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Tuesday, 19 May 2015

What's new for 'birdRS' in PubMed. May 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).
View complete results in PubMed (results may change over time).


PubMed Results
1. PLoS One. 2015 May 15;10(5):e0126854. doi: 10.1371/journal.pone.0126854.
 
Integrating Taxonomic, Functional and Phylogenetic Beta Diversities: Interactive Effects with the Biome and Land Use across Taxa.  
 
Corbelli JM(1), Zurita GA(2), Filloy J(1), Galvis JP(3), Vespa NI(4), Bellocq I(1) 

Author information:  

(1)Departamento de Ecología, Genética y Evolución, IEGEBA, (CONICET-UBA), Facultad de Ciencias Exactas y Naturales, Universidad de, Buenos Aires, Ciudad Universitaria, Pabellón 2, Piso 4, CA Buenos Aires (1428), Argentina.  
(2)Instituto de Biología Subtropical-Facultad de Ciencias Forestales, Universidad Nacional de Misiones-CONICET, Bertoni 85, Pto Iguazú (3770), Misiones, Argentina.  
(3)División Paleozoología Invertebrados, Facultad de Ciencias Naturales y Museo (FCNyM), Universidad Nacional de La Plata, Museo de Ciencias Naturales de La Plata, Paseo del Bosque s/n. La Plata (1900), Buenos Aires, Argentina.  
(4)Departamento de Ecología, Genética y Evolución, IEGEBA, (CONICET-UBA), Facultad de Ciencias Exactas y Naturales, Universidad de, Buenos Aires, Ciudad Universitaria, Pabellón 2, Piso 4, CA Buenos Aires (1428), Argentina; Instituto de Biología Subtropical-Facultad de Ciencias Forestales, Universidad Nacional de Misiones-CONICET, Bertoni 85, Pto Iguazú (3770), Misiones, Argentina.  

Abstract
The spatial distribution of species, functional traits and phylogenetic relationships at both the regional and local scales provide complementary approaches to study patterns of biodiversity and help to untangle the mechanisms driving community assembly. Few studies have simultaneously considered the taxonomic (TBD), functional (FBD) and phylogenetic (PBD) facets of beta diversity. Here we analyze the associations between TBD, FBD, and PBD with the biome (representing different regional species pools) and land use, and investigate whether TBD, FBD and PBD were correlated. In the study design we considered two widely used indicator taxa (birds and ants) from two contrasting biomes (subtropical forest and grassland) and land uses (tree plantations and cropfields) in the southern Neotropics. Non-metric multidimensional scaling showed that taxonomic, functional and phylogenetic distances were associated to biome and land use; study sites grouped into four groups on the bi-dimensional space (cropfields in forest and grassland, and tree plantations in forest and grassland), and that was consistent across beta diversity facets and taxa. Mantel and PERMANOVA tests showed that TBD, FBD and PBD were positively correlated for both bird and ant assemblages; in general, partial correlations were also significant. Some of the functional traits considered here were conserved along phylogeny. Our results will contribute to the development of sound land use planning and beta diversity conservation.  

PMID: 25978319 [PubMed - as supplied by publisher]  



2. J Wildl Dis. 2015 May 14. [Epub ahead of print]  

Avian Bornaviruses in North American Gulls.
 
Guo J(1), Tizard I, Baroch J, Shivaprasad HL, Payne SL. 
 
Author information:  
(1) Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843, USA.  

Abstract
Avian bornaviruses, recently described members of the family Bornaviridae, have been isolated from captive parrots and passerines as well as wild waterfowl in which they may cause lethal neurologic disease. We report detection of avian bornavirus RNA in the brains of apparently healthy gulls. We tested 439 gull brain samples from 18 states, primarily in the northeastern USA, using a reverse-transcriptase PCR assay with primers designed to detect a conserved region of the bornavirus M gene. Nine birds yielded a PCR product of appropriate size. Sequencing of PCR products indicated that the virus was closely related to aquatic bird bornavirus 1 (ABBV-1). Viral RNA was detected in Herring Gulls (Larus argentatus), Ring-billed Gulls (Larus delawarensis), and Laughing Gulls (Leucophaeus atricilla). Eight of the nine positive birds came from the New York/New Jersey area. One positive Herring Gull came from New Hampshire. Histopathologic examination of one well-preserved brain from a Herring Gull from Union County New Jersey, showed a lymphocytic encephalitis similar to that observed in bornavirus-infected parrots and geese. Bornavirus N protein was confirmed in two Herring Gull brains by immunohistochemistry. Thus ABBV-1 can infect gulls and cause encephalitic brain lesions similar to those observed in other birds.  

PMID: 25973630 [PubMed - as supplied by publisher]  



3. Poult Sci. 2015 May 12. pii: pev088. [Epub ahead of print]  

Evaluation of inclusion level of wheat distillers dried grains with solubles with and without protease or β-mannanase on performance and water intake of turkey hens.  

Opoku EY(1), Classen HL(1), Scott TA(2). 
  
Author information:  
(1)Department of Animal and Poultry Science, University of Saskatchewan, Saskatoon, SK, Canada S7N5A8. (2)Department of Animal and Poultry Science, University of Saskatchewan, Saskatoon, SK, Canada S7N5A8 tom.scott@usask.ca.  

Abstract
It is becoming a common practice to use higher levels of wheat distillers dried grains with solubles (wDDGS) in poultry diets. The objective of this study was to determine the effects of level of inclusion of wDDGS with or without enzyme (E-, i.e., wDDGSE-) supplementation on performance and water consumption of turkey hens (0 to 72 d). Two diets (0 or 30% wDDGS) were formulated to meet the nutrient requirements of Hybrid Converter turkeys. Diets (0 or 30% wDDGS; starter, grower, and finisher) were then blended to obtain a different level of inclusion (15%) of wDDGS. The 30% wDDGS diet was divided into 3 fractions and 2 fractions supplemented with either protease (P+, i.e., wDDGSP+; 0.126 g/kg) or β-mannanase (M+, i.e., wDDGSM+; 0.05 g/kg). All 5 diets were fed ad libitum as mash. The 700 0-d turkey hens were randomly allocated into groups of 35 birds per replicate with 4 replicate floor pens per treatment, in a completely randomized design. Water consumption per pen was recorded beginning at 7 d. There was no effect of dietary treatment on feed intake. BW of turkey hens (52 d; grower) was significantly higher for 30% wDDGSP+ as compared to 0% wDDGSE- or 15% wDDGSE- diets; but was not different from 30% wDDGSE- or 30% wDDGSM+ diets. FCR (P < 0.01; 28 to 52 d), and total FCR (P < 0.05; 0 to 72 d) was significantly improved for birds fed 15 or 30% wDDGS regardless of enzyme treatment compared to 0% wDDGSE-. Water intake (WI, in mL per bird per day) tended to be higher (P = 0.08) between 7 and 28 d for 30% wDDGSP+ diets compared to other treatments. Similarly, WI of birds fed 30% wDDGSP+ was higher (P < 0.05; 28 to 52 and 52 to 72 d) and total WI (P = 0.07; 7 to 72 d) tended to be higher than other treatments. This study is the first to report the impact of wDDGS on WI. As high as 30% wDDGS can be substituted in turkey hen diets. No effect of P+ or M+ at the inclusion level tested was found on performance. © 2015 Poultry Science Association Inc.  

PMID: 25971948 [PubMed - as supplied by publisher]  

 

4. Avian Pathol. 2015 May 14:1-12. [Epub ahead of print]  

Molecular detection of Neospora caninum in house sparrows (Passer domesticus) in Iran.  

Abdoli A(1), Arbabi M, Dalimi A, Pirestani M.  

Author information:  
1) Department of Parasitology, Faculty of Medical Sciences , Kashan University of Medical Science , Kashan , Iran.  

Abstract
Neospora caninum is an intracellular protozoan parasite with a wide range of intermediate animal hosts. There is little information describing the prevalence and genetic characterization of N. caninum in bird hosts worldwide and in Iran. In this study, a total 217 brain samples of house sparrow (Passer domesticus) were examined for N. caninum presence by nested-PCR targeting the Nc-5 gene. Neospora caninum DNA was detected in 3.68% (8/217) of sparrows. Sequencing of the Nc5 genomic DNA revealed 97-99% of similarity with N. caninum sequences deposited in Genbank. To our knowledge, this study is the first molecular evidence of N. caninum DNA in bird hosts in Iran. The results of this study highlight the role of the house sparrow (Passer domesticus) in maintaining and spreading N. caninum infection to canines in the feral and domestic environment. 
  
PMID: 25971651 [PubMed - as supplied by publisher]  

5. PLoS One. 2015 May 13;10(5):e0126383. doi: 10.1371/journal.pone.0126383. eCollection 2015.
  
Topological data analysis of biological aggregation models. 

Topaz CM(1), Ziegelmeier L(1), Halverson T(1).  

Author information:  
(1)Department of Mathematics, Statistics, and Computer Science, Macalester College, Saint Paul, Minnesota, United States of America.  
AbstractWe apply tools from topological data analysis to two mathematical models inspired by biological aggregations such as bird flocks, fish schools, and insect swarms. Our data consists of numerical simulation output from the models of Vicsek and D'Orsogna. These models are dynamical systems describing the movement of agents who interact via alignment, attraction, and/or repulsion. Each simulation time frame is a point cloud in position-velocity space. We analyze the topological structure of these point clouds, interpreting the persistent homology by calculating the first few Betti numbers. These Betti numbers count connected components, topological circles, and trapped volumes present in the data. To interpret our results, we introduce a visualization that displays Betti numbers over simulation time and topological persistence scale. We compare our topological results to order parameters typically used to quantify the global behavior of aggregations, such as polarization and angular momentum. The topological calculations reveal events and structure not captured by the order parameters. 
  
PMID: 25970184 [PubMed - in process]  


6. Gigascience. 2015 May 12;4:24. doi: 10.1186/s13742-015-0062-9. eCollection 2015.  

Improving the ostrich genome assembly using optical mapping data. 

  
Zhang J(1), Li C(2), Zhou Q(3), Zhang G(4).
  
Author information:  
(1)China National GeneBank, BGI-Shenzhen, Shenzhen,, 518083 China. (2)China National GeneBank, BGI-Shenzhen, Shenzhen,, 518083 China ; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark. (3)Department of Integrative Biology, University of California, Berkeley, USA. (4)China National GeneBank, BGI-Shenzhen, Shenzhen,, 518083 China ; Department of Biology, Centre for Social Evolution, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, DK Denmark.  

Abstract
BACKGROUND: The ostrich (Struthio camelus) is the tallest and heaviest living bird. Ostrich meat is considered a healthy red meat, with an annual worldwide production ranging from 12,000 to 15,000 tons. As part of the avian phylogenomics project, we sequenced the ostrich genome for phylogenetic and comparative genomics analyses. The initial Illumina-based assembly of this genome had a scaffold N50 of 3.59 Mb and a total size of 1.23 Gb. Since longer scaffolds are critical for many genomic analyses, particularly for chromosome-level comparative analysis, we generated optical mapping (OM) data to obtain an improved assembly. The OM technique is a non-PCR-based method to generate genome-wide restriction enzyme maps, which improves the quality of de novo genome assembly. FINDINGS: In order to generate OM data, we digested the ostrich genome with KpnI, which yielded 1.99 million DNA molecules (>250 kb) and covered the genome at least 500×. The pattern of molecules was subsequently assembled to align with the Illumina-based assembly to achieve sequence extension. This resulted in an OM assembly with a scaffold N50 of 17.71 Mb, which is 5 times as large as that of the initial assembly. The number of scaffolds covering 90% of the genome was reduced from 414 to 75, which means an average of ~3 super-scaffolds for each chromosome. Upon integrating the OM data with previously published FISH (fluorescence in situ hybridization) markers, we recovered the full PAR (pseudoatosomal region) on the ostrich Z chromosome with 4 super-scaffolds, as well as most of the degenerated regions. CONCLUSIONS: The OM data significantly improved the assembled scaffolds of the ostrich genome and facilitated chromosome evolution studies in birds. Similar strategies can be applied to other genome sequencing projects to obtain better assemblies.  

PMID: 25969728 [PubMed]  

7. Oecologia. 2015 May 14. [Epub ahead of print]  

Traits influencing range contraction in New Zealand's endemic forest birds.  

Parlato EH(1), Armstrong DP, Innes JG.  

Author information:  
(1)Wildlife Ecology Group, Institute of Agriculture and Environment, Massey University, Private Bag 11 222, Palmerston North, 4442, New Zealand, e.parlato@massey.ac.nz.  

Abstract
Understanding vulnerability of endemic taxa to predation is clearly important for conservation management. In New Zealand, predation by introduced mammals such as rats and mustelids is widely recognized as the primary factor responsible for declines of indigenous fauna. The aim of our study was to evaluate the vulnerability of New Zealand's surviving endemic forest bird species to impacts of introduced mammalian predators, and identify key life history attributes underlying this vulnerability. We measured range contraction following the introduction of exotic mammalian predators for 23 endemic forest bird species using information on both pre-human and current distributions. We used Bayesian modeling techniques to analyze whether variation in range contraction was associated with life history traits potentially influencing species' predation vulnerability, while accounting for phylogenetic relatedness. Our results showed that the extent of range contraction varied greatly among species, with some species remaining in available forest habitat throughout most of their pre-human range, and others having disappeared completely from the main islands. Cavity nesting was the key trait associated with more extensive range decline, suggesting that cavity-nesting species are more vulnerable to predation than species that nest in more open sites. 
  
PMID: 25969334 [PubMed - as supplied by publisher]  

8. Parasitology. 2015 May 13:1-6. [Epub ahead of print]  

Detecting transmission areas of malaria parasites in a migratory bird species.  

Garcia-Longoria L(1), Hellgren O(2), Bensch S(2), DE Lope F(1), Marzal A(1).  

Author information:  
(1)Departamento de Biología Animal,Universidad de Extremadura,E-06071 Badajoz,Spain. (2)Department of Biology,Molecular Ecology and Evolution Lab,Ecology Building,Lund University,SE- 22362 Lund,Sweden.  

Abstract
The identification of the regions where vector-borne diseases are transmitted is essential to study transmission patterns and to recognize future changes in environmental conditions that may potentially influence the transmission areas. SGS1, one of the lineages of Plasmodium relictum, is known to have active transmission in tropical Africa and temperate regions of Europe. Nuclear sequence data from isolates infected with SGS1 (based on merozoite surface protein 1 (MSP1) allelic diversity) have provided new insights on the distribution and transmission areas of these allelic variants. For example, MSP1 alleles transmitted in Africa differ from those transmitted in Europe, suggesting the existence of two populations of SGS1 lineages. However, no study has analysed the distribution of African and European transmitted alleles in Afro-Palearctic migratory birds. With this aim, we used a highly variable molecular marker to investigate whether juvenile house martins become infected in Europe before their first migration to Africa. We explored the MSP1 allelic diversity of P. relictum in adult and juvenile house martins. We found that juveniles were infected with SGS1 during their first weeks of life, confirming active transmission of SGS1 to house martins in Europe. Moreover, we found that all the juveniles and most of adults were infected with one European transmitted MSP1 allele, whereas two adult birds were infected with two African transmitted MSP1 alleles. These findings suggest that house martins are exposed to different strains of P. relictum in their winter and breeding quarters.  

PMID: 25968571 [PubMed - as supplied by publisher]  

9. Biomaterials. 2015 May 8;59:125-143. doi: 10.1016/j.biomaterials.2015.04.038. [Epub ahead of print]  

Phytomolecule icaritin incorporated PLGA/TCP scaffold for steroid-associated osteonecrosis: Proof-of-concept for prevention of hip joint collapse in bipedal emus and mechanistic study in quadrupedal rabbits.  

Qin L(1), Yao D(2), Zheng L(2), Liu WC(2), Liu Z(2), Lei M(3), Huang L(2), Xie X(2), Wang X(4), Chen Y(5), Yao X(6), Peng J(7), Gong H(8), Griffith JF(9), Huang Y(10), Zheng Y(10), Feng JQ(11), Liu Y(11), Chen S(2), Xiao D(3), Wang D(5), Xiong J(5), Pei D(12), Zhang P(13), Pan X(14), Wang X(15), Lee KM(16), Cheng CY(2). 
  
Author information:  
(1)Musculoskeletal Research Laboratory, Department of Orthopaedics & Traumatology, The Chinese University of Hong Kong, Hong Kong SAR, PR China; Translational Medicine R&D Center, Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, PR China. Electronic address: lingqin@cuhk.edu.hk.  
(2)Musculoskeletal Research Laboratory, Department of Orthopaedics & Traumatology, The Chinese University of Hong Kong, Hong Kong SAR, PR China.  
(3)Department of Orthopaedics, Peking University Shenzhen Hospital, Shenzhen, PR China. 
(4)Musculoskeletal Research Laboratory, Department of Orthopaedics & Traumatology, The Chinese University of Hong Kong, Hong Kong SAR, PR China; Translational Medicine R&D Center, Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, PR China. 
(5)Department of Orthopaedics, The Second People's Hospital of Shenzhen, Shenzhen, PR China. 
(6)Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Jinan University, Guangzhou, PR China. 
(7)Musculoskeletal Research Laboratory, Department of Orthopaedics & Traumatology, The Chinese University of Hong Kong, Hong Kong SAR, PR China; Orthopaedic Research Institute, Chinese People's Liberation Army General Hospital, Beijing, PR China. (8)School of Biological Science and Medical Engineering, Beihang University, Beijing, PR China. 
(9)Department of Imaging and Interventional Radiology, The Chinese University of Hong Kong, Hong Kong SAR, PR China. 
(10)Interdisciplinary Division of Biomedical Engineering, The Hong Kong Polytechnic University, Hong Kong SAR, PR China. 
(11)Baylor College of Dentistry, Texas A&M University, Dallas, USA. (12)Guangzhou Institutes of Biomedical and Health, Chinese Academy of Sciences, Guangzhou, PR China. 
(13)Translational Medicine R&D Center, Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, PR China. 
(14)Department of Orthopaedics, The First Peoples' Hospital, Shenzhen, PR China. 
(15)Department of Mechanical Engineering, Tsinghua University, Beijing, PR China. 
(16)Lee Hysan Clinical Research Laboratories, The Chinese University of Hong Kong, Hong Kong SAR, PR China.  

Abstract
Steroid-associated osteonecrosis (SAON) may lead to joint collapse and subsequent joint replacement. Poly lactic-co-glycolic acid/tricalcium phosphate (P/T) scaffold providing sustained release of icaritin (a metabolite of Epimedium-derived flavonoids) was investigated as a bone defect filler after surgical core-decompression (CD) to prevent femoral head collapse in a bipedal SAON animal model using emu (a large flightless bird). The underlying mechanism on SAON was evaluated using a well-established quadrupedal rabbit model. Fifteen emus were established with SAON, and CD was performed along the femoral neck for the efficacy study. In this CD bone defect, a P/T scaffold with icaritin (P/T/I group) or without icaritin (P/T group) was implanted while no scaffold implantation was used as a control. For the mechanistic study in rabbits, the effects of icaritin and composite scaffolds on bone mesenchymal stem cells (BMSCs) recruitment, osteogenesis, and anti-adipogenesis were evaluated. Our efficacy study showed that P/T/I group had the significantly lowest incidence of femoral head collapse, better preserved cartilage and mechanical properties supported by more new bone formation within the bone tunnel. For the mechanistic study, our in vitro tests suggested that icaritin enhanced the expression of osteogenesis related genes COL1α, osteocalcin, RUNX2, and BMP-2 while inhibited adipogenesis related genes C/EBP-ß, PPAR-γ, and aP2 of rabbit BMSCs. Both P/T and P/T/I scaffolds were demonstrated to recruit BMSCs both in vitro and in vivo but a higher expression of migration related gene VCAM1 was only found in P/T/I group in vitro. In conclusion, both efficacy and mechanistic studies show the potential of a bioactive composite porous P/T scaffold incorporating icaritin to enhance bone defect repair after surgical CD and prevent femoral head collapse in a bipedal SAON emu model.  

Copyright © 2015 Elsevier Ltd. All rights reserved.  

PMID: 25968462  [PubMed - as supplied by publisher]  

10. Environ Sci Pollut Res Int. 2015 May 13. [Epub ahead of print]
  
Temporal and spatial variations in phytoplankton: correlations with environmental factors in Shengjin Lake, China.  

Wang L(1), Wang C, Deng D, Zhao X, Zhou Z.  

Author information:  
(1)School of Resources and Environmental Engineering, Anhui Biodiversity Information Center, Anhui University, Hefei, 230601, China. 
  
Abstract
Temporal and spatial variations in the phytoplankton community and environmental variables were investigated from February to July 2014, in the upper lake of Shengjin Lake, China. We identified 192 species of phytoplankton belonging to 8 phyla and 84 genera, of which 46.4 % of Chlorophyta, 29.2 % of Bacillariophyta, and 12.5 % of Cyanophyta. There were 14 predominant species. Marked temporal and spatial variations were observed in the phytoplankton community. The total abundance of phytoplankton ranged from 3.66 × 10(5) to 867.93 × 10(5) cells/L and total biomass ranging from 0.40 to 20.89 mg/L. The Shannon-Wiener diversity index varied from 3.50 to 8.35 with an average of 5.58, revealing high biodiversity in the phytoplankton community. There were substantial temporal changes in the dominant species, from Bacillariophyta and Cryptophyta to Cyanophyta and Chlorophyta. Phytoplankton biomass and abundance showed a similar increasing trend from February to July. Pearson correlations and Redundancy analysis revealed that the most significant environmental factors influencing phytoplankton community were water temperature (T), transparency (SD), and nutrient concentration. The positive correlation between the key water bird areas and phytoplankton biomass indicated that the droppings of wintering water birds had an important influence on the phytoplankton community in the upper lake of Shengjin Lake.  

PMID: 25966883 [PubMed - as supplied by publisher]  

11. J Therm Biol. 2015 Jul;51:119-25. doi: 10.1016/j.jtherbio.2015.04.003. Epub 2015 Apr 14.  

Circannual rhythm of resting metabolic rate of a small Afrotropical bird.  

Thompson LJ(1), Brown M(2), Downs CT(3).  

Author information:  
(1)School of Life Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville 3201, South Africa. Electronic address: lindojano@yahoo.com.  
(2)School of Life Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville 3201, South Africa. 
(3)School of Life Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville 3201, South Africa. Electronic address: downs@ukzn.ac.za.  

Abstract
Seasonal variation in avian metabolic rate is well established in Holarctic and temperate species, while trends in Afrotropical species are relatively poorly understood. Furthermore, given the paucity of data on circannual rhythm in avian metabolism, it is not known whether seasonal measurements made in summer and winter correspond with annual peaks and troughs in avian metabolic rate. Thus, we investigated how mean body mass, resting metabolic rate (RMR) and evaporative water loss (EWL) of a small Afrotropical bird, the Cape white-eye (Zosterops virens), changed monthly over the course of a year at 20°C and 25°C. Mean body mass was 12.2±1.0g throughout the study period. However, both EWL and RMR varied monthly, and peaks and troughs in RMR occurred in March and October respectively, which did not correspond to peaks and troughs in mean monthly outdoor ambient temperatures. These results suggest that measuring RMR at the height of summer and winter may underestimate the flexibility of which birds are capable in terms of their metabolic rate. We encourage further studies on this topic, to establish whether the lag between environmental temperature and RMR is consistent in other species. 
  
Copyright © 2015 Elsevier Ltd. All rights reserved.  
PMID: 25965025 [PubMed - in process]  

12. Biol Open. 2015 May 11. pii: bio.012211. doi: 10.1242/bio.012211. [Epub ahead of print]  

The cuticle modulates ultraviolet reflectance of avian eggshells. 
  
Fecheyr-Lippens DC(1), Igic B(2), D'Alba L(2), Hanley D(3), Verdes A(4), Holford M(4), Waterhouse GI(5), Grim T(3), Hauber ME(6), Shawkey MD(2).  

Author information:  
(1)Department of Biology, University of Akron, Akron, OH, USA daphne@fecheyr.be.  
(2)Department of Biology, University of Akron, Akron, OH, USA. 
(3)Department of Zoology and Laboratory of Ornithology, Palacký University, Olomouc, Czech Republic. 
(4)Department of Chemistry, Hunter College and the Graduate Center, City University of New York, New York, NY, USA. 
(5)School of Chemical Sciences, University of Auckland, Auckland, New Zealand. 
(6)Department of Psychology, Hunter College and the Graduate Center, City University of New York, New York, NY, USA.  

Abstract
Avian eggshells are variedly coloured, yet only two pigments, biliverdin and protoporphyrin XI, are known to contribute to the dramatic diversity of their colours. By contrast, the contributions of structural or other chemical components of the eggshell are poorly understood. For example, unpigmented eggshells, which appear white to the human eye, vary in their ultraviolet (UV) reflectance, which may be detectable by birds. We investigated the proximate mechanisms for the variation in UV-reflectance of unpigmented bird eggshells, using spectrophotometry, electron microscopy, chemical analyses, and experimental manipulations. We specifically tested how UV-reflectance is affected by the eggshell cuticle, the outermost layer of most avian eggshells. The chemical dissolution of the outer eggshell layers, including the cuticle, increased UV-reflectance for only eggshells that contained a cuticle. Our findings demonstrate that the outer eggshell layers, including the cuticle, absorb UV-light, probably because they contain higher levels of organic components and other chemicals, such as calcium phosphates, compared to the predominantly calcite-based eggshell matrix. These data highlight the need to examine factors other than the known pigments in studies of avian eggshell colour.  

© 2015. Published by The Company of Biologists Ltd.  
PMID: 25964661 [PubMed - as supplied by publisher]  

13. J Exp Biol. 2015 May 11. pii: jeb.111039. [Epub ahead of print]  
Is oxidative status influenced by dietary carotenoid and physical activity after moult in the great tit (Parus major)?  

Vaugoyeau M(1), Decencière B(2), Perret S(2), Karadas F(3), Meylan S(4), Biard C(5). 
  
Author information:  
(1)Sorbonne universités, UPMC Univ Paris 06, UPEC, Paris 7, CNRS, INRA, IRD, Institut d'Écologie et des Sciences de l'Environnement de Paris, 7 Quai St. Bernard, F-75005 Paris, France marie.vaugoyeau@gmail.com. 
(2)CNRS ENS, UMS 3194, CEREEP - Ecotron IleDeFrance, Ecole Normale Supérieure, St-Pierre-lès-Nemours, France. 
(3)Department of Animal Science, University of Yüzüncü Yil, Van, Turkey.  
(4)Sorbonne universités, UPMC Univ Paris 06, UPEC, Paris 7, CNRS, INRA, IRD, Institut d'Écologie et des Sciences de l'Environnement de Paris, 7 Quai St. Bernard, F-75005 Paris, France ESPE de Paris, Université Sorbonne Paris IV, 10 rue Molitor, 75016 Paris, France. 
(5)Sorbonne universités, UPMC Univ Paris 06, UPEC, Paris 7, CNRS, INRA, IRD, Institut d'Écologie et des Sciences de l'Environnement de Paris, 7 Quai St. Bernard, F-75005 Paris, France.  

Abstract
In the context of sexual and natural selection, an allocation trade-off for carotenoid pigments may exist because of their obligate dietary origin and their role both in the antioxidant and immune systems and in the production of coloured signals in various taxa, particularly birds. When birds have expended large amounts of carotenoids to feather growth such as after autumn moult, bird health and oxidative status might be more constrained. We tested this hypothesis in a bird species with carotenoid-based plumage colour, by manipulating dietary carotenoids and physical activity, which can decrease antioxidant capacity and increase reactive oxygen metabolites (ROM) concentration. Great tits were captured after moult and kept in aviaries, under three treatments: physical handicap and dietary supplementation with carotenoids, physical handicap and control diet, and no handicap and control diet. We measured plasma composition (antioxidant capacity, ROM concentration, vitamin A, E and total carotenoid concentrations), immune system activation (blood sedimentation) and stress response (heterophil/lymphocyte ratio) and predicted that handicap treatment should influence these negatively and carotenoid supplementation positively. Colouration of yellow feathers was also measured. Carotenoid supplementation increased total plasma carotenoid concentrations, decreased feather carotenoid chroma and marginally increased ROM concentration. Handicap increased blood sedimentation only in males but had no clear influence on oxidative stress, which contradicted previous studies. Further studies are needed to investigate how physical activity and carotenoid availability might interact and influence oxidative stress outside the moult period, and their combined potential influence on attractiveness and reproductive investment later during the breeding season.  

© 2015. Published by The Company of Biologists Ltd.  
PMID: 25964421 [PubMed - as supplied by publisher]  

14. Proc Natl Acad Sci U S A. 2015 May 11. pii: 201418414. [Epub ahead of print] 
  
Climatic dipoles drive two principal modes of North American boreal bird irruption.  

Strong C(1), Zuckerberg B(2), Betancourt JL(3), Koenig WD(4).  

Author information:  
(1)Department of Atmospheric Sciences, University of Utah, Salt Lake City, UT 84112-0110; court.strong@utah.edu. 
(2)Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI 53706-1598; 
(3)National Research Program, US Geological Survey, Reston, VA 20192; 
(4)Cornell Lab of Ornithology and Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14850.  

Abstract
Pine Siskins exemplify normally boreal seed-eating birds that can be sparse or absent across entire regions of North America in one year and then appear in large numbers the next. These dramatic avian "irruptions" are thought to stem from intermittent but broadly synchronous seed production (masting) in one year and meager seed crops in the next. A prevalent hypothesis is that widespread masting in the boreal forest at high latitudes is driven primarily by favorable climate during the two to three consecutive years required to initiate and mature seed crops in most conifers. Seed production is expensive for trees and is much reduced in the years following masting, driving boreal birds to search elsewhere for food and overwintering habitat. Despite this plausible logic, prior efforts to discover climate-irruption relationships have been inconclusive. Here, analysis of more than 2 million Pine Siskin observations from Project FeederWatch, a citizen science program, reveals two principal irruption modes (North-South and West-East), both of which are correlated with climate variability. The North-South irruption mode is, in part, influenced by winter harshness, but the predominant climate drivers of both modes manifest in the warm season as continental-scale pairs of oppositely signed precipitation and temperature anomalies (i.e., dipoles). The climate dipoles juxtapose favorable and unfavorable conditions for seed production and wintering habitat, motivating a push-pull paradigm to explain irruptions of Pine Siskins and possibly other boreal bird populations in North America.  

PMID: 25964328 [PubMed - as supplied by publisher]  

15. Evolution. 2015 May 12. doi: 10.1111/evo.12684. [Epub ahead of print] 
  
A molecular mechanism for the origin of a key evolutionary innovation, the bird beak and palate, revealed by an integrative approach to major transitions in vertebrate history.  

Bhullar BA(1,)(2,)(3), Morris ZS(4), Sefton EM(4,)(5), Tok A(4), Tokita M(4), Namkoong B(4), Camacho J(4), Burnham DA(6), Abzhanov A(7).  

Author information:  
(1)Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave, Cambridge, MA, 02138, USA. bhart-anjan.bhullar@yale.edu.  
(2)Department of Organismal Biology and Anatomy, University of Chicago, 1027 E. 57th St, Anatomy 306, Chicago, IL, 60637, USA. bhart-anjan.bhullar@yale.edu.  
(3)Department of Geology & Geophysics and Peabody Museum of Natural History, Yale University, P.O. Box 208109, New Haven, CT, 06520, USA. bhart-anjan.bhullar@yale.edu. 
(4)Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave, Cambridge, MA, 02138, USA.  
(5)Museum of Comparative Zoology, Harvard University, 26 Oxford St, Cambridge, MA, 02138, USA. 
(6)University of Kansas Biodiversity Institute and Natural History Museum, 1345 Jayhawk Blvd, Lawrence, KS, 66045, USA. 
(7)Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave, Cambridge, MA, 02138, USA. abzhanov@fas.harvard.edu. 
  
Abstract
The avian beak is a key evolutionary innovation whose flexibility has permitted birds to diversify into a range of disparate ecological niches. We approached the problem of the mechanism behind this innovation using an approach bridging paleontology, comparative anatomy, and experimental developmental biology. First we used fossil and extant data to show the beak is distinctive in consisting of fused premaxillae that are geometrically distinct from those of ancestral archosaurs. To elucidate underlying developmental mechanisms, we examined candidate gene expression domains in the embryonic face: the earlier frontonasal ectodermal zone (FEZ) and the later midfacial Wnt-responsive region, in birds and several reptiles. This permitted the identification of an autapomorphic median gene expression region in Aves. In order to test the mechanism, we used inhibitors of both pathways to replicate in chicken the ancestral amniote expression. Altering the FEZ altered later Wnt responsiveness to the ancestral pattern. Skeletal phenotypes from both types of experiments had premaxillae that clustered geometrically with ancestral fossil forms instead of beaked birds. The palatal region was also altered to a more ancestral phenotype. This is consistent with the fossil record and with the tight functional association of avian premaxillae and palate in forming a kinetic beak. 

This article is protected by copyright. All rights reserved.  
PMID: 25964090 [PubMed - as supplied by publisher]  

16. Evol Dev. 2015 Jun;17(3):185-94. doi: 10.1111/ede.12123.
  
Nuclear β-catenin localization supports homology of feathers, avian scutate scales, and alligator scales in early development.  

Musser JM(1,)(2), Wagner GP(1,)(2), Prum RO(1).  

Author information:  
(1)Department of Ecology and Evolutionary Biology, and Peabody Museum of Natural History, Yale University, 21 Sachem St, New Haven, CT 06511, USA. 
(2)Systems Biology Institute, Yale University, 840 West Campus Drive, West Haven, CT 06516, USA.  

Abstract
Feathers are an evolutionary novelty found in all extant birds. Despite recent progress investigating feather development and a revolution in dinosaur paleontology, the relationship of feathers to other amniote skin appendages, particularly reptile scales, remains unclear. Disagreement arises primarily from the observation that feathers and avian scutate scales exhibit an anatomical placode-defined as an epidermal thickening-in early development, whereas alligator and other avian scales do not. To investigate the homology of feathers and archosaur scales we examined patterns of nuclear β-catenin localization during early development of feathers and different bird and alligator scales. In birds, nuclear β-catenin is first localized to the feather placode, and then exhibits a dynamic pattern of localization in both epidermis and dermis of the feather bud. We found that asymmetric avian scutate scales and alligator scales share similar patterns of nuclear β-catenin localization with feathers. This supports the hypothesis that feathers, scutate scales, and alligator scales are homologous during early developmental stages, and are derived from early developmental stages of an asymmetric scale present in the archosaur ancestor. Furthermore, given that the earliest stage of β-catenin localization in feathers and archosaur scales is also found in placodes of several mammalian skin appendages, including hair and mammary glands, we hypothesize that a common skin appendage placode originated in the common ancestor of all amniotes. We suggest a skin placode should not be defined by anatomical features, but as a local, organized molecular signaling center from which an epidermal appendage develops.  

© 2015 Wiley Periodicals, Inc.  

PMID: 25963196 [PubMed - in process]  

17. PLoS One. 2015 May 11;10(5):e0126639. doi: 10.1371/journal.pone.0126639. eCollection 2015.  

Arthropod but not bird predation in ethiopian homegardens is higher in tree-poor than in tree-rich landscapes.  

Lemessa D(1), Hambäck PA(2), Hylander K(2).  

Author information:  
(1)Leuphana University Luneburg, Scharnhorststr 1, Germany. 
(2)Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden.  

Abstract
Bird and arthropod predation is often associated with natural pest control in agricultural landscapes, but the rates of predation may vary with the amount of tree cover or other environmental factors. We examined bird and arthropod predation in three tree-rich and three tree-poor landscapes across southwestern Ethiopia. Within each landscape we selected three tree-rich and three tree-poor homegardens in which we recorded the number of tree species and tree stems within 100 × 100 m surrounding the central house. To estimate predation rates, we attached plasticine caterpillars on leaves of two coffee and two avocado shrubs in each homegarden, and recorded the number of attacked caterpillars for 7-9 consecutive weeks. The overall mean daily predation rate was 1.45% for birds and 1.60% for arthropods. The rates of arthropod predation varied among landscapes and were higher in tree-poor landscapes. There was no such difference for birds. Within landscapes, predation rates from birds and arthropods did not vary between tree-rich and tree-poor homegardens in either tree-rich or tree-poor landscapes. The most surprising result was the lack of response by birds to tree cover at either spatial scale. Our results suggest that in tree-poor landscapes there are still enough non-crop habitats to support predatory arthropods and birds to deliver strong top-down effect on crop pests.  

PMID: 25961306 [PubMed - in process]  


18. Vet Microbiol. 2015 Apr 22. pii: S0378-1135(15)00154-6. doi: 10.1016/j.vetmic.2015.04.009. [Epub ahead of print]  

Mechanisms of antimicrobial resistant Salmonella enterica transmission associated with starling-livestock interactions. 
  
Carlson JC(1), Hyatt DR(2), Ellis JW(3), Pipkin DR(4), Mangan AM(3), Russell M(2), Bolte DS(2), Engeman RM(3), DeLiberto TJ(3), Linz GM(5).  

Author information:  
(1)U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, 4101 LaPorte Avenue, Fort Collins, CO 80521, USA. Electronic address: James.C.Carlson@aphis.usda.gov.  
(2)Colorado State University, Veterinary Diagnostic Laboratories, College of Veterinary Medicine and Biomedical Science, 1644 Campus Delivery, Fort Collins, CO 80523-1644, USA. 
(3)U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, 4101 LaPorte Avenue, Fort Collins, CO 80521, USA. 
(4)U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Texas Wildlife Services, P.O. Box 690170, San Antonio, TX 78269, USA. 
(5)U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, 2110 Miriam Circle, Suite B, Bismarck, ND 58501-2502, USA. 
  
Abstract
Bird-livestock interactions have been implicated as potential sources for bacteria within concentrated animal feeding operations (CAFO). European starlings (Sturnus vulgaris) in particular are known to contaminate cattle feed and water with Salmonella enterica through their fecal waste. We propose that fecal waste is not the only mechanisms through which starlings introduce S. enterica to CAFO. The goal of this study was to assess if starlings can mechanically move S. enterica. We define mechanical movement as the transportation of media containing S. enterica, on the exterior of starlings within CAFO. We collected 100 starlings and obtained external wash and gastrointestinal tract (GI) samples. We also collected 100 samples from animal pens. Within each pen we collected one cattle fecal, feed, and water trough sample. Isolates from all S. enterica positive samples were subjected to antimicrobial susceptibility testing. All sample types, including 17% of external starling wash samples, contained S. enterica. All sample types had at least one antimicrobial resistant (AMR) isolate and starling GI samples harbored multidrug resistant S. enterica. The serotypes isolated from the starling external wash samples were all found in the farm environment and 11.8% (2/17) of isolates from positive starling external wash samples were resistant to at least one class of antibiotics. This study provides evidence of a potential mechanism of wildlife introduced microbial contamination in CAFO. Mechanical movement of microbiological hazards, by starlings, should be considered a potential source of bacteria that is of concern to veterinary, environmental and public health. 
  
Published by Elsevier B.V.  
PMID: 25960334 [PubMed - as supplied by publisher]  

19. Environ Toxicol Chem. 2015 May 8. doi: 10.1002/etc.3062. [Epub ahead of print]  

CYP-mediated warfarin metabolic ability is not a critical determinant of warfarin sensitivity in avian species; in vitro assays in several birds and in vivo assays in chicken.  


Watanabe KP(1), Kawata M(1), Ikenaka Y(1,)(2), Nakayama SM(1), Ishii C(1), Darwish WS(1,)(3), Saengtienchai A(1,)(4), Mizukawa H(1), Ishizuka M(1).  

Author information:  
(1)Laboratory of Toxicology, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido, Japan. 
(2)Water Research Group, Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa. 
(3)Food Control Department, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt. 
(4)Department of Pharmacology, Faculty of Veterinary Medicine, Kasetsart University, Lat Yao Chatuchak, Bangkok, Thailand.  

Abstract
Coumarin derivative anticoagulant rodenticides used for rodent control are posing a serious risk to wild bird populations. For warfarin (WF) a classic coumarin derivative, chicken have a high LD50 while mammalian species generally have much lower LD50 . Large interspecies differences in sensitivity to WF are to be expected. We previously reported substantial differences in WF metabolism among avian species, however the actual in vivo pharmacokinetics have yet to be elucidated, even in the chicken. In the present study, we sought to provide an in-depth characterization of WF metabolism in birds using in vivo and in vitro approaches. We performed a kinetic analysis of WF metabolism using liver microsomes of four avian species and found that the metabolic ability of the chicken and crow are much higher in comparison to the mallard and ostrich. Analysis of in vivo metabolites from chicken showed that excretions predominantly consisted of 4'-hydroxywarfarin, which was consistent with the in vitro results. Pharmacokinetic analysis suggested that chickens have an unexpectedly long half-life despite showing high metabolic ability in vitro. These results suggest that the half-life of WF in other bird species could be longer than in chicken, and that WF metabolism may not be a critical determinant of species difference with respect to WF sensitivity. 

This article is protected by copyright. All rights reserved.  
PMID: 25959534 [PubMed - as supplied by publisher]  

20. Parasitol Res. 2015 May 10. [Epub ahead of print]  

Complete sporogony of Plasmodium relictum (lineage pGRW4) in mosquitoes Culex pipiens pipiens, with implications on avian malaria epidemiology.  

Valkiūnas G(1), Žiegytė R, Palinauskas V, Bernotienė R, Bukauskaitė D, Ilgūnas M, Dimitrov D, Iezhova TA.  

Author information:  
(1)Nature Research Centre, Akademijos 2, LT-08412, Vilnius 2100, Lithuania, gedvalk@ekoi.lt.  

Abstract
Plasmodium relictum (lineage pGRW4) causes malaria in birds and is actively transmitted in countries with warm climates and also temperate regions of the New World. In Europe, the lineage pGRW4 has been frequently reported in many species of Afrotropical migrants after their arrival from wintering grounds, but is rare in European resident birds. Obstacles for transmission of this parasite in Europe have not been identified. Culex quinquefasciatus is an effective vector of pGRW4 malaria, but this mosquito is absent from temperate regions of Eurasia. It remains unclear if the lineage pGRW4 completes sporogony in European species of mosquitoes. Here we compare the sporogonic development of P. relictum (pGRW4) in experimentally infected mosquitoes Culex pipiens pipiens form molestus, C. quinquefasciatus, and Ochlerotatus cantans. The pGRW4 parasite was isolated from a garden warbler Sylvia borin, multiplied, and used to infect laboratory-reared Culex spp. and wild-caught Ochlerotatus mosquitoes by allowing them to take blood meals on infected birds. The exposed females were maintained at a mean laboratory temperature of 19 °C, which ranged between 14 °C at night and 24 °C during daytime. They were dissected on intervals to study the development of sporogonic stages. Only ookinetes developed in O. cantans; sporogonic development was abortive. The parasite completed sporogony in both Culex species, with similar patterns of development, and sporozoites were reported in the salivary glands 16 days after infection. The presence of sporogonic stages of the lineage pGRW4 in mosquitoes was confirmed by PCR-based testing of (1) the sporozoites present in salivary glands and (2) the single oocysts, which were obtained by laser microdissection from infected mosquito midguts. This study shows that P. relictum (pGRW4) completes sporogony in C. p. pipiens at relatively low temperatures. We conclude that there are no restrictions for spreading this bird infection in Europe from the point of view of vector availability and temperature necessary for sporogony. Other factors should be considered and were discussed for the explanation of rare reports of this malaria parasite in Europe.  

PMID: 25958156 [PubMed - as supplied by publisher]

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