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Monday, 12 January 2015

What's new for 'birdRS' in PubMed: January 2015, Week 1

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).

Search: (bird[TIAB] OR songbird[TIAB]) NOT (flu[TIAB] OR influenza[TIAB] OR bird[AUTH]) AND (2014/04/01[PDAT]:2020/01/01[PDAT])

View complete results in PubMed (results may change over time).

PubMed Results

1. Environ Res. 2015 Jan 5;137C:185-198. doi: 10.1016/j.envres.2014.12.017. [Epub ahead of print]

Delta-aminolevulinic acid dehydratase (δALAD) activity in four free-living bird species exposed to different levels of lead under natural conditions.

Espín S1, Martínez-López E2, Jiménez P3, María-Mojica P4, García-Fernández AJ5.


The purposes of this study were: (1) to determine the δALAD activity and δALAD ratio in blood of four free-living bird species (Griffon vulture, Eagle owl, Slender-billed gull and Audouin's gull); (2) and to investigate the correlations between δALAD activity/ratio and Pb concentrations in blood samples. A decrease was observed in δALAD activity in Griffon vultures and Eagle owls exposed to Pb. In addition, negative relationships were found between δALAD ratio or δALAD activity and Log blood Pb levels in Griffon vultures and Eagle owls, and these relationships were stronger in areas with the highest Pb exposure. We provide equations that may be helpful to estimate δALAD activity and δALAD ratio using blood Pb concentrations. Regarding gull species, δALAD activity found in the present study may be considered the normal activity in Slender-billed gull and Audouin's gull species, since very low blood Pb concentrations and no correlations were found in these species. Although both δALAD activity and δALAD ratio are sensitive biomarkers of Pb exposure and effect in birds, the use of δALAD ratio may improve the results. Besides, this study provides blood threshold concentrations at which Pb bears effects on δALAD enzyme (5µg/dl in Eagle owl; 8µg/dl in Griffon vulture; and probably >2µg/dl in Slender-billed gull and Audouin's gull). Our findings show that Eagle owl seems to be more sensitive to δALAD enzymatic inhibition by Pb than Griffon vultures. Eagle owls and Griffon vultures exhibited up to 79% and 94% decrease in δALAD activity when blood Pb concentrations exceeded 19 and 30µg/dl, respectively. Regarding the effects related with δALAD inhibition, significant negative correlations were found between δALAD activity and hematocrit in Eagle owls and Griffon vultures, which may be related to compensatory response associated with a decrease in δALAD activity. In addition, an effect on creatine kinase activity and total proteins in plasma was found in Griffon vultures. The significant negative correlations found between δALAD activity and tGSH in Griffon vulture, and between δALAD activity and Log CAT activity in Eagle owls, may be related to a protective response of antioxidant system against reactive oxygen species (ROS). The negative relationship found between δALAD activity and TBARS levels in Griffon vulture is probably related to an induction of lipid peroxidation by ROS that may be generated by δALA accumulation when δALAD activity is depressed. δALAD activity and δALAD ratio in blood are suggested as important nondestructive biomarkers for Pb exposure and effect for future biomonitoring studies in Griffon vulture and Eagle owl. Further studies are recommended to provide new data on Pb concentrations at which δALAD activity is affected in different wild bird species and to elucidate why different species tolerate Pb in different ways.
Copyright © 2014 Elsevier Inc. All rights reserved.
PMID: 25569843 [PubMed - as supplied by publisher]

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2. J Anim Sci. 2015 Jan;93(1):238-46. doi: 10.2527/jas.2014-7219.

Dietary β-galactomannans have beneficial effects on the intestinal morphology of chickens challenged with Salmonella enterica serovar Enteritidis.

Brufau MT1, Martín-Venegas R2, Guerrero-Zamora AM1, Pérez-Vendrell AM3, Vilà B3, Brufau J3, Ferrer R1.


Salmonella enterica serovar Enteritidis is one of the leading causes of food-borne salmonellosis in humans. Poultry is the single largest reservoir, and the consumption of incorrectly processed chicken meat and egg products is the major source of infection. Since 2006, the use of antibiotics as growth promoters has been banned in the European Union, and the dietary inclusion of β-galactomannans (βGM) has become a promising strategy to control and prevent intestinal infections. The aim of this study was to investigate the effect of various βGM-rich products on intestinal morphology in chickens challenged with Salmonella Enteritidis. To assess this effect, a total of 280 male Ross 308 chickens were studied (40 animals per treatment housed in 5 cages). There were 7 treatments, including controls: uninoculated birds fed the basal diet (negative control) and inoculated birds fed the basal diet (positive control) or the basal diet supplemented with Salmosan (1 g/kg), Duraió gum (1 g/kg), Cassia gum (1 g/kg), the cell walls of Saccharomyces cerevisiae (0.5 g/kg), or the antibiotic colistine (0.8 g/kg). The birds were fed these diets from the d 1 to 23, except the animals in the colistine group, which were fed the diet containing the antibiotic only from d 5 to 11. The inoculated animals were orally infected on d 7 with 10(8) cfu of Salmonella Enteritidis. Bird performance per replicate was determined for the whole study period (23 d), and the distal ileum and cecal tonsil of 5 animals per treatment (1 animal per replicate) were observed at different magnification levels (scanning electron, light, and laser confocal microscopy). In the images corresponding to the treatments containing βGM we observed more mucus, an effect that can be associated with the observation of more goblet cells. Moreover, the images also show fewer M cells, which are characteristic of infected animals. Regarding the morphometric parameters, the animals that received Duraió and Cassia gums show greater (P = 0.001 and P = 0.016, respectively) villus length compared with the animals in the positive control, thus indicating the capacity of these products to increase epithelial surface area. However, no effect (P > 0.05) on microvillus dimensions was detected. In conclusion, the results obtained indicating the beneficial effects of these βGM on intestinal morphology give more evidence of the positive effects of these supplements in poultry nutrition.
PMID: 25568372 [PubMed - in process]

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3. J Neurosci. 2015 Jan 7;35(1):299-307. doi: 10.1523/JNEUROSCI.3698-14.2015.

Motor Origin of Precise Synaptic Inputs onto Forebrain Neurons Driving a Skilled Behavior.

Vallentin D1, Long MA2.


Sensory feedback is crucial for learning and performing many behaviors, but its role in the execution of complex motor sequences is poorly understood. To address this, we consider the forebrain nucleus HVC in the songbird, which contains the premotor circuitry for song production and receives multiple convergent sensory inputs. During singing, projection neurons within HVC exhibit precisely timed synaptic events that may represent the ongoing motor program or song-related sensory feedback. To distinguish between these possibilities, we recorded the membrane potential from identified HVC projection neurons in singing zebra finches. External auditory perturbations during song production did not affect synaptic inputs in these neurons. Furthermore, the systematic removal of three sensory feedback streams (auditory, proprioceptive, and vagal) did not alter the frequency or temporal precision of synaptic activity observed. These findings support a motor origin for song-related synaptic events and suggest an updated circuit model for generating behavioral sequences.
Copyright © 2015 the authors 0270-6474/15/350299-09$15.00/0.
PMID: 25568122 [PubMed - in process]

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4. Avian Pathol. 2015 Jan 7:1-31. [Epub ahead of print]

High stocking density as a predisposing factor for necrotic enteritis in broiler chicks.

Tsiouris V1, Georgopoulou I, Batzios C, Pappaioannou N, Ducatelle R, Fortomaris P.


Stocking density is a management factor which has critical implications for the poultry industry. The aim of the present study was to investigate the effect of high stocking density as a predisposing factor in an experimental model of necrotic enteritis in broiler chicks. The experimental challenge model included an oral inoculation with 10-fold dose of attenuated anticoccidial vaccine and multiple oral inoculations with a specific strain of Clostridium perfringens. Two hundred and forty as hatched day-old broiler chicks were randomly allocated to four treatment groups according to the following experimental design: group N, with normal stocking density (15 birds/m2) and no challenge, group D, with high stocking density (30 birds/m2) and no challenge, group P, with normal stocking density and positive challenge and group DP, with high stocking density and positive challenge. From each bird, the intestine, gizzard and liver were collected and scored for gross lesions. The intestinal digesta was collected for pH and viscosity determination. One caecum from each bird was taken for microbiological analysis. The statistical analysis and evaluation of the experimental data revealed significant interaction effects between "stocking density" and "challenge", regarding gross lesion scores in intestine and liver, pH values in jejunum, ileum and caeca as well as C. perfringens counts in the caeca (P ≤ 0.05). High stocking density in challenged birds increased the gross lesion score in intestine (P ≤ 0.05), contrary to unchallenged birds. It can be concluded that high stocking density affects unfavorably the welfare and gut health of broiler chicks, predisposes to necrotic enteritis in a subclinical experimental model and increases further its importance as management factor for the poultry industry.
PMID: 25563065 [PubMed - as supplied by publisher]

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5. Ann Am Thorac Soc. 2015 Jan 6. [Epub ahead of print]

Validation of Inhalation Provocation Test in Chronic Bird-related Hypersensitivity Pneumonitis and New Prediction Score.

Ishizuka M1, Miyazaki Y, Tateishi T, Tsutsui T, Tsuchiya K, Inase N.


Rationale: Hypersensitivity pneumonitis (HP) is an immunologically mediated lung disease induced by the inhalation of any of a wide variety of antigens. For example, bird-related hypersensitivity pneumonitis (BRHP) results from the inhalation of avian antigens. The clinical features of chronic HP, including imaging and histological findings, are similar to those of idiopathic pulmonary fibrosis. Despite its status as the "gold standard," the inhalation provocation test (IPT) is rarely performed because the methods and the criteria are not standardized. In 2000, we reported the utility of IPT for pigeon dropping extracts (PDE). Objective: The purpose of the current study was to validate the utility and the safety of the test and to differentiate chronic HP from other interstitial lung diseases. Methods: Twenty-eight patients with chronic BRHP and 19 control subjects were evaluated in this retrospective study. We validated the previous criteria and proposed new criteria using prediction scores. Measurements and Main Results: In the IPT using PDE, the previous criteria showed a sensitivity of 78.6% and a specificity of 94.7% in this retrospective study. The increases in the peripheral white blood cell count and C-reactive protein levels are good indicators of a positive response to the inhalation challenge. We propose the use of the IPT prediction score (IPT-PS = 1 × ∆WBC (%) + 2 × ∆ P (A-a) O2 (mmHg)) and the prediction rule, which showed high sensitivity and specificity values of 92.9% and 94.7%, respectively. Two (1.5%) out of a total of 130 subjects who underwent the tests required treatment after the challenge. Conclusions: The IPT is a useful and safe tool for the diagnosis of chronic HP. The IPT-PS that we have proposed has high sensitivity and specificity in the diagnosis of chronic BRHP.
PMID: 25562381 [PubMed - as supplied by publisher]

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6. Philos Trans R Soc Lond B Biol Sci. 2015 Feb 19;370(1662). pii: 20140013. doi: 10.1098/rstb.2014.0013.

Global evolutionary isolation measures can capture key local conservation species in Nearctic and Neotropical bird communities.

Redding DW1, Mooers AO2, Şekercioğlu ÇH3, Collen B4.


Understanding how to prioritize among the most deserving imperilled species has been a focus of biodiversity science for the past three decades. Though global metrics that integrate evolutionary history and likelihood of loss have been successfully implemented, conservation is typically carried out at sub-global scales on communities of species rather than among members of complete taxonomic assemblages. Whether and how global measures map to a local scale has received little scrutiny. At a local scale, conservation-relevant assemblages of species are likely to be made up of relatively few species spread across a large phylogenetic tree, and as a consequence there are potentially relatively large amounts of evolutionary history at stake. We ask to what extent global metrics of evolutionary history are useful for conservation priority setting at the community level by evaluating the extent to which three global measures of evolutionary isolation (evolutionary distinctiveness (ED), average pairwise distance (APD) and the pendant edge or unique phylogenetic diversity (PD) contribution) capture community-level phylogenetic and trait diversity for a large sample of Neotropical and Nearctic bird communities. We find that prioritizing the most ED species globally safeguards more than twice the total PD of local communities on average, but that this does not translate into increased local trait diversity. By contrast, global APD is strongly related to the APD of those same species at the community level, and prioritizing these species also safeguards local PD and trait diversity. The next step for biologists is to understand the variation in the concordance of global and local level scores and what this means for conservation priorities: we need more directed research on the use of different measures of evolutionary isolation to determine which might best capture desirable aspects of biodiversity.
Free Article
PMID: 25561674 [PubMed - in process]

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7. Proc Natl Acad Sci U S A. 2015 Jan 5. pii: 201410844. [Epub ahead of print]

Context-dependent categorical perception in a songbird.

Lachlan RF1, Nowicki S2.


Some of the psychological abilities that underlie human speech are shared with other species. One hallmark of speech is that linguistic context affects both how speech sounds are categorized into phonemes, and how different versions of phonemes are produced. We here confirm earlier findings that swamp sparrows categorically perceive the notes that constitute their learned songs and then investigate how categorical boundaries differ according to context. We clustered notes according to their acoustic structure, and found statistical evidence for clustering into 10 population-wide note types. Examining how three related types were perceived, we found, in both discrimination and labeling tests, that an "intermediate" note type is categorized with a "short" type when it occurs at the beginning of a song syllable, but with a "long" type at the end of a syllable. In sum, three produced note-type clusters appear to be underlain by two perceived categories. Thus, in birdsong, as in human speech, categorical perception is context-dependent, and as is the case for human phonology, there is a complex relationship between underlying categorical representations and surface forms. Our results therefore suggest that complex phonology can evolve even in the absence of rich linguistic components, like syntax and semantics.
PMID: 25561538 [PubMed - as supplied by publisher]

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8. Am Nat. 2015 Jan;185(1):135-41. doi: 10.1086/679106. Epub 2014 Nov 26.

Morphological and behavioral evidence of batesian mimicry in nestlings of a lowland amazonian bird.

Londoño GA1, García DA, Sánchez Martínez MA.


Abstract Because predation is the main cause of avian nest failure, selection should favor strategies that reduce the probability of nest predation. We describe apparent Batesian mimicry in the morphology and behavior of a Laniocera hypopyrra nestling. On hatching, the nestling had a distinctive bright orange color and modified feathers all over its body, and 6 days after hatching, it started to move its head very slowly from side to side (in a "caterpillar" movement) when disturbed. These traits gave it a resemblance to a hairy, aposematic caterpillar. This species has a long nestling period for its size (20 days), perhaps due to slow provisioning rates (about one feeding per hour). We argue that the slow growth rate, combined with high nest predation, favors the evolution of antipredation mechanisms such as the unique morphological and behavioral characteristics of L. hypopyrra nestlings.
PMID: 25560558 [PubMed - in process]

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9. Am Nat. 2015 Jan;185(1):13-27. doi: 10.1086/679012. Epub 2014 Nov 19.

Life-history differences in age-dependent expressions of multiple ornaments and behaviors in a lekking bird.

Kervinen M1, Lebigre C, Alatalo RV, Siitari H, Soulsbury CD.


Abstract Age is a major factor explaining variation in life-history traits among individuals with typical patterns of increasing trait values early in life, maximum trait expression, and senescence. However, age-dependent variation in the expressions of sexually selected traits has received less attention, although such variation underpins differences in male competitive abilities and female preference, which are central to sexual selection. In contrast to previous studies focusing on single traits, we used repeated measures of seven sexually selected morphological and behavioral traits in male black grouse (Tetrao tetrix) to quantify the effects of age and life span on their expressions and quantified this variation in relation to male reproductive effort. Trait expression increased with age, but long-lived males had a slower increase and delayed maxima in trait values compared with short-lived males. There was evidence of terminal investment (increasing trait values during the last breeding season) in some traits and senescence in all traits. These trait dynamics were largely explained by the timing of male peak lekking effort. This study shows that fully understanding the variation in sexually selected traits and fitness benefits associated with sexual selection requires accounting for the complex interaction among individual age, life span, and the timing of individuals' investment in reproduction.
PMID: 25560550 [PubMed - in process]

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10. Ecol Lett. 2015 Jan 6. doi: 10.1111/ele.12395. [Epub ahead of print]

A new dynamic null model for phylogenetic community structure.

Pigot AL1, Etienne RS.


Phylogenies are increasingly applied to identify the mechanisms structuring ecological communities but progress has been hindered by a reliance on statistical null models that ignore the historical process of community assembly. Here, we address this, and develop a dynamic null model of assembly by allopatric speciation, colonisation and local extinction. Incorporating these processes fundamentally alters the structure of communities expected due to chance, with speciation leading to phylogenetic overdispersion compared to a classical statistical null model assuming equal probabilities of community membership. Applying this method to bird and primate communities in South America we show that patterns of phylogenetic overdispersion - often attributed to negative biotic interactions - are instead consistent with a species neutral model of allopatric speciation, colonisation and local extinction. Our findings provide a new null expectation for phylogenetic community patterns and highlight the importance of explicitly accounting for the dynamic history of assembly when testing the mechanisms governing community structure.
© 2014 The Authors. Ecology Letters published by John Wiley & Sons Ltd and CNRS.
PMID: 25560516 [PubMed - as supplied by publisher]

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11. J Comp Neurol. 2015 Jan 5. doi: 10.1002/cne.23738. [Epub ahead of print]

Efferent innervation of turtle semicircular canal cristae: Comparisons with bird and mouse.

Jordan PM1, Fettis M, Holt JC.


In the vestibular periphery of nearly every vertebrate, cholinergic vestibular efferent neurons give rise to numerous presynaptic varicosities that target hair cells and afferent processes in the sensory neuroepithelium. Although pharmacological studies have described the postsynaptic actions of vestibular efferent stimulation in several species, characterization of efferent innervation patterns and the relative distribution of efferent varicosities among hair cells and afferents are also integral to understanding how efferent synapses operate. Vestibular efferent markers, however, have not been well characterized in the turtle, one of the animal models utilized by our laboratory. Here, we sought to identify reliable efferent neuronal markers in the vestibular periphery of turtle, to utilize these markers to understand how efferent synapses are organized, and to compare efferent neuronal labeling patterns in turtle with two other amniotes using some of the same markers. Efferent fibers and varicosities were visualized in the semicircular canal of Red-Eared Turtles (Trachemys scripta elegans), Zebra Finches (Taeniopygia guttata), and mice (Mus musculus) utilizing fluorescent immunohistochemistry with antibodies against choline acetyltransferase (ChAT). Vestibular hair cells and afferents were counterstained using antibodies to myosin VIIa and calretinin. In all species, ChAT labeled a population of small diameter fibers giving rise to numerous spherical varicosities abutting type II hair cells and afferent processes. That these ChAT-positive varicosities represent presynaptic release sites were demonstrated by colabeling with antibodies against the synaptic vesicle proteins synapsin I, SV2, or syntaxin and the neuropeptide calcitonin gene-related peptide (CGRP). Comparisons of efferent innervation patterns among the three species are discussed. This article is protected by copyright. All rights reserved.
© 2015 Wiley Periodicals, Inc.
PMID: 25560461 [PubMed - as supplied by publisher]

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12. Ecol Evol. 2014 Dec;4(24):4578-88. doi: 10.1002/ece3.1306. Epub 2014 Nov 26.

Step selection techniques uncover the environmental predictors of space use patterns in flocks of Amazonian birds.

Potts JR1, Mokross K2, Stouffer PC2, Lewis MA3.


Understanding the behavioral decisions behind animal movement and space use patterns is a key challenge for behavioral ecology. Tools to quantify these patterns from movement and animal-habitat interactions are vital for transforming ecology into a predictive science. This is particularly important in environments undergoing rapid anthropogenic changes, such as the Amazon rainforest, where animals face novel landscapes. Insectivorous bird flocks are key elements of avian biodiversity in the Amazonian ecosystem. Therefore, disentangling and quantifying the drivers behind their movement and space use patterns is of great importance for Amazonian conservation. We use a step selection function (SSF) approach to uncover environmental drivers behind movement choices. This is used to construct a mechanistic model, from which we derive predicted utilization distributions (home ranges) of flocks. We show that movement decisions are significantly influenced by canopy height and topography, but depletion and renewal of resources do not appear to affect movement significantly. We quantify the magnitude of these effects and demonstrate that they are helpful for understanding various heterogeneous aspects of space use. We compare our results to recent analytic derivations of space use, demonstrating that the analytic approximation is only accurate when assuming that there is no persistence in the animals' movement. Our model can be translated into other environments or hypothetical scenarios, such as those given by proposed future anthropogenic actions, to make predictions of spatial patterns in bird flocks. Furthermore, our approach is quite general, so could potentially be used to understand the drivers of movement and spatial patterns for a wide variety of animal communities.
Free Article
PMID: 25558353 [PubMed]

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13. J Appl Ecol. 2014 Oct;51(5):1387-1395. Epub 2014 Jul 25.

Agriculture modifies the seasonal decline of breeding success in a tropical wild bird population.

Cartwright SJ1, Nicoll MA1, Jones CG2, Tatayah V3, Norris K1.


Habitat conversion for agriculture is a major driver of biodiversity loss, but our understanding of the demographic processes involved remains poor. We typically investigate the impacts of agriculture in isolation even though populations are likely to experience multiple, concurrent changes in the environment (e.g. land and climate change). Drivers of environmental change may interact to affect demography, but the mechanisms have yet to be explored fully in wild populations.Here, we investigate the mechanisms linking agricultural land use with breeding success using long-term data for the formerly Critically Endangered Mauritius kestrel Falco punctatus, a tropical forest specialist that also occupies agricultural habitats. We specifically focused on the relationship between breeding success, agriculture and the timing of breeding because the latter is sensitive to changes in climatic conditions (spring rainfall) and enables us to explore the interactive effects of different (land and climate) drivers of environmental change.Breeding success, measured as egg survival to fledging, declines seasonally in this population, but we found that the rate of this decline became increasingly rapid as the area of agriculture around a nest site increased. If the relationship between breeding success and agriculture was used in isolation to estimate the demographic impact of agriculture, it would significantly under-estimate breeding success in dry (early) springs and over-estimate breeding success in wet (late) springs.Analysis of prey delivered to nests suggests that the relationship between breeding success and agriculture might be due, in part, to spatial variation in the availability of native, arboreal geckos.Synthesis and applications. Agriculture modifies the seasonal decline in breeding success in this population. As springs are becoming wetter in our study area and since the kestrels breed later in wetter springs, the impact of agriculture on breeding success will become worse over time. Our results suggest that forest restoration designed to reduce the detrimental impacts of agriculture on breeding may also help reduce the detrimental effects of breeding late due to wetter springs. Our results therefore highlight the importance of considering the interactive effects of environmental change when managing wild populations.
PMID: 25558086 [PubMed]
Related citations

14. Syst Parasitol. 2015 Jan;90(1):1-25. doi: 10.1007/s11230-014-9530-3. Epub 2015 Jan 4.

A re-assessment of species diversity within the 'revolutum' group of Echinostoma Rudolphi, 1809 (Digenea: Echinostomatidae) in Europe.

Faltýnková A1, Georgieva S, Soldánová M, Kostadinova A .


Species of Echinostoma Rudolphi, 1809 (Digenea: Echinostomatidae) belonging to the 'revolutum' species complex were re-examined based on material gathered in an extensive sampling programme in eight countries in Europe. The morphology of the life-cycle stages was studied in naturally and experimentally infected snail and bird hosts. A review, with an updated synonymy, is presented for six European species, including one new to science, i.e. Echinostoma revolutum (Frölich, 1802) (sensu stricto) (type-species), E. bolschewense (Kotova, 1939), E. miyagawai Ishii, 1932, E. nasincovae n. sp., E. paraulum Dietz, 1909 and Echinostoma sp. IG), and keys to the identification of their cercariae and adults are provided.
PMID: 25557744 [PubMed - in process]

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15. Integr Environ Assess Manag. 2014 Dec 30. doi: 10.1002/ieam.1612. [Epub ahead of print]

Interactive effects of climate change with nutrients, mercury, and freshwater acidification on key taxa in the North Atlantic Landscape Conservation Cooperative region.

Pinkney AE1, Driscoll CT, Evers DC, Hooper MJ, Horan J, Jones JW, Lazarus RS, Marshall HG, Milliken A, Rattner BA, Schmerfeld J, Sparling DW.


The North Atlantic Landscape Conservation Cooperative LCC (NA LCC) is a public-private partnership that provides information to support conservation decisions that may be affected by global climate change (GCC) and other threats. The NA LCC region extends from southeast Virginia to the Canadian Maritime Provinces. Within this region, the U.S. National Climate Assessment documented increases in air temperature, total precipitation, frequency of heavy precipitation events, and rising sea level, and predicted more drastic changes. Here we synthesize literature on the effects of GCC interacting with selected contaminant, nutrient, and environmental processes to adversely affect natural resources within this region. Using a case study approach, we focused on three stressors with sufficient NA LCC region-specific information for an informed discussion. We describe GCC interactions with a contaminant (mercury), and two complex environmental phenomena-freshwater acidification and eutrophication. We also prepared taxa case studies on GCC- and GCC-contaminant/nutrient/process effects on amphibians and freshwater mussels. Several avian species of high conservation concern have blood mercury concentrations that have been associated with reduced nesting success. Freshwater acidification has adversely affected terrestrial and aquatic ecosystems in the Adirondacks and other areas of the region that are slowly recovering due to decreased emissions of nitrogen and sulfur oxides. Eutrophication in many estuaries within the region is projected to increase from greater storm runoff and less denitrification in riparian wetlands. Estuarine hypoxia may be exacerbated by increased stratification. Elevated water temperature favors algal species that produce harmful algal blooms (HABs). In several of the region's estuaries, HABs have been associated with bird die-offs. In the NA LCC region, amphibian populations appear to be declining. Some species may be adversely affected by GCC through higher temperatures and more frequent droughts. GCC may affect freshwater mussel populations via altered stream temperatures, and increased sediment loading during heavy storms. Freshwater mussels are sensitive to un-ionized ammonia which is more toxic at higher temperatures. We recommend studying the interactive effects of GCC on generation and bioavailability of methylmercury and how GCC-driven shifts in bird species distributions will affect avian exposure to methylmercury. Research is needed on how decreases in acid deposition concurrent with GCC will alter the structure and function of sensitive watersheds and surface waters. Studies are needed to determine how GCC will affect HABs and avian disease, and how more severe and extensive hypoxia will affect fish and shellfish populations. Regarding amphibians, we suggest research on 1) thermal tolerance and moisture requirements of species of concern; 2) effects of multiple stressors (temperature, desiccation, contaminants, nutrients); and 3) approaches to mitigate impacts of increased temperature and seasonal drought. We recommend studies to assess which mussel species and populations are vulnerable and which are resilient to rising stream temperatures, hydrological shifts, and ionic pollutants, all of which are influenced by GCC. This article is protected by copyright. All rights reserved.
This article is protected by copyright. All rights reserved.
PMID: 25556986 [PubMed - as supplied by publisher]

16. FEMS Microbiol Ecol. 2014 Oct;90(1):300-12. doi: 10.1111/1574-6941.12392. Epub 2014 Aug 26.

Marek's disease virus influences the core gut microbiome of the chicken during the early and late phases of viral replication.

Perumbakkam S1, Hunt HD, Cheng HH.


Marek's disease (MD) is an important neoplastic disease of chickens caused by the Marek's disease virus (MDV), an oncogenic alphaherpesvirus. In this study, dysbiosis induced by MDV on the core gut flora of chicken was assessed using next generation sequence (NGS) analysis. Total fecal and cecum-derived samples from individual birds were used to estimate the influence of MDV infection on the gut microbiome of chicken. Our analysis shows that MDV infection alters the core gut flora in the total fecal samples relatively early after infection (2-7 days) and in the late phase of viral infection (28-35 days) in cecal samples, corresponding well with the life cycle of MDV. Principle component analyses of total fecal and cecal samples showed clustering at the early and late time points, respectively. The genus Lactobacillus was exclusively present in the infected samples in both total fecal and cecal bird samples. The community colonization of core gut flora was altered by viral infection, which manifested in the enrichment of several genera during the early and late phases of MDV replication. The results suggest a relationship between viral infection and microbial composition of the intestinal tract that may influence inflammation and immunosuppression of T and B cells in the host.
Published 2014. This article is a U.S. Government work and is in the public domain in the USA.
PMID: 25065611 [PubMed - indexed for MEDLINE]

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17. J R Soc Interface. 2014 Aug 6;11(97):20140451. doi: 10.1098/rsif.2014.0451.

Magnetic orientation of garden warblers (Sylvia borin) under 1.4 MHz radiofrequency magnetic field.

Kavokin K, Chernetsov N, Pakhomov A, Bojarinova J, Kobylkov D, Namozov B.


We report on the experiments on orientation of a migratory songbird, the garden warbler (Sylvia borin), during the autumn migration period on the Courish Spit, Eastern Baltics. Birds in experimental cages, deprived of visual information, showed the seasonally appropriate direction of intended flight with respect to the magnetic meridian. Weak radiofrequency (RF) magnetic field (190 nT at 1.4 MHz) disrupted this orientation ability. These results may be considered as an independent replication of earlier experiments, performed by the group of R. and W. Wiltschko with European robins (Erithacus rubecula). Confirmed outstanding sensitivity of the birds' magnetic compass to RF fields in the lower megahertz range demands for a revision of one of the mainstream theories of magnetoreception, the radical-pair model of birds' magnetic compass.
© 2014 The Author(s) Published by the Royal Society. All rights reserved.
PMCID: PMC4208380 [Available on 2015/8/6]
PMID: 24942848 [PubMed - indexed for MEDLINE]

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18. Bioinspir Biomim. 2014 Jun;9(2):025013. doi: 10.1088/1748-3182/9/2/025013. Epub 2014 May 22.

Robust post-stall perching with a simple fixed-wing glider using LQR-Trees.

Moore J1, Cory R, Tedrake R.


Birds routinely execute post-stall maneuvers with a speed and precision far beyond the capabilities of our best aircraft control systems. One remarkable example is a bird exploiting post-stall pressure drag in order to rapidly decelerate to land on a perch. Stall is typically associated with a loss of control authority, and it is tempting to attribute this agility of birds to the intricate morphology of the wings and tail, to their precision sensing apparatus, or their ability to perform thrust vectoring. Here we ask whether an extremely simple fixed-wing glider (no propeller) with only a single actuator in the tail is capable of landing precisely on a perch from a large range of initial conditions. To answer this question, we focus on the design of the flight control system; building upon previous work which used linear feedback control design based on quadratic regulators (LQR), we develop nonlinear feedback control based on nonlinear model-predictive control and 'LQR-Trees'. Through simulation using a flat-plate model of the glider, we find that both nonlinear methods are capable of achieving an accurate bird-like perching maneuver from a large range of initial conditions; the 'LQR-Trees' algorithm is particularly useful due to its low computational burden at runtime and its inherent performance guarantees. With this in mind, we then implement the 'LQR-Trees' algorithm on real hardware and demonstrate a 95 percent perching success rate over 147 flights for a wide range of initial speeds. These results suggest that, at least in the absence of significant disturbances like wind gusts, complex wing morphology and sensing are not strictly required to achieve accurate and robust perching even in the post-stall flow regime.
PMID: 24852406 [PubMed - indexed for MEDLINE]

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19. Bioinspir Biomim. 2014 Jun;9(2):025012. doi: 10.1088/1748-3182/9/2/025012. Epub 2014 May 22.

Flocking algorithm for autonomous flying robots.

Virágh C1, Vásárhelyi G, Tarcai N, Szörényi T, Somorjai G, Nepusz T, Vicsek T.


Animal swarms displaying a variety of typical flocking patterns would not exist without the underlying safe, optimal and stable dynamics of the individuals. The emergence of these universal patterns can be efficiently reconstructed with agent-based models. If we want to reproduce these patterns with artificial systems, such as autonomous aerial robots, agent-based models can also be used in their control algorithms. However, finding the proper algorithms and thus understanding the essential characteristics of the emergent collective behaviour requires thorough and realistic modeling of the robot and also the environment. In this paper, we first present an abstract mathematical model of an autonomous flying robot. The model takes into account several realistic features, such as time delay and locality of communication, inaccuracy of the on-board sensors and inertial effects. We present two decentralized control algorithms. One is based on a simple self-propelled flocking model of animal collective motion, the other is a collective target tracking algorithm. Both algorithms contain a viscous friction-like term, which aligns the velocities of neighbouring agents parallel to each other. We show that this term can be essential for reducing the inherent instabilities of such a noisy and delayed realistic system. We discuss simulation results on the stability of the control algorithms, and perform real experiments to show the applicability of the algorithms on a group of autonomous quadcopters. In our case, bio-inspiration works in two ways. On the one hand, the whole idea of trying to build and control a swarm of robots comes from the observation that birds tend to flock to optimize their behaviour as a group. On the other hand, by using a realistic simulation framework and studying the group behaviour of autonomous robots we can learn about the major factors influencing the flight of bird flocks.
PMID: 24852272 [PubMed - indexed for MEDLINE]

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