here, we characterized the CYP2 family across 48 novel avian whole genomes representing all major extant bird clades. Overall, 12 CYP2 subfamilies were identified, including the first description of the CYP2F, CYP2G and several CYP2AF genes in avian genomes. Some of the CYP2 genes previously described as being lineage-specific, such as CYP2K and CYP2W, are ubiquitous to all avian groups. Furthermore, we identified a large number of CYP2J copies, which have been associated previously with water reabsorption. We detected positive selection in the avian CYP2C, CYP2D, CYP2H, CYP2J, CYP2K and CYP2AC subfamilies. Moreover, we identified new substrate recognition sites (SRS0, SRS2_SRS3 and SRS3.1) and heme binding areas that influence CYP2 structure and function of functional importance as under significant positive selection. Some of the positively selected sites in avian CYP2D are located within the same SRS1 region that was previously linked with the metabolism of plant toxins. Additionally, we find that selective constraint variations in some avian CYP2 subfamilies are consistently associated with different feeding habits (CYP2H and CYP2J), habitats (CYP2D, CYP2H, CYP2J and CYP2K) and migratory behaviors (CYP2D, CYP2H and CYP2J). Overall, our findings indicate that there has been active enzyme site selection on CYP2 subfamilies and differential selection associated with different life history traits among birds. © The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. PMID: 26979796 [PubMed - as supplied by publisher] 


12. G3 (Bethesda). 2016 Mar 14. pii: g3.116.027946. doi: 10.1534/g3.116.027946. [Epub ahead of print] 

Gene Regulatory Evolution During Speciation in a Songbird. 
Davidson JH(1), Balakrishnan CN(2). Author information: (1)East Carolina University. (2)East Carolina University balakrishnanc@ecu.edu. 

Abstract
Over the last decade tremendous progress has been made towards a comparative understanding of gene regulatory evolution. However, we know little about how gene regulation evolves in birds, and how divergent genomes interact in their hybrids. Because of the unique features of birds - female heterogamety, a highly conserved karyotype, and the slow evolution of reproductive incompatibilities - an understanding of regulatory evolution in birds is critical to a comprehensive understanding of regulatory evolution and its implications for speciation. Using a novel complement of analyses of replicated RNA-seq libraries, we demonstrate abundant divergence in brain gene expression between zebra finch (Taeniopygia guttata) subspecies. By comparing parental populations and their F1 hybrids, we also show that gene misexpression is relatively rare among brain-expressed transcripts in male birds. If this pattern is consistent across tissues and sexes, it may partially explain the slow buildup of postzygotic reproductive isolation observed in birds relative to other taxa. Although we expected that the action of genetic drift on the island-dwelling zebra finch subspecies would be manifested in a higher rate of trans regulatory divergence, we found that most divergence was in cis regulation, following a pattern commonly observed in other taxa. Thus our study highlights both unique and shared features of avian regulatory evolution. Copyright © 2016 Author et al. PMID: 26976438 [PubMed - as supplied by publisher] 


13. Mol Phylogenet Evol. 2016 Mar 12. pii: S1055-7903(16)00072-5. doi: 10.1016/j.ympev.2016.03.004. [Epub ahead of print] 

Diverse sampling of East African haemosporidians reveals chiropteran origin of malaria parasites in primates and rodents. 
Lutz HL(1), Patterson BD(2), Kerbis Peterhans JC(3), Stanley WT(2), Webala PW(4), Gnoske TP(2), Hackett SJ(2), Stanhope MJ(5). Author information: (1)Department of Ecology and Evolutionary Biology, College of Agricultural and Life Sciences, Cornell University, Ithaca, NY 14853, United States; Cornell Lab of Ornithology, Cornell University, Ithaca, NY 14853, United States; Science & Education, Field Museum of Natural History, Chicago, IL 60605, United States; Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, United States. Electronic address: hll47@cornell.edu. (2)Science & Education, Field Museum of Natural History, Chicago, IL 60605, United States. (3)Science & Education, Field Museum of Natural History, Chicago, IL 60605, United States; College of Professional Studies, Roosevelt University, Chicago, IL 60605, United States. (4)Department of Tourism and Wildlife Management, Maasai Mara University, Narok 20500, Kenya. (5)Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, United States. 

Abstract
Phylogenies of parasites provide hypotheses on the history of their movements between hosts, leading to important insights regarding the processes of host switching that underlie modern-day epidemics. Haemosporidian (malaria) parasites lack a well resolved phylogeny, which has impeded the study of evolutionary processes associated with host-switching in this group. Here we present a novel phylogenetic hypothesis that suggests bats served as the ancestral hosts of malaria parasites in primates and rodents. Expanding upon current taxon sampling of Afrotropical bat and bird parasites, we find strong support for all major nodes in the haemosporidian tree using both Bayesian and maximum likelihood approaches. Our analyses support a single transition of haemosporidian parasites from saurian to chiropteran hosts, and do not support a monophyletic relationship between Plasmodium parasites of birds and mammals. We find, for the first time, that Hepatocystis and Plasmodium parasites of mammals represent reciprocally monophyletic evolutionary lineages. These results highlight the importance of broad taxonomic sampling when analyzing phylogenetic relationships, and have important implications for our understanding of key host switching events in the history of malaria parasite evolution. Copyright © 2016 Elsevier Inc. All rights reserved. PMID: 26975691 [PubMed - as supplied by publisher] 


14. Front Cell Infect Microbiol. 2016 Mar 4;6:26. doi: 10.3389/fcimb.2016.00026. eCollection 2016. 

Identification of Biomarkers for Footpad Dermatitis Development and Wound Healing. 
Chen J(1), Tellez G(2), Escobar J(1). Author information: (1)Research and Development, Novus International Inc. St. Charles, MO, USA. (2)Department of Poultry Science, University of Arkansas Fayetteville, AR, USA. 

Abstract
Footpad dermatitis (FPD) is a type of skin inflammation that causes necrotic lesions on the plantar surface of the footpads in commercial poultry, with significant animal welfare, and economic implications. To identify biomarkers for FPD development and wound healing, a battery cage trial was conducted in which a paper sheet was put on the bottom of cages to hold feces to induce FPD of broilers. Day-of-hatch Ross 308 male broiler chicks were fed a corn-soybean meal diet and assigned to 3 treatments with 8 cages per treatment and 11 birds per cage. Cages without paper sheets were used as a negative control (NEG). Cages with paper sheets during the entire growth period (d 0-30) were used as a positive control (POS) to continually induce FPD. Cages with paper sheets during d 0-13 and without paper sheets during d 14-30 were used to examine the dynamic of FPD development and lesion wound healing (LWH). Footpad lesions were scored to grade (G) 1-5 with no lesion in G1 and most severe lesion in G5. Covering with paper sheets in POS and LWH induced 99% incidence of G3 footpads on d 13. Removing paper sheets from LWH healed footpad lesions by d 30. One representative bird, with lesions most close to pen average lesion score, was chosen to collect footpad skin samples for biomarker analysis. Total collagen protein and mRNA levels of tenascin X (TNX), type I α1 collagen (COL1A1), type III α1 collagen (COL3A1), tissue inhibitor of metalloproteinase 3 (TIMP3), and integrin α1 (ITGA1) mRNA levels were decreased (P < 0.05), while mRNA levels of tenascin C (TNC), tumor necrosis factor (TNF) α, Toll-like receptor (TLR) 4 and vascular endothelial growth factor (VEGF), IL-1β, and the ratio of MMP2 to all TIMP were increased (P < 0.03) in G3 footpads in POS and LWH compared to G1 footpads in NEG on d 14. These parameters continued to worsen with development of more severe lesions in POS. After paper sheets were removed (i.e., LWH), levels of these parameters gradually or rapidly returned to levels measured in NEG. Regression analysis indicated significant quadratic changes of these parameters to footpad lesion scores. In summary, these biomarkers were interrelated with dynamic changes of footpad lesion scores, suggesting they may be used as potential biomarkers for footpad lesion development and wound healing process. PMCID: PMC4777922 PMID: 26973819 [PubMed - in process] 


15. Gen Comp Endocrinol. 2016 Mar 10. pii: S0016-6480(16)30058-2. doi: 10.1016/j.ygcen.2016.03.013. [Epub ahead of print] 

The ecological and physiological bases of variation in the phenology of gonad growth in an urban and desert songbird. 
Davies S(1), Lane S(2), Meddle SL(3), Tsutsui K(4), Deviche P(2). Author information: (1)School of Life Sciences, Arizona State University, Tempe, Arizona 85287, USA. Electronic address: Scott.Davies@asu.edu. (2)School of Life Sciences, Arizona State University, Tempe, Arizona 85287, USA. (3)The Roslin Institute & Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, Midlothian EH25 9PS, UK. (4)Laboratory of Integrative Brain Sciences, Department of Biology and Center for Medical Life Science, Waseda University, Tokyo 162-8480, Japan. 

Abstract
Birds often adjust to urban areas by advancing the timing (phenology) of vernal gonad growth. However, the ecological and physiological bases of this adjustment are unclear. We tested whether the habitat-related disparity in gonad growth phenology of male Abert's towhees, Melozone aberti, is due to greater food availability in urban areas of Phoenix, Arizona USA or, alternatively, a habitat-related difference in the phenology of key food types. To better understand the physiological mechanism underlying variation in gonad growth phenology, we compared the activity of the reproductive system at all levels of hypothalamo-pituitary-gonadal (HPG) axis. We found no habitat-associated difference in food availability (ground arthropod biomass), but, in contrast to the seasonal growth of leaves on desert trees, the leaf foliage of urban trees was already developed at the beginning of our study. Multiple estimates of energetic status did not significantly differ between the non-urban and urban populations during three years that differed in the habitat-related disparity in gonad growth and winter precipitation levels. Thus, our results provide no support for the hypothesis that greater food abundance in urban areas of Phoenix drives the habitat-related disparity in gonad growth phenology in Abert's towhees. By contrast, they suggest that differences in the predictability and magnitude of change in food availability between urban and desert areas of Phoenix contribute to the observed habitat-related disparity in gonad growth. Endocrine responsiveness of the gonads may contribute to this phenomenon as desert - but not urban - towhees had a marked plasma T response to GnRH challenge. Copyright © 2016. Published by Elsevier Inc. PMID: 26972152 [PubMed - as supplied by publisher] 


16. Mar Pollut Bull. 2016 Mar 9. pii: S0025-326X(16)30120-5. doi: 10.1016/j.marpolbul.2016.02.069. [Epub ahead of print] 

Plastic mistaken for prey by a colony-breeding Eleonora's falcon (Falco eleonorae) in the Mediterranean Sea, revealed by camera-trap. Steen R(1), Torjussen CS(2), Jones DW(3), Tsimpidis T(3), Miliou A(3). Author information: (1)Department of Ecology and Natural Resource Management, Norwegian University of Life Science, P.O. Box 5003, 1432 Ås, Norway. Electronic address: ronny.steen@nmbu.no. (2)Department of Ecology and Natural Resource Management, Norwegian University of Life Science, P.O. Box 5003, 1432 Ås, Norway. (3)Archipelagos, Institute of Marine Conservation, Marine Research Base, P.O. Box 42, Pythagorio 83102, Samos, Greece. 

Abstract
Discarded plastic is known to be harmful for marine animals through ingestion and entanglement. Here we report the first documentation of Eleonora's falcons providing plastic waste to dependent nestlings. Eleonora's falcons breed colonially on sea cliffs and islets in areas of the Mediterranean Sea and the Canary Islands in which they normally feed their nestlings exclusively with small migratory birds. Copyright © 2016 Elsevier Ltd. All rights reserved. PMID: 26971232 [PubMed - as supplied by publisher] 


17. Sci Total Environ. 2016 Mar 10;556:80-88. doi: 10.1016/j.scitotenv.2016.02.205. [Epub ahead of print] 

Persistent organic pollutant and mercury concentrations in eggs of ground-nesting marine birds in the Canadian high Arctic. 
Peck LE(1), Gilchrist HG(2), Mallory CD(3), Braune BM(2), Mallory ML(4). Author information: (1)Department of Biology, Acadia University, Wolfville, Nova Scotia B4P 2R6, Canada. (2)Environment Canada, National Wildlife Research Centre, Carleton University, Ottawa, Ontario K1A 0H3, Canada. (3)Department of Environment, Government of Nunavut, Iqaluit, Nunavut X0A 0H0, Canada. (4)Department of Biology, Acadia University, Wolfville, Nova Scotia B4P 2R6, Canada. Electronic address: Mark.mallory@acadiau.ca. 

Abstract
We collected eggs of eight marine bird species from several colony sites in the Canadian high Arctic located at approximately 76°N and analyzed them for concentrations of legacy persistent organic pollutants (POPs) and mercury. We provide the first report on concentrations of POPs in eggs of three Arctic species (Thayer's gull Larus thayeri, Sabine's gull Xema sabini, Ross's Gull Rhodostethia rosea), and we found significant differences in each of the POP profiles among the five species with sufficient data for statistical comparisons (Thayer's gull, black guillemot Cepphus grylle, Sabine's gull, Arctic tern Sterna paradisaea and common eider Somateria mollissima borealis). The Ross's Gull had unexpectedly high POP concentrations relative to the other species examined, although this was based on a single egg, while glaucous gull Larus hyperboreus eggs from our sampling location had very low POPs. Sabine's gulls had the lowest Hg of the eggs studied, consistent with their low trophic position, but concentrations of their legacy POPs were higher than expected. We also noted that total hexachlorocyclohexanes were higher than reported elsewhere in the circumpolar Arctic in three species. Copyright © 2016 Elsevier B.V. All rights reserved. PMID: 26971212 [PubMed - as supplied by publisher] 


18. Malar J. 2016 Mar 11;15(1):154. doi: 10.1186/s12936-016-1198-5. 

A method to preserve low parasitaemia Plasmodium-infected avian blood for host and vector infectivity assays. 
Carlson JS(1), Giannitti F(2,)(3,)(4), Valkiūnas G(5), Tell LA(6), Snipes J(6), Wright S(7), Cornel AJ(8,)(9). Author information: (1)Mosquito Control Research Laboratory, Department of Entomology and Nematology, Kearney Agriculture Center, University of California, Parlier, Davis, USA. jennysaracarlson@gmail.com. (2)Veterinary Diagnostic Laboratory, Veterinary Population Medicine Department, College of Veterinary Medicine, University of Minnesota, Saint Paul, USA. (3)Instituto Nacional de Investigación Agropecuaria, La Estanzuela, Colonia, Uruguay. (4)California Animal Health and Food Safety Laboratory, School of Veterinary Medicine, University of California, Davis, USA. (5)Nature Research Centre, Akademijos 2, 08412, Vilnius, Lithuania. (6)Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, USA. (7)Sacramento-Yolo Mosquito Vector and Control District, Elk Grove, USA. (8)Mosquito Control Research Laboratory, Department of Entomology and Nematology, Kearney Agriculture Center, University of California, Parlier, Davis, USA. (9)Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, University of California, Davis, USA. 

Abstract
BACKGROUND: Avian malaria vector competence studies are needed to understand more succinctly complex avian parasite-vector-relations. The lack of vector competence trials may be attributed to the difficulty of obtaining gametocytes for the majority of Plasmodium species and lineages. To conduct avian malaria infectivity assays for those Plasmodium spp. and lineages that are refractory to in vitro cultivation, it is necessary to obtain and preserve for short periods sufficient viable merozoites to infect naïve donor birds to be used as gametocyte donors to infect mosquitoes. Currently, there is only one described method for long-term storage of Plasmodium spp.-infected wild avian blood and it is reliable at a parasitaemia of at least 1 %. However, most naturally infected wild-caught birds have a parasitaemia of much less that 1 %. To address this problem, a method for short-term storage of infected wild avian blood with low parasitaemia (even ≤0.0005 %) has been explored and validated. METHODS: To obtain viable infective merozoites, blood was collected from wild birds using a syringe containing the anticoagulant and the red blood cell preservative citrate phosphate dextrose adenine solution (CPDA). Each blood sample was stored at 4 °C for up to 48 h providing sufficient time to determine the species and parasitaemia of Plasmodium spp. in the blood by morphological examination before injecting into donor canaries. Plasmodium spp.-infected blood was inoculated intravenously into canaries and once infection was established, Culex stigmatosoma, Cx. pipiens and Cx. quinquefasciatus mosquitoes were then allowed to feed on the infected canaries to validate the efficacy of this method for mosquito vector competence assays. RESULTS: Storage of Plasmodium spp.-infected donor blood at 4 °C yielded viable parasites for 48 h. All five experimentally-infected canaries developed clinical signs and were infectious. Pathologic examination of three canaries that later died revealed splenic lesions typical of avian malaria infection. Mosquito infectivity assays demonstrated that Cx. stigmatosoma and Cx. pipiens were competent vectors for Plasmodium cathemerium. CONCLUSIONS: A simple method of collecting and preserving avian whole blood with malaria parasites of low parasitaemia (≤0.0005 %) was developed that remained viable for further experimental bird and mosquito infectivity assays. This method allows researchers interested in conducting infectivity assays on target Plasmodium spp. to collect these parasites directly from nature with minimal impact on wild birds. PMCID: PMC4787182 PMID: 26969510 [PubMed - in process] 


19. Genet Sel Evol. 2015 Sep 28;47:75. doi: 10.1186/s12711-015-0152-2. 

Predicting direct and indirect breeding values for survival time in laying hens using repeated measures. 
Brinker T(1), Ellen ED(2), Veerkamp RF(3), Bijma P(4). Author information: (1)Animal Breeding and Genomics Centre, Wageningen UR, P.O. Box 338, 6700 AH, Wageningen, The Netherlands. tessa.brinker@wur.nl. (2)Animal Breeding and Genomics Centre, Wageningen UR, P.O. Box 338, 6700 AH, Wageningen, The Netherlands. Esther.Ellen@wur.nl. (3)Animal Breeding and Genomics Centre, Wageningen UR, P.O. Box 338, 6700 AH, Wageningen, The Netherlands. Roel.Veerkamp@wur.nl. (4)Animal Breeding and Genomics Centre, Wageningen UR, P.O. Box 338, 6700 AH, Wageningen, The Netherlands. Piter.Bijma@wur.nl. 

Abstract
BACKGROUND: Minimizing bird losses is important in the commercial layer industry. Selection against mortality is challenging because heritability is low, censoring is high, and individual survival depends on social interactions among cage members. With cannibalism, mortality depends not only on an individual's own genes (direct genetic effects; DGE) but also on genes of its cage mates (indirect genetic effects; IGE). To date, studies using DGE-IGE models have focussed on survival time but their shortcomings are that censored records were considered as exact lengths of life and models assumed that IGE were continuously expressed by all cage members even after death. However, since dead animals no longer express IGE, IGE should ideally be time-dependent in the model. Neglecting censoring and timing of IGE expression may reduce accuracy of estimated breeding values (EBV). Thus, our aim was to improve prediction of breeding values for survival time in layers that present cannibalism. METHODS: We considered four DGE-IGE models to predict survival time in layers. One model was an analysis of survival time and the three others treated survival in consecutive months as a repeated binomial trait (repeated measures models). We also tested whether EBV were improved by including timing of IGE expression in the analyses. Approximate EBV accuracies were calculated by cross-validation. The models were fitted to survival data on two purebred White Leghorn layer lines W1 and WB, each having monthly survival records over 13 months. RESULTS: Including the timing of IGE expression in the DGE-IGE model reduced EBV accuracy compared to analysing survival time. EBV accuracy was higher when repeated measures models were used. However, there was no universal best model. Using repeated measures instead of analysing survival time increased EBV accuracy by 10 to 21 and 2 to 12 % for W1 and WB, respectively. We showed how EBV and variance components estimated with repeated measures models can be translated into survival time. CONCLUSIONS: Our results suggest that prediction of breeding values for survival time in laying hens can be improved using repeated measures models. This is an important result since more accurate EBV contribute to higher rates of genetic gain. PMCID: PMC4587788 PMID: 26416791 [PubMed - indexed for MEDLINE]



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