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Thursday, 17 March 2016

What's new for 'birdRS' in PubMed. March Week 2, 2016

birdRS Latest News

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



PubMed Results

1. Cell. 2016 Mar 10;164(6):1269-1276. doi: 10.1016/j.cell.2016.02.039. 

Insights into the Neural and Genetic Basis of Vocal Communication. 
Konopka G(1), Roberts TF(2). Author information: (1)Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA. Electronic address: genevieve.konopka@utsouthwestern.edu. (2)Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA. Electronic address: todd.roberts@utsouthwestern.edu. 

Abstract
The use of vocalizations to communicate information and elaborate social bonds is an adaptation seen in many vertebrate species. Human speech is an extreme version of this pervasive form of communication. Unlike the vocalizations exhibited by the majority of land vertebrates, speech is a learned behavior requiring early sensory exposure and auditory feedback for its development and maintenance. Studies in humans and a small number of other species have provided insights into the neural and genetic basis for learned vocal communication and are helping to delineate the roles of brain circuits across the cortex, basal ganglia, and cerebellum in generating vocal behaviors. This Review provides an outline of the current knowledge about these circuits and the genes implicated in vocal communication, as well as a perspective on future research directions in this field. Copyright © 2016 Elsevier Inc. All rights reserved. PMID: 26967292 [PubMed - as supplied by publisher] 


2. PeerJ. 2016 Feb 25;4:e1728. doi: 10.7717/peerj.1728. eCollection 2016. 

Familiarity breeds content: assessing bird species popularity with culturomics. 
Correia RA(1), Jepson PR(2), Malhado AC(3), Ladle RJ(1). Author information: (1)Institute of Biological and Health Sciences, Federal University of Alagoas, Maceió, Alagoas, Brazil; School of Geography and the Environment, University of Oxford, Oxford, United Kingdom. (2)School of Geography and the Environment, University of Oxford , Oxford , United Kingdom. (3)Institute of Biological and Health Sciences, Federal University of Alagoas , Maceió, Alagoas , Brazil. 

Abstract
Understanding public perceptions of biodiversity is essential to ensure continued support for conservation efforts. Despite this, insights remain scarce at broader spatial scales, mostly due to a lack of adequate methods for their assessment. The emergence of new technologies with global reach and high levels of participation provide exciting new opportunities to study the public visibility of biodiversity and the factors that drive it. Here, we use a measure of internet saliency to assess the national and international visibility of species within four taxa of Brazilian birds (toucans, hummingbirds, parrots and woodpeckers), and evaluate how much of this visibility can be explained by factors associated with familiarity, aesthetic appeal and conservation interest. Our results strongly indicate that familiarity (human population within the range of a species) is the most important factor driving internet saliency within Brazil, while aesthetic appeal (body size) best explains variation in international saliency. Endemism and conservation status of a species had small, but often negative, effects on either metric of internet saliency. While further studies are needed to evaluate the relationship between internet content and the cultural visibility of different species, our results strongly indicate that internet saliency can be considered as a broad proxy of cultural interest. PMID: 26966663 [PubMed] 


3. PeerJ. 2016 Feb 29;4:e1723. doi: 10.7717/peerj.1723. eCollection 2016. 

Identifying key conservation threats to Alpine birds through expert knowledge. 
Chamberlain DE(1), Pedrini P(2), Brambilla M(3), Rolando A(1), Girardello M(4). Author information: (1)Department of Life Sciences and Systems Biology, University of Turin , Turin , Italy. (2)Museo delle Scienze di Trento , Trento , Italy. (3)Sezione Zoologia dei Vertebrati, Museo delle Scienze di Trento, Trento, Italy; Settore biodiversità e aree protette, Fondazione Lombardia per l'Ambiente, Seveso (MB), Italy. (4)Department of Bioscience, Aarhus University , Aarhus , Denmark. 

Abstract
Alpine biodiversity is subject to a range of increasing threats, but the scarcity of data for many taxa means that it is difficult to assess the level and likely future impact of a given threat. Expert opinion can be a useful tool to address knowledge gaps in the absence of adequate data. Experts with experience in Alpine ecology were approached to rank threat levels for 69 Alpine bird species over the next 50 years for the whole European Alps in relation to ten categories: land abandonment, climate change, renewable energy, fire, forestry practices, grazing practices, hunting, leisure, mining and urbanization. There was a high degree of concordance in ranking of perceived threats among experts for most threat categories. The major overall perceived threats to Alpine birds identified through expert knowledge were land abandonment, urbanization, leisure and forestry, although other perceived threats were ranked highly for particular species groups (renewable energy and hunting for raptors, hunting for gamebirds). For groups of species defined according to their breeding habitat, open habitat species and treeline species were perceived as the most threatened. A spatial risk assessment tool based on summed scores for the whole community showed threat levels were highest for bird communities of the northern and western Alps. Development of the approaches given in this paper, including addressing biases in the selection of experts and adopting a more detailed ranking procedure, could prove useful in the future in identifying future threats, and in carrying out risk assessments based on levels of threat to the whole bird community. PMID: 26966659 [PubMed] 


4. Gen Comp Endocrinol. 2016 Mar 7. pii: S0016-6480(16)30053-3. doi: 10.1016/j.ygcen.2016.03.009. [Epub ahead of print] 

Wound-healing ability is conserved during periods of chronic stress and costly life history events in a wild-caught bird. 
DuRant SE(1), de Bruijn R(2), Tran MN(2), Romero LM(2). Author information: (1)Department of Biology, Tufts University, Medford, MA 02155; Department of Zoology, Oklahoma State University, Stillwater, OK 74078. Electronic address: sarah.durant@okstate.edu. (2)Department of Biology, Tufts University, Medford, MA 02155. 

Abstract
Chronic stress, potentially through the actions of corticosterone, is thought to directly impair the function of immune cells. However, chronic stress may also have an indirect effect by influencing allocation of energy, ultimately shifting resources away from the immune system. If so, the effects of chronic stress on immune responses may be greater during energetically-costly life history events. To test whether the effects of chronic stress on immune responses differ during expensive life history events we measured wound healing rate in molting and non-molting European starlings (Sturnus vulgaris) exposed to control or chronic stress conditions. To determine whether corticosterone correlated with wound healing rates before starting chronic stress, we measured baseline and stress-induced corticosterone and two estimates of corticosterone release and regulation, negative feedback (using dexamethasone injection), and maximal capacity of the adrenals to secrete corticosterone (using adrenocorticotropin hormone [ACTH] injection). After eight days of exposure to chronic stress, we wounded both control and chronically stressed birds and monitored healing daily. We monitored nighttime heart rate, which strongly correlates with energy expenditure, and body mass throughout the study. Measures of corticosterone did not differ with molt status. Contrary to work on lizards and small mammals, all birds, regardless of stress or molt status, fully-healed wounds at similar rates. Although chronic stress did not influence healing rates, individuals with low baseline corticosterone or strong negative feedback had faster healing rates than individuals with high baseline corticosterone or weak negative feedback. In addition, wound healing does appear to be linked to energy expenditure and body mass. Non-molting, chronically stressed birds decreased nighttime heart rate during healing, but this pattern did not exist in molting birds. Additionally, birds of heavier body mass at the start of the experiment healed wounds more rapidly than lighter birds. Finally, chronically stressed birds lost body mass at the start of chronic stress, but after wounding all birds regardless of stress or molt status started gaining weight, which continued for the remainder of the study. Increased body mass could suggest compensatory feeding to offset energetic or resource demands (e.g., proteins) of wound healing. Although chronic stress did not inhibit healing, our data suggest that corticosterone may play an important role in mediating healing processes and that molt could influence energy saving tactics during periods of chronic stress. Although the experiment was designed to test allostasis, interpretation of data through reactive scope appears to be a better fit. Copyright © 2016. Published by Elsevier Inc. PMID: 26965949 [PubMed - as supplied by publisher] 


5. Parasitol Res. 2016 Mar 11. [Epub ahead of print] 

New host records of Haemaphysalis leporispalustris (Acari: Ixodidae) on birds in Brazil. 
Zeringóta V(1), Maturano R(2), Santolin ÍD(2), McIntosh D(2), Famadas KM(2), Daemon E(3), Faccini JL(2). Author information: (1)Program in Veterinary Sciences, Parasitology Animal Department, Rio de Janeiro Federal Rural University, UFRRJ, Seropédica, Rio de Janeiro, Brazil. vivianezr@yahoo.com.br. (2)Program in Veterinary Sciences, Parasitology Animal Department, Rio de Janeiro Federal Rural University, UFRRJ, Seropédica, Rio de Janeiro, Brazil. (3)Program in Animal Behavior and Biology, Juiz de Fora Federal University, UFJF, Juiz de Fora, Minas Gerais, Brazil. 

Abstract
Birds are an important component of the life histories and bioecology of a number of tick species and of some tick associated pathogens. An examination of the data concerning bird/tick associations in the Neotropics, showed that the tick Haemaphysalis leporispalustrisis (Packard, 1869) was rarely recorded infesting birds. The current study reports parasitism by H. leporispalustris in wild birds collected from Atlantic rain forest environments in the states of Rio de Janeiro (4LL) and Minas Gerais (17LL, 1NN), Brazil. All ticks were identified morphologically to the genus level; total DNA was extracted from each Haemaphysalis tick and examined by PCR and nucleotide sequencing of fragments of the eukaryotic genes encoding 16S rRNA and 12S rRNA. The bird species Arremon semitorquatus, Corythopis delalandi, Fluvicola nengeta, Troglodytes musculus, and Volatinia jacarina were recorded as hosts for H. leporispalustris for the first time in South America, and Turdus rufiventris represented a new record for Brazil. PMID: 26965425 [PubMed - as supplied by publisher] 


6. PLoS One. 2016 Mar 10;11(3):e0150813. doi: 10.1371/journal.pone.0150813. eCollection 2016. 

Prioritizing Avian Species for Their Risk of Population-Level Consequences from Wind Energy Development. 
Beston JA(1), Diffendorfer JE(1), Loss SR(2), Johnson DH(3). Author information: (1)Geosciences and Environmental Change Science Center, U.S. Geological Survey, Denver, Colorado, United States of America. (2)Department of Natural Resource Ecology and Management, Oklahoma State University, Stillwater, Oklahoma, United States of America. (3)Northern Prairie Wildlife Research Center, U.S. Geological Survey, Saint Paul, Minnesota, United States of America. 

Abstract
Recent growth in the wind energy industry has increased concerns about its impacts on wildlife populations. Direct impacts of wind energy include bird and bat collisions with turbines whereas indirect impacts include changes in wildlife habitat and behavior. Although many species may withstand these effects, species that are long-lived with low rates of reproduction, have specialized habitat preferences, or are attracted to turbines may be more prone to declines in population abundance. We developed a prioritization system to identify the avian species most likely to experience population declines from wind facilities based on their current conservation status and their expected risk from turbines. We developed 3 metrics of turbine risk that incorporate data on collision fatalities at wind facilities, population size, life history, species' distributions relative to turbine locations, number of suitable habitat types, and species' conservation status. We calculated at least 1 measure of turbine risk for 428 avian species that breed in the United States. We then simulated 100,000 random sets of cutoff criteria (i.e., the metric values used to assign species to different priority categories) for each turbine risk metric and for conservation status. For each set of criteria, we assigned each species a priority score and calculated the average priority score across all sets of criteria. Our prioritization system highlights both species that could potentially experience population decline caused by wind energy and species at low risk of population decline. For instance, several birds of prey, such as the long-eared owl, ferruginous hawk, Swainson's hawk, and golden eagle, were at relatively high risk of population decline across a wide variety of cutoff values, whereas many passerines were at relatively low risk of decline. This prioritization system is a first step that will help researchers, conservationists, managers, and industry target future study and management activity. PMID: 26963254 [PubMed - in process] 


7. PLoS One. 2016 Mar 10;11(3):e0150899. doi: 10.1371/journal.pone.0150899. eCollection 2016. 

Avian Assemblages at Bird Baths: A Comparison of Urban and Rural Bird Baths in Australia. 
Cleary GP(1,)(2), Parsons H(3), Davis A(4), Coleman BR(5), Jones DN(6), Miller KK(2), Weston MA(2). Author information: (1)National Parks Association of New South Wales, PO Box 337, Newtown, New South Wales, Australia. (2)Deakin University, Geelong, Australia. Centre for Integrative Ecology, School of Life and Environmental Sciences, Burwood Campus, Burwood, Victoria, Australia. (3)BirdLife Australia, Sydney Olympic Park, New South Wales, Australia. (4)The University of Sydney, School of Biological Sciences, Botany Annex A13, Sydney, New South Wales, Australia. (5)Evolve Information Services, Level 8, Melbourne, Victoria, Australia. (6)Environmental Futures Research Institute, Griffith University, Nathan, Queensland, Australia. 

Abstract
Private gardens provide habitat and resources for many birds living in human-dominated landscapes. While wild bird feeding is recognised as one of the most popular forms of human-wildlife interaction, almost nothing is known about the use of bird baths. This citizen science initiative explores avian assemblages at bird baths in private gardens in south-eastern Australia and how this differs with respect to levels of urbanisation and bioregion. Overall, 992 citizen scientists collected data over two, four-week survey periods during winter 2014 and summer 2015 (43% participated in both years). Avian assemblages at urban and rural bird baths differed between bioregions with aggressive nectar-eating species influenced the avian assemblages visiting urban bird baths in South Eastern Queensland, NSW North Coast and Sydney Basin while introduced birds contributed to differences in South Western Slopes, Southern Volcanic Plains and Victorian Midlands. Small honeyeaters and other small native birds occurred less often at urban bird baths compared to rural bird baths. Our results suggest that differences between urban versus rural areas, as well as bioregion, significantly influence the composition of avian assemblages visiting bird baths in private gardens. We also demonstrate that citizen science monitoring of fixed survey sites such as bird baths is a useful tool in understanding large-scale patterns in avian assemblages which requires a vast amount of data to be collected across broad areas. PMID: 26962857 [PubMed - in process] 


8. An Acad Bras Cienc. 2016 Mar 4. pii: S0001-37652016005003110. [Epub ahead of print] 

Composition and structure of bird communities in vegetational gradients of Bodoquena Mountains, western Brazil. 
Godoi MN(1), Souza FL(2), Laps RR(3), Ribeiro DB(3). Author information: (1)Programa de Pós-Graduação em Ecologia e Conservação, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brazil. (2)Departamento de Zoologia, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brazil. (3)Departamento de Ecologia, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brazil. 

Abstract
The informations of bird species distribution in different habitats and the structure of their communities are crucial for bird conservation. We tested the differences in composition, richness and abundance of birds in different phytophysiognomies at Bodoquena Mountains, western Brazil, and we demonstrated the variations in richness and abundance of birds between different trophic groups. Sampling was conducted between July 2011 and June 2012 in 200 point counts arranged in the study area. A total of 3350 contacts were obtained belonging to 156 bird species. Woodland savannas, seasonal forests and arboreal savannas had higher bird abundance and richness, while riparian forests, clean pastures and dirty pastures had smaller values of these parameters. The bird community was organized according to local vegetational gradient, with communities of forests, open areas and savannas, although many species occurred in more than one vegetation type. The insectivorous, omnivorous, frugivorous and gramnivorous birds composed most of the community. These data showed how important environmental heterogeneity is to bird communities. Furthermore, the presence of extensive patches of natural habitats, the small distance between these patches and the permeability of pastures, with high arboreal and shrubby cover, are indicated as important factors to maintain the bird diversity. PMID: 26959319 [PubMed - as supplied by publisher] 


9. Poult Sci. 2016 Mar 8. pii: pew061. [Epub ahead of print] 

Impact of dietary branched chain amino acids concentration on broiler chicks during aflatoxicosis. 
Chen X(1), Zhang Q(1), Applegate TJ(2). Author information: (1)Department of Animal Sciences, Purdue University, West Lafayette, IN 47906. (2)Department of Animal Sciences, Purdue University, West Lafayette, IN 47906 applegt@uga.edu. 

Abstract
A 20-day trial was conducted to determine the effects of dietary branched-chain amino acids (BCAA) on performance, nutrient digestibility, and gene expression of the mTOR pathway in broiler chicks when exposed to aflatoxin B1 (AFB1). The 6 dietary treatments were arranged in a 2 × 3 factorial with 3 BCAA concentrations (1.16, 1.94, and 2.73%) with or without 1.5 mg/kg AFB1 (1.77 mg/kg analyzed). Each diet was fed to 8 replicate cages (6 chicks per cage) from 6 to 20 d of age. Exposure to AFB1 significantly reduced gain:feed ratio and breast muscle weight (P < 0.05), and tended to decrease cumulative BW gain (P = 0.087), while increasing dietary BCAA improved all performance measures (P ≤ 0.0002), except relative breast muscle weight. Apparent ileal digestibility of N and 9 amino acids were increased by AFB1 (P ≤ 0.05), but were reduced by higher dietary BCAA (P ≤ 0.023). Jejunum histology was not affected by AFB1, while higher dietary BCAA tended to increase villus height (P = 0.08). Additionally, the gene expression of mTOR pathway (mTOR, 4EBP1, and S6K1) from liver and jejunum were not affected by dietary treatments, while muscle expression of S6K1 tended to be increased by AFB1 (P = 0.07). No significant interaction between AFB1 and dietary BCAA were observed for any measures in the current study. Results from this study suggested that feed AFB1 contamination can significantly reduce growth performance and breast muscle growth in broiler chicks at 20 d. Higher BCAA supply may have beneficial impact on bird performance, but this effect is independent of AFB1 exposure. © 2016 Poultry Science Association Inc. PMID: 26957625 [PubMed - as supplied by publisher] 


10. Curr HIV Res. 2016;14(3):183-210. 

The Early Bird Catches the Worm - Can Evolution Teach us Lessons in Fighting HIV? 
Schaller T(1), Herold N. Author information: (1)Institute for Infectious Diseases, Virology, Heidelberg University Hospital, Im Neuenheimer Feld 324, Heidelberg, 69120, Germany. torsten.schaller@med.uni-heidelberg.de. 

Abstract
BACKGROUND: Human immunodeficiency virus 1 (HIV-1) infection is the primary cause of the acquired immunodeficiency syndrome (AIDS). Worldwide, approximately 37 million people are infected (UNAIDS, 2014), most of them in developing countries. A vaccine is not available and current treatment strategies and diagnostics are expensive and require appropriate medical infrastructure. As a lentivirus of the family Retroviridae, HIV-1 reverse transcribes its RNA into double stranded DNA that integrates into the host genome during infection, establishing a stably integrated provirus that serves as a template for the production of progeny virus. The earliest steps during infection are critical for onset of disease, progression and clinical outcome. METHODS: Here we review the current literature of known interactions between host cell factors and HIV-1 in the early infection steps and discuss them as possible targets for new treatment strategies. RESULTS: Targeting the earliest interactions of the virus with host cell factors is an attractive way to prevent provirus formation, underlined by the evolution of multiple antiviral host cell barriers at this stage. HIV-1 has to overcome these restrictions by either counteracting them directly or by escape mutations. At the same time, viral fitness requires preservation of viral structures that interact with host components, thereby avoiding recognition of viral nucleic acids, like reverse transcription intermediates, by innate pattern recognition receptors. CONCLUSION: Future drug development, improvement of existing drugs acting in the earliest stages of the HIV-1 replication cycle as well as specifically targeting interactions of viral components with host cell factors required for HIV-1 infection will likely advance current therapy strategies. PMID: 26957195 [PubMed - in process] 


11. Environ Manage. 2016 Mar 8. [Epub ahead of print] 

Composition and Diversity of Avian Communities Using a New Urban Habitat: Green Roofs. 
Washburn BE(1), Swearingin RM(2), Pullins CK(2), Rice ME(2). Author information: (1)United States Department of Agriculture, Animal Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, 6100 Columbus Avenue, Sandusky, OH, 44870, USA. brian.e.washburn@aphis.usda.gov. (2)United States Department of Agriculture, Animal Plant Health Inspection Service, Wildlife Services, Chicago, IL, USA. 

Abstract
Green roofs on buildings are becoming popular and represent a new component of the urban landscape. Public benefits of green roof projects include reduced stormwater runoff, improved air quality, reduced urban heat island effects, and aesthetic values. As part of a city-wide plan, several green roofs have been constructed at Chicago's O'Hare International Airport (ORD). Like some other landscaping features, green roofs on or near an airport might attract wildlife and thus increase the risk of bird-aircraft collisions. During 2007-2011, we conducted a series of studies to evaluate wildlife use of newly constructed green roofs and traditional (gravel) roofs on buildings at ORD. These green roofs were 0.04-1.62 ha in area and consisted of primarily stonecrop species for vegetation. A total of 188 birds were observed using roofs during this research. Of the birds using green roofs, 66, 23, and 4 % were Killdeer, European Starlings, and Mourning Doves, respectively. Killdeer nested on green roofs, whereas the other species perched, foraged, or loafed. Birds used green roofs almost exclusively between May and October. Overall, avian use of the green roofs was minimal and similar to that of buildings with traditional roofs. Although green roofs with other vegetation types might offer forage or cover to birds and thus attract potentially hazardous wildlife, the stonecrop-vegetated green roofs in this study did not increase the risk of bird-aircraft collisions. PMID: 26956765 [PubMed - as supplied by publisher] 


12. Avian Pathol. 2016 Mar 9:1-38. [Epub ahead of print] 

Effect of yeast-derived products and distillers dried grains with solubles (DDGS) on growth performance and local innate immune response of broiler chickens challenged with Clostridium perfringens. 
Alizadeh M(1), Rogiewicz A(1), McMillan E(2), Rodriguez-Lecompte JC(3), Patterson R(4), Slominski BA(1). Author information: (1)a Department of Animal Science , University of Manitoba , Winnipeg , Canada , R3T 2N2. (2)b Nutreco Canada Agresearch , Burford , ON , Canada , N0E 1A0. (3)c Department of Pathology and Microbiology , Atlantic Veterinary College, University of Prince Edward Island , PE , Canada C1A 4P3. (4)d Canadian Bio-Systems Inc ., Calgary , Alberta , Canada T2C 0J7. 

Abstract
This study evaluated the effect of yeast-derived products on growth performance, gut lesion score, intestinal population of Clostridium perfringens, and local innate immunity of broiler chickens challenged with C. perfringens. One-d-old broiler chickens were randomly assigned to 8 dietary treatments providing 6 replicate pens of 55 birds each per treatment. Dietary treatments consisted of Control diets without and with C. perfringens challenge, and diets containing bacitracin methylene disalicylate (BMD, 55 g/tonne), nucleotides (150 g/tonne), yeast cell wall (YCW, 300 g/tonne), and a commercial product Maxi-Gen Plus (1 kg/tonne) fed to chickens challenged with C. perfringens. Diets containing 10% DDGS without and with C. perfringens challenge were also used. Birds were orally challenged with C. perfringens (10(8) CFU/bird) on d 14. On d 21, intestinal samples were collected for gene expression analysis. Pathogen challenge significantly (P<0.05) impaired feed intake, body weight gain, and FCR shortly after the challenge (14-21d). Increased C. perfringens counts and intestinal lesion score were observed for challenged birds except the BMD-containing diet. Over the entire trial (1-35d), no difference in growth performance was observed except the BMD diet which improved FCR over the Control, challenged group. Birds receiving nucleotides showed increased expression of toll-like receptors and cytokines interleukin (IL)-4 and IL-18 compared to the Control, challenged group. Expression of macrophage mannose receptor and IL-18 was upregulated in birds receiving YCW. Increased expression of cytokines and receptors involved in innate immunity in broilers receiving nucleotides and YCW suggests the immunomodulatory properties of these products under pathogen challenge conditions. PMID: 26956683 [PubMed - as supplied by publisher] 


13. J Proteome Res. 2016 Mar 8. [Epub ahead of print] 

Serum and muscle metabolomics for the prediction of ultimate pH, a key factor for chicken meat quality. 
Beauclercq S, Nadal-Desbarats L, Hennequet-Antier C, Collin A, Tesseraud S, Bourin M, Le Bihan-Duval E, Berri C. 

Abstract
Variations in muscle glycogen storage are highly correlated with variations in meat ultimate pH (pHu), a key factor for poultry meat quality. Two chicken lines were divergently selected on breast pHu to understand the biological basis for variations in meat quality, i.e. the pHu- and the pHu+ lines that are characterized by a 17% difference in muscle glycogen content. The effects of this selection on bird metabolism were investigated by quantifying muscle metabolites by high resolution NMR (1H, 31P) and serum metabolites by 1H-NMR. Twenty and 26 discriminating metabolites between the two lines were identified by Orthogonal Partial Least Squares Discriminant Analysis (OPLS DA) in the serum and muscle, respectively. There was over-representation of carbohydrate metabolites in the serum and muscle of the pHu- line, consistent with its high level of muscle glycogen. On the other hand, the pHu+ line was characterized by markers of oxidative stress and muscle catabolism, probably because of its low level of energy substrates. After OPLS-DA multiblock analysis a metabolic set of fifteen high-confidence biomarkers was identified that could be used to predict the quality of poultry meat after validation on independent population. PMID: 26954775 [PubMed - as supplied by publisher] 


14. Asian-Australas J Anim Sci. 2016 Jan 29. doi: 10.5713/ajas.15.0648. [Epub ahead of print] 

Performance of Broiler Chickens fed Low Protein, Limiting Amino Acid Supplemented Diets Formulated either on Total or Standardized Ileal Digestible Amino Acid Basis. 
C BK(1), R GG(2), K CS(1), T M P(3), B N S(4). Author information: (1)Department of Animal Nutrition, Bangalore, India. (2)Department of Instructional Livestock Farming Complex, Bangalore, India. (3)Livestock Research and Information Centre (Sheep), Nagamangala, India. (4)Department of Instructional Livestock Farming Complex, Hassan, India. 

Abstract
The aim of present experiment was to investigate the effect of protein reduction in commercial broiler chicken rations with incorporation of de-oiled rice bran (DORB) and supplementation of limiting amino acids (valine, isoleucine and/or tryptophan) with ration formulation either on total amino acid (TAA) or standardized ileal digestible amino acids (SIDAA). The experimental design consisted of T1-TAA control; T2 & T3-0.75% and 1.5% protein reduction by 3% and 6% DORB incorporation, respectively by replacing soybean meal with supplemental limiting amino acids to meet TAA requirement; T4-SIDAA control, T5 & T6-0.75% and 1.5% protein reduction by DORB incorporation (3% and 6%) with supplemental limiting amino acids on SIDAA basis. A total of 360 d-old fast growing broiler chicks (Vencobb-400) were divided into 36 homogenous groups of ten chicks each, and six dietary treatments described were allocated randomly with six replications. During 42 days trial, the feed intake was significantly (p<0.05) reduced by TAA factor compared to SIDAA factor and protein factor significantly (p<0.05) reduced the feed intake at 1.5% reduction compared to normal protein group. This was observed only during pre-starter phase but not thereafter. The cumulative body weight gain (BWG) was significantly (p<0.05) reduced in TAA formulations with protein step-down of 1.5% (T3-1993 g) compared to control (T1-2067 g), while under SIDAA formulations, BWG was not affected with protein reduction of 1.5% (T6-2076 g) compared to T4 (2129 g). The feed conversion ratio was significantly (P<0.05) reduced in both TAA and SIDAA formulations with 1.5% protein step-down (T3-1.741; T6-1.704) compared to respective controls (T1-1.696; T4-1.663). The SIDAA formulation revealed significantly (p<0.05) higher BWG (2095 g) and better FCR (1.684) compared to TAA formulation (2028 g; 1.721). Intake of CP and all limiting amino acids (SID basis) was higher in SIDAA group than TAA group with resultant higher nitrogen retention (4.438 v/s 4.027 g/bird/d). The nitrogen excretion was minimized with 1.5% protein reduction (1.608 g/bird) compared to normal protein group (1.794 g/bird). The serum uric acid concentration was significantly reduced in T3 (9.45 mg/dl) as compared to T4 (10.75 mg/dl). All carcass parameters were significantly (p<0.05) higher in SIDAA formulation over TAA formulation and 1.5% protein reduction significantly reduced carcass, breast and thigh yields. In conclusion, the dietary protein can be reduced by 0.75% with TAA formulation and 1.5% with SIDAA formulation through DORB incorporation and supplementation of limiting amino acids and among formulations, SIDAA formulation was better than TAA formulation. PMID: 26954211 [PubMed - as supplied by publisher] 


15. Asian-Australas J Anim Sci. 2015 Dec 18. doi: 10.5713/ajas.15.0757. [Epub ahead of print] 

Red Color Light at Different Intensities Affects the Performance, Behavioral Activities and Welfare of Broilers. 
Senaratna D(1), Samarakone TS(2), Gunawardena A(1). Author information: (1)University of Ruhuna, Matara, Sri Lanka. (2)University of Peradeniya, Peradeniya, Sri Lanka. 

Abstract
Red light (RL) marked higher weight gain (WG) and preference of broilers compared to other light colors. This study aimed to investigate how different intensities of RL affect the performance, behavior and welfare of broilers. RL treatments were T1=high intensity (320 lux), T2= medium intensity (20 lux); T3= dim intensity (5 lux), T4=control/ white light (WL) at (20 lux) provided on 20L: 4D schedule and T5=negative control (-VEC); 12 hours dark: 12 hours day light. Strain Cobb was used by adopting Complete Randomize Design with 6 replicates. WG, water/feed intake, FCR, mortality, behavior and welfare were assessed. At 35d, significantly (p<0.05) highest body weight (2147.06g±99) was recorded by T3. Lowest body weight (1640.55g±56) and FCR (1.34) were recorded by -VEC. Skin weight was the only carcass parameter showed a significant (p<0.05) influence giving the highest (56.2g) and the lowest (12.6g) values for -VEC and T1 respectively. Reduced welfare status indicated by significantly (p<0.05) higher foot pad lesions, hock burns and breast blisters was found under T3, due to reduced expression of behavior. Highest walking (2.08% ± 1) was performed under T1 in the evening during 29-35days. Highest dust bathing (3.01% ± 2) was performed in the morning during 22-28 days and highest bird interaction [BI] (4.87% ±4) was observed in the evening by -VEC during 14-21days. Light intensity*day session*age interaction was significantly (p<0.05) affected walking, dust bathing and BI. Light intensity significantly (p<0.05) affected certain behaviors such as lying, eating, drinking, standing, walking, preening while lying, wing/leg stretching, sleeping, dozing, BI, vocalization, idling. In conclusion, birds essentially required provision of light in the night for better performance. Exposed to 5 lux contributed to higher WG, potentially indicating compromised welfare status. Further researches are suggested to investigate RL intensity based lighting regimen that favors for both production and welfare of Broilers. PMID: 26954120 [PubMed - as supplied by publisher] 


16. Nat Commun. 2016 Mar 8;7:10986. doi: 10.1038/ncomms10986. 

Experimental evidence for compositional syntax in bird calls. 
Suzuki TN(1,)(2), Wheatcroft D(3), Griesser M(4). Author information: (1)Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Kamiyamaguchi 1560-35, Hayama, Kanagawa 240-0193, Japan. (2)Department of Life Science, Rikkyo University, Nishi-Ikebukuro 3-34-1, Toshima, Tokyo 171-8501, Japan. (3)Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden. (4)Anthropological Institute and Museum, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland. 

Abstract
Human language can express limitless meanings from a finite set of words based on combinatorial rules (i.e., compositional syntax). Although animal vocalizations may be comprised of different basic elements (notes), it remains unknown whether compositional syntax has also evolved in animals. Here we report the first experimental evidence for compositional syntax in a wild animal species, the Japanese great tit (Parus minor). Tits have over ten different notes in their vocal repertoire and use them either solely or in combination with other notes. Experiments reveal that receivers extract different meanings from 'ABC' (scan for danger) and 'D' notes (approach the caller), and a compound meaning from 'ABC-D' combinations. However, receivers rarely scan and approach when note ordering is artificially reversed ('D-ABC'). Thus, compositional syntax is not unique to human language but may have evolved independently in animals as one of the basic mechanisms of information transmission. PMID: 26954097 [PubMed - in process] 


17. PLoS One. 2016 Mar 8;11(3):e0147819. doi: 10.1371/journal.pone.0147819. eCollection 2016. 

Localisation of the Putative Magnetoreceptive Protein Cryptochrome 1b in the Retinae of Migratory Birds and Homing Pigeons. 
Bolte P(1,)(2), Bleibaum F(1,)(2), Einwich A(1,)(2), Günther A(1,)(2), Liedvogel M(3), Heyers D(1,)(2), Depping A(1,)(2), Wöhlbrand L(4), Rabus R(4), Janssen-Bienhold U(5), Mouritsen H(1,)(2). Author information: (1)Institute for Biology and Environmental Sciences, University of Oldenburg, Oldenburg, Germany. (2)Research Centre for Neurosensory Sciences, University of Oldenburg, Oldenburg, Germany. (3)Max-Planck-Institute for Evolutionary Biology, Plön, Germany. (4)Institute for Chemistry and Biology of the Marine Environment, Carl-von-Ossietzky University, Oldenburg, Germany. (5)Department of Neurobiology, University of Oldenburg, Oldenburg, Germany. 

Abstract
Cryptochromes are ubiquitously expressed in various animal tissues including the retina. Some cryptochromes are involved in regulating circadian activity. Cryptochrome proteins have also been suggested to mediate the primary mechanism in light-dependent magnetic compass orientation in birds. Cryptochrome 1b (Cry1b) exhibits a unique carboxy terminus exclusively found in birds so far, which might be indicative for a specialised function. Cryptochrome 1a (Cry1a) is so far the only cryptochrome protein that has been localised to specific cell types within the retina of migratory birds. Here we show that Cry1b, an alternative splice variant of Cry1a, is also expressed in the retina of migratory birds, but it is primarily located in other cell types than Cry1a. This could suggest different functions for the two splice products. Using diagnostic bird-specific antibodies (that allow for a precise discrimination between both proteins), we show that Cry1b protein is found in the retinae of migratory European robins (Erithacus rubecula), migratory Northern Wheatears (Oenanthe oenanthe) and pigeons (Columba livia). In all three species, retinal Cry1b is localised in cell types which have been discussed as potentially well suited locations for magnetoreception: Cry1b is observed in the cytosol of ganglion cells, displaced ganglion cells, and in photoreceptor inner segments. The cytosolic rather than nucleic location of Cry1b in the retina reported here speaks against a circadian clock regulatory function of Cry1b and it allows for the possible involvement of Cry1b in a radical-pair-based magnetoreception mechanism. PMID: 26953791 [PubMed - in process] 


18. PLoS One. 2016 Mar 8;11(3):e0150377. doi: 10.1371/journal.pone.0150377. eCollection 2016. 

Seasonally Changing Cryptochrome 1b Expression in the Retinal Ganglion Cells of a Migrating Passerine Bird. 
Nießner C(1), Gross JC(1,)(2), Denzau S(1), Peichl L(3), Fleissner G(1), Wiltschko W(1), Wiltschko R(1). Author information: (1)Fachbereich Biowissenschaften der Goethe-Universität Frankfurt, Max-von-Laue-Str. 13, D-60438, Frankfurt am Main, Germany. (2)Haematology and Oncology and Developmental Biochemistry, University Medicine Göttingen, Justus-von-Liebig Weg 11, 37077, Göttingen, Germany. (3)Max Planck Institute for Brain Research, Max-von-Laue-Str. 4, D-60438, Frankfurt am Main, Germany. 

Abstract
Cryptochromes, blue-light absorbing proteins involved in the circadian clock, have been proposed to be the receptor molecules of the avian magnetic compass. In birds, several cryptochromes occur: Cryptochrome 2, Cryptochrome 4 and two splice products of Cryptochrome 1, Cry1a and Cry1b. With an antibody not distinguishing between the two splice products, Cryptochrome 1 had been detected in the retinal ganglion cells of garden warblers during migration. A recent study located Cry1a in the outer segments of UV/V-cones in the retina of domestic chickens and European robins, another migratory species. Here we report the presence of cryptochrome 1b (eCry1b) in retinal ganglion cells and displaced ganglion cells of European Robins, Erithacus rubecula. Immuno-histochemistry at the light microscopic and electron microscopic level showed eCry1b in the cell plasma, free in the cytosol as well as bound to membranes. This is supported by immuno-blotting. However, this applies only to robins in the migratory state. After the end of the migratory phase, the amount of eCry1b was markedly reduced and hardly detectable. In robins, the amount of eCry1b in the retinal ganglion cells varies with season: it appears to be strongly expressed only during the migratory period when the birds show nocturnal migratory restlessness. Since the avian magnetic compass does not seem to be restricted to the migratory phase, this seasonal variation makes a role of eCry1b in magnetoreception rather unlikely. Rather, it could be involved in physiological processes controlling migratory restlessness and thus enabling birds to perform their nocturnal flights. PMID: 26953690 [PubMed - in process] 


19. Proc Natl Acad Sci U S A. 2016 Mar 7. pii: 201523754. [Epub ahead of print] 

Focal expression of mutant huntingtin in the songbird basal ganglia disrupts cortico-basal ganglia networks and vocal sequences. 
Tanaka M(1), Singh Alvarado J(1), Murugan M(2), Mooney R(3). Author information: (1)Department of Neurobiology, Duke University Medical Center, Durham, NC 27710; (2)Department of Psychology, Princeton University, Princeton, NJ 08544. (3)Department of Neurobiology, Duke University Medical Center, Durham, NC 27710; mooney@neuro.duke.edu. 

Abstract
The basal ganglia (BG) promote complex sequential movements by helping to select elementary motor gestures appropriate to a given behavioral context. Indeed, Huntington's disease (HD), which causes striatal atrophy in the BG, is characterized by hyperkinesia and chorea. How striatal cell loss alters activity in the BG and downstream motor cortical regions to cause these disorganized movements remains unknown. Here, we show that expressing the genetic mutation that causes HD in a song-related region of the songbird BG destabilizes syllable sequences and increases overall vocal activity, but leave the structure of individual syllables intact. These behavioral changes are paralleled by the selective loss of striatal neurons and reduction of inhibitory synapses on pallidal neurons that serve as the BG output. Chronic recordings in singing birds revealed disrupted temporal patterns of activity in pallidal neurons and downstream cortical neurons. Moreover, reversible inactivation of the cortical neurons rescued the disorganized vocal sequences in transfected birds. These findings shed light on a key role of temporal patterns of cortico-BG activity in the regulation of complex motor sequences and show how a genetic mutation alters cortico-BG networks to cause disorganized movements. PMID: 26951661 [PubMed - as supplied by publisher] 


20. Glob Chang Biol. 2016 Mar 7. doi: 10.1111/gcb.13273. [Epub ahead of print] 

Choice of baseline climate data impacts projected species' responses to climate change. 
Baker DJ(1), Hartley AJ(2), Butchart SH(3,)(4), Willis SG(1). Author information: (1)School of Biological & Biomedical Sciences, Durham University, Mountjoy Site, Durham, DH1 3LE, UK. (2)Met Office Hadley Centre, FitzRoy Road, Exeter, Devon, EX1 3PB, UK. (3)BirdLife International, David Attenborough Building, Pembroke Street, Cambridge, CB2 3QZ, UK. (4)Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB23EJ, UK. 

Abstract
Climate data created from historic climate observations are integral to most assessments of potential climate change impacts, and frequently comprise the baseline period used to infer species-climate relationships. They are often also central to downscaling coarse resolution climate simulations from General Circulation Models (GCMs) in order to project future climate scenarios at ecologically relevant spatial scales. Uncertainty in these baseline data can be large, particularly where weather observations are sparse and climate dynamics are complex (e.g. over mountainous or coastal regions). Yet, importantly, this uncertainty is almost universally overlooked when assessing potential responses of species to climate change. Here we assessed the importance of historic baseline climate uncertainty for projections of species' responses to future climate change. We built species distribution models (SDMs) for 895 African bird species of conservation concern, using six different climate baselines. We projected these models to two future periods (2040-2069, 2070-2099), using downscaled climate projections, and calculated species turnover and changes in species-specific climate suitability. We found that the choice of baseline climate data constituted an important source of uncertainty in projections of both species turnover and species-specific climate suitability, often comparable with, or more important than, uncertainty arising from the choice of GCM. Importantly, the relative contribution of these factors to projection uncertainty varied spatially. Moreover, when projecting SDMs to sites of biodiversity importance (Important Bird and Biodiversity Areas), these uncertainties altered site-level impacts, which could affect conservation prioritisation. Our results highlight that projections of species' responses to climate change are sensitive to uncertainty in the baseline climatology. We recommend that this should be considered routinely in such analyses. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved. PMID: 26950769 [PubMed - as supplied by publisher]



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