PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Shielding effects of myelin sheath on axolemma depolarization under transverse electric field stimulation
items: When and where to hatch? Red-eyed treefrog embryos use light cues in two contexts
items: Coral disease prevalence estimation and sampling design
items: Intestinal microbiome and its potential functions in bighead carp (Aristichthys nobilis) under different feeding strategies
items: In-situ incubation of a coral patch for community-scale assessment of metabolic and chemical processes on a reef slope
items: Urbanisation and wing asymmetry in the western honey bee (Apis mellifera, Linnaeus 1758) at multiple scales
items: Characterization of bacterioplankton communities and quantification of organic carbon pools off the Galapagos Archipelago under contrasting environmental conditions
items: The proportion of core species in a community varies with spatial scale and environmental heterogeneity
items: Between extreme simplification and ideal optimization: antennal sensilla morphology of miniaturized Megaphragma wasps (Hymenoptera: Trichogrammatidae)
items: Analyses of long non-coding RNA and mRNA profiling in the spleen of diarrheic piglets caused by Clostridium perfringens type C

Shielding effects of myelin sheath on axolemma depolarization under transverse electric field stimulation
type: item
type: AcademicArticle
description: Axonal stimulation with electric currents is an effective method for controlling neural activity. An electric field parallel to the axon is widely accepted as the predominant component in the activation of an axon. However, recent studies indicate that the transverse component to the axolemma is also effective in depolarizing the axon. To quantitatively investigate the amount of axolemma polarization induced by a transverse electric field, we computed the transmembrane potential (Vm) for a conductive body that represents an unmyelinated axon (or the bare axon between the myelin sheath in a myelinated axon). We also computed the transmembrane potential of the sheath-covered axonal segment in a myelinated axon. We then systematically analyzed the biophysical factors that affect axonal polarization under transverse electric stimulation for both the bare and sheath-covered axons. Geometrical patterns of polarization of both axon types were dependent on field properties (magnitude and field orientation to the axon). Polarization of both axons was also dependent on their axolemma radii and electrical conductivities. The myelin provided a significant “shielding effect” against the transverse electric fields, preventing excessive axolemma depolarization. Demyelination could allow for prominent axolemma depolarization in the transverse electric field, via a significant increase in myelin conductivity. This shifts the voltage drop of the myelin sheath to the axolemma. Pathological changes at a cellular level should be considered when electric fields are used for the treatment of demyelination diseases. The calculated term for membrane polarization (Vm) could be used to modify the current cable equation that describes axon excitation by an external electric field to account for the activating effects of both parallel and transverse fields surrounding the target axon.
format: application/pdf
format: text/html
creator: Hui Ye
creator: Jeffrey Ng
subject: Biophysics
subject: Computational Biology
subject: Mathematical Biology
subject: Neurology
description: doi:10.7717/peerj.6020
publisher: PeerJ Inc.
rights: © 2018 Ye and Ng
abstract: Axonal stimulation with electric currents is an effective method for controlling neural activity. An electric field parallel to the axon is widely accepted as the predominant component in the activation of an axon. However, recent studies indicate that the transverse component to the axolemma is also effective in depolarizing the axon. To quantitatively investigate the amount of axolemma polarization induced by a transverse electric field, we computed the transmembrane potential (Vm) for a conductive body that represents an unmyelinated axon (or the bare axon between the myelin sheath in a myelinated axon). We also computed the transmembrane potential of the sheath-covered axonal segment in a myelinated axon. We then systematically analyzed the biophysical factors that affect axonal polarization under transverse electric stimulation for both the bare and sheath-covered axons. Geometrical patterns of polarization of both axon types were dependent on field properties (magnitude and field orientation to the axon). Polarization of both axons was also dependent on their axolemma radii and electrical conductivities. The myelin provided a significant “shielding effect” against the transverse electric fields, preventing excessive axolemma depolarization. Demyelination could allow for prominent axolemma depolarization in the transverse electric field, via a significant increase in myelin conductivity. This shifts the voltage drop of the myelin sheath to the axolemma. Pathological changes at a cellular level should be considered when electric fields are used for the treatment of demyelination diseases. The calculated term for membrane polarization (Vm) could be used to modify the current cable equation that describes axon excitation by an external electric field to account for the activating effects of both parallel and transverse fields surrounding the target axon.
bibliographic citation: Ye et al. (2018) Shielding effects of myelin sheath on axolemma depolarization under transverse electric field stimulation. PeerJ 6:e6020 https://doi.org/10.7717/peerj.6020
date submitted: 2018-05-15
date accepted: 2018-10-29
issued: 2018-12-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ye
  given name: Hui
author list: Agent
  family name: Ng
  given name: Jeffrey
doi: 10.7717/peerj.6020
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-03
copyright: © 2018 Ye and Ng
attribution name: Ye and Ng

When and where to hatch? Red-eyed treefrog embryos use light cues in two contexts
type: item
type: AcademicArticle
description: Hatching timing is under strong selection and environmentally cued in many species. Embryos use multiple sensory modalities to inform hatching timing and many have spontaneous hatching patterns adaptively synchronized to natural cycles. Embryos can also adaptively shift their hatching timing in response to environmental cues indicating immediate threats or opportunities. Such cued shifts in hatching are widespread among amphibians; however, we know little about what, if anything, regulates their spontaneous hatching. Moreover, in addition to selection on hatching timing, embryos may experience benefits or suffer costs due to the spatial orientation of hatching. Amphibian eggs generally lack internal constraints on hatching direction but embryos might, nonetheless, use external cues to inform hatching orientation. The terrestrial embryos of red-eyed treefrogs, Agalychnis callidryas, hatch rapidly and prematurely in response to vibrational cues in egg-predator attacks and hypoxia if flooded. Here we examined A. callidryas’ use of light cues in hatching timing and orientation. To assess patterns of spontaneous hatching and the role of light cues in their diel timing, we recorded hatching times for siblings distributed across three light environments: continuous light, continuous dark, and a 12L:12D photoperiod. Under a natural photoperiod, embryos showed a clear diel pattern of synchronous hatching shortly after nightfall. Hatching was desynchronized in both continuous light and continuous darkness. It was also delayed by continuous light, but not accelerated by continuous dark, suggesting the onset of dark serves as a hatching cue. We examined hatching orientation and light as a potential directional cue for flooded embryos. Embryos flooded in their clutches almost always hatched toward open water, whereas individual eggs flooded in glass cups often failed to do so, suggesting the natural context provides a directional cue. To test if flooded embryos orient hatching t…
format: application/pdf
format: text/html
creator: Brandon A. Güell
creator: Karen M. Warkentin
subject: Animal Behavior
subject: Zoology
description: doi:10.7717/peerj.6018
publisher: PeerJ Inc.
rights: © 2018 Güell and Warkentin
abstract: Hatching timing is under strong selection and environmentally cued in many species. Embryos use multiple sensory modalities to inform hatching timing and many have spontaneous hatching patterns adaptively synchronized to natural cycles. Embryos can also adaptively shift their hatching timing in response to environmental cues indicating immediate threats or opportunities. Such cued shifts in hatching are widespread among amphibians; however, we know little about what, if anything, regulates their spontaneous hatching. Moreover, in addition to selection on hatching timing, embryos may experience benefits or suffer costs due to the spatial orientation of hatching. Amphibian eggs generally lack internal constraints on hatching direction but embryos might, nonetheless, use external cues to inform hatching orientation. The terrestrial embryos of red-eyed treefrogs, Agalychnis callidryas, hatch rapidly and prematurely in response to vibrational cues in egg-predator attacks and hypoxia if flooded. Here we examined A. callidryas’ use of light cues in hatching timing and orientation. To assess patterns of spontaneous hatching and the role of light cues in their diel timing, we recorded hatching times for siblings distributed across three light environments: continuous light, continuous dark, and a 12L:12D photoperiod. Under a natural photoperiod, embryos showed a clear diel pattern of synchronous hatching shortly after nightfall. Hatching was desynchronized in both continuous light and continuous darkness. It was also delayed by continuous light, but not accelerated by continuous dark, suggesting the onset of dark serves as a hatching cue. We examined hatching orientation and light as a potential directional cue for flooded embryos. Embryos flooded in their clutches almost always hatched toward open water, whereas individual eggs flooded in glass cups often failed to do so, suggesting the natural context provides a directional cue. To test if flooded embryos orient hatching t…
bibliographic citation: Güell et al. (2018) When and where to hatch? Red-eyed treefrog embryos use light cues in two contexts. PeerJ 6:e6018 https://doi.org/10.7717/peerj.6018
date submitted: 2018-07-05
date accepted: 2018-10-27
issued: 2018-12-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Güell
  given name: Brandon A.
author list: Agent
  family name: Warkentin
  given name: Karen M.
doi: 10.7717/peerj.6018
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-03
copyright: ©2018 Güell and Warkentin
attribution name: Güell and Warkentin

Coral disease prevalence estimation and sampling design
type: item
type: AcademicArticle
description: In the last decades diseases have changed coral communities’ structure and function in reefs worldwide. Studies conducted to evaluate the effect of diseases on corals frequently use modified adaptations of sampling designs that were developed to study ecological aspects of coral reefs. Here we evaluate how efficient these sampling protocols are by generating virtual data for a coral population parameterized with mean coral density and disease prevalence estimates from the Caribbean scleractinian Orbicella faveolata at the Mexican Caribbean. Six scenarios were tested consisting of three patterns of coral colony distribution (random, randomly clustered and randomly over-dispersed) and two disease transmission modes (random and contagious). The virtual populations were sampled with the commonly used method of belt-transects with variable sample-unit sizes (10 × 1, 10 × 2, 25 × 2, 50 × 2 m). Results showed that the probability of obtaining a mean coral disease prevalence estimate of ±5% of the true prevalence value was low (range: 11–48%) and that two-sample comparisons achieved rather low power, unless very large effect sizes existed. Such results imply low statistical confidence to assess differences or changes in coral disease prevalence. The main problem identified was insufficient sample size because local mean colony size, density and spatial distribution of targeted coral species was not taken into consideration to properly adjust the sampling protocols.
format: application/pdf
format: text/html
creator: Eric Jordán-Dahlgren
creator: Adán G. Jordán-Garza
creator: Rosa E. Rodríguez-Martínez
subject: Ecology
subject: Statistics
description: doi:10.7717/peerj.6006
publisher: PeerJ Inc.
rights: © 2018 Jordán-Dahlgren et al.
abstract: In the last decades diseases have changed coral communities’ structure and function in reefs worldwide. Studies conducted to evaluate the effect of diseases on corals frequently use modified adaptations of sampling designs that were developed to study ecological aspects of coral reefs. Here we evaluate how efficient these sampling protocols are by generating virtual data for a coral population parameterized with mean coral density and disease prevalence estimates from the Caribbean scleractinian Orbicella faveolata at the Mexican Caribbean. Six scenarios were tested consisting of three patterns of coral colony distribution (random, randomly clustered and randomly over-dispersed) and two disease transmission modes (random and contagious). The virtual populations were sampled with the commonly used method of belt-transects with variable sample-unit sizes (10 × 1, 10 × 2, 25 × 2, 50 × 2 m). Results showed that the probability of obtaining a mean coral disease prevalence estimate of ±5% of the true prevalence value was low (range: 11–48%) and that two-sample comparisons achieved rather low power, unless very large effect sizes existed. Such results imply low statistical confidence to assess differences or changes in coral disease prevalence. The main problem identified was insufficient sample size because local mean colony size, density and spatial distribution of targeted coral species was not taken into consideration to properly adjust the sampling protocols.
bibliographic citation: Jordán-Dahlgren et al. (2018) Coral disease prevalence estimation and sampling design. PeerJ 6:e6006 https://doi.org/10.7717/peerj.6006
date submitted: 2018-06-11
date accepted: 2018-10-26
issued: 2018-12-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jordán-Dahlgren
  given name: Eric
author list: Agent
  family name: Jordán-Garza
  given name: Adán G.
author list: Agent
  family name: Rodríguez-Martínez
  given name: Rosa E.
doi: 10.7717/peerj.6006
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-03
copyright: © 2018 Jordán-Dahlgren et al.
attribution name: Jordán-Dahlgren et al.

Intestinal microbiome and its potential functions in bighead carp (Aristichthys nobilis) under different feeding strategies
type: item
type: AcademicArticle
description: Bighead carps (Aristichthys nobilis) were divided into four groups with different feeding strategies: group A, nature live food only (fertiliser only, 200 g urea + 160 g ethylamine phosphate + 250 g Huangjintai bio-fertiliser); group B, nature live food + 1/2 formulated feed; group C, nature live food + formulated feed; and group D, formulated feed only. The intestinal microbiomes of the different groups were compared through the Illumina MiSeq sequencing of the bacterial 16S rRNA gene. The specific growth rate (SGR), survival and blood biochemical factors of the fish were also investigated. Results showed that feeding treatment influenced the intestinal communities in the fish. In specific, more bacterial phyla dominated in groups A and B (phyla Bacteroidetes, Fusobacteria, Firmicutes and Proteobacteria in group A, phyla Proteobacteria and Fusobacteria in group B) than in groups C and D (phylum Proteobacteria). The diversity was also lower in groups C and D than in groups A and B. Unweighted pair-group method analysis revealed a clear difference in intestinal microbiota among the different feeding treatments. No difference in survival rate was found among the treatment groups, but the SGR was significantly higher (P < 0.01) in groups B, C and D than in group A. Functional analysis showed that the intestinal bacteria correlated with fish glucose metabolism in group A but with lipid metabolic activity in groups B, C and D. In summary, the intestinal microbiomes and their potential functions vary in bighead carp under different feeding treatments. This study provides new insights into the gut microbiomes of filter-feeding and formulated diet-fed fish.
format: application/pdf
format: text/html
creator: Xuemei Li
creator: Yongjiu Zhu
creator: Einar Ringø
creator: Xuge Wang
creator: Jinling Gong
creator: Deguo Yang
subject: Aquaculture, Fisheries and Fish Science
subject: Microbiology
description: doi:10.7717/peerj.6000
publisher: PeerJ Inc.
rights: © 2018 Li et al.
abstract: Bighead carps (Aristichthys nobilis) were divided into four groups with different feeding strategies: group A, nature live food only (fertiliser only, 200 g urea + 160 g ethylamine phosphate + 250 g Huangjintai bio-fertiliser); group B, nature live food + 1/2 formulated feed; group C, nature live food + formulated feed; and group D, formulated feed only. The intestinal microbiomes of the different groups were compared through the Illumina MiSeq sequencing of the bacterial 16S rRNA gene. The specific growth rate (SGR), survival and blood biochemical factors of the fish were also investigated. Results showed that feeding treatment influenced the intestinal communities in the fish. In specific, more bacterial phyla dominated in groups A and B (phyla Bacteroidetes, Fusobacteria, Firmicutes and Proteobacteria in group A, phyla Proteobacteria and Fusobacteria in group B) than in groups C and D (phylum Proteobacteria). The diversity was also lower in groups C and D than in groups A and B. Unweighted pair-group method analysis revealed a clear difference in intestinal microbiota among the different feeding treatments. No difference in survival rate was found among the treatment groups, but the SGR was significantly higher (P < 0.01) in groups B, C and D than in group A. Functional analysis showed that the intestinal bacteria correlated with fish glucose metabolism in group A but with lipid metabolic activity in groups B, C and D. In summary, the intestinal microbiomes and their potential functions vary in bighead carp under different feeding treatments. This study provides new insights into the gut microbiomes of filter-feeding and formulated diet-fed fish.
bibliographic citation: Li et al. (2018) Intestinal microbiome and its potential functions in bighead carp (Aristichthys nobilis) under different feeding strategies. PeerJ 6:e6000 https://doi.org/10.7717/peerj.6000
date submitted: 2018-06-07
date accepted: 2018-10-25
issued: 2018-12-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Xuemei
author list: Agent
  family name: Zhu
  given name: Yongjiu
author list: Agent
  family name: Ringø
  given name: Einar
author list: Agent
  family name: Wang
  given name: Xuge
author list: Agent
  family name: Gong
  given name: Jinling
author list: Agent
  family name: Yang
  given name: Deguo
doi: 10.7717/peerj.6000
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-03
copyright: © 2018 Li et al.
attribution name: Li et al.

In-situ incubation of a coral patch for community-scale assessment of metabolic and chemical processes on a reef slope
type: item
type: AcademicArticle
description: Anthropogenic pressures threaten the health of coral reefs globally. Some of these pressures directly affect coral functioning, while others are indirect, for example by promoting the capacity of bioeroders to dissolve coral aragonite. To assess the coral reef status, it is necessary to validate community-scale measurements of metabolic and geochemical processes in the field, by determining fluxes from enclosed coral reef patches. Here, we investigate diurnal trends of carbonate chemistry, dissolved organic carbon, oxygen, and nutrients on a 20 m deep coral reef patch offshore from the island of Saba, Dutch Caribbean by means of tent incubations. The obtained trends are related to benthic carbon fluxes by quantifying net community calcification (NCC) and net community production (NCP). The relatively strong currents and swell-induced near-bottom surge at this location caused minor seawater exchange between the incubated reef and ambient water. Employing a compensating interpretive model, the exchange is used to our advantage as it maintains reasonably ventilated conditions, which conceivably prevents metabolic arrest during incubation periods of multiple hours. No diurnal trends in carbonate chemistry were detected and all net diurnal rates of production were strongly skewed towards respiration suggesting net heterotrophy in all incubations. The NCC inferred from our incubations ranges from −0.2 to 1.4 mmol CaCO3 m−2 h−1 (−0.2 to 1.2 kg CaCO3 m−2 year−1) and NCP varies from −9 to −21.7 mmol m−2 h−1 (net respiration). When comparing to the consensus-based ReefBudget approach, the estimated NCC rate for the incubated full planar area (0.36 kg CaCO3 m−2 year−1) was lower, but still within range of the different NCC inferred from our incubations. Field trials indicate that the tent-based incubation as presented here, coupled with an appropriate interpretive model, is an effective tool to investigate, in situ, the state of coral reef patches even when located in a relati…
format: application/pdf
format: text/html
creator: Steven M.A.C. van Heuven
creator: Alice E. Webb
creator: Didier M. de Bakker
creator: Erik Meesters
creator: Fleur C. van Duyl
creator: Gert-Jan Reichart
creator: Lennart J. de Nooijer
subject: Biodiversity
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.5966
publisher: PeerJ Inc.
rights: © 2018 van Heuven et al.
abstract: Anthropogenic pressures threaten the health of coral reefs globally. Some of these pressures directly affect coral functioning, while others are indirect, for example by promoting the capacity of bioeroders to dissolve coral aragonite. To assess the coral reef status, it is necessary to validate community-scale measurements of metabolic and geochemical processes in the field, by determining fluxes from enclosed coral reef patches. Here, we investigate diurnal trends of carbonate chemistry, dissolved organic carbon, oxygen, and nutrients on a 20 m deep coral reef patch offshore from the island of Saba, Dutch Caribbean by means of tent incubations. The obtained trends are related to benthic carbon fluxes by quantifying net community calcification (NCC) and net community production (NCP). The relatively strong currents and swell-induced near-bottom surge at this location caused minor seawater exchange between the incubated reef and ambient water. Employing a compensating interpretive model, the exchange is used to our advantage as it maintains reasonably ventilated conditions, which conceivably prevents metabolic arrest during incubation periods of multiple hours. No diurnal trends in carbonate chemistry were detected and all net diurnal rates of production were strongly skewed towards respiration suggesting net heterotrophy in all incubations. The NCC inferred from our incubations ranges from −0.2 to 1.4 mmol CaCO3 m−2 h−1 (−0.2 to 1.2 kg CaCO3 m−2 year−1) and NCP varies from −9 to −21.7 mmol m−2 h−1 (net respiration). When comparing to the consensus-based ReefBudget approach, the estimated NCC rate for the incubated full planar area (0.36 kg CaCO3 m−2 year−1) was lower, but still within range of the different NCC inferred from our incubations. Field trials indicate that the tent-based incubation as presented here, coupled with an appropriate interpretive model, is an effective tool to investigate, in situ, the state of coral reef patches even when located in a relati…
bibliographic citation: van Heuven et al. (2018) In-situ incubation of a coral patch for community-scale assessment of metabolic and chemical processes on a reef slope. PeerJ 6:e5966 https://doi.org/10.7717/peerj.5966
date submitted: 2018-04-04
date accepted: 2018-10-18
issued: 2018-12-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: van Heuven
  given name: Steven M.A.C.
author list: Agent
  family name: Webb
  given name: Alice E.
author list: Agent
  family name: de Bakker
  given name: Didier M.
author list: Agent
  family name: Meesters
  given name: Erik
author list: Agent
  family name: van Duyl
  given name: Fleur C.
author list: Agent
  family name: Reichart
  given name: Gert-Jan
author list: Agent
  family name: de Nooijer
  given name: Lennart J.
doi: 10.7717/peerj.5966
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-03
copyright: © 2018 van Heuven et al.
attribution name: van Heuven et al.

Urbanisation and wing asymmetry in the western honey bee (Apis mellifera, Linnaeus 1758) at multiple scales
type: item
type: AcademicArticle
description: Changes in the mean and variance of phenotypic traits like wing and head morphology are frequently used as indicators of environmental stress experienced during development and may serve as a convenient index of urbanization exposure. To test this claim, we collected adult western honey bee (Apis mellifera Linnaeus 1758, Hymenoptera, Apidae) workers from colonies located across an urbanization gradient, and quantified associations between the symmetries of both wing size and wing shape, and several landscape traits associated with urbanization. Landscape traits were assessed at two spatial scales (three km and 500 m) and included vegetation and anthropogenic land cover, total road length, road proximity and, population and dwelling density. We then used geometric morphometric techniques to determine two wing asymmetry scores—centroid size, a measure of wing size asymmetry and Procrustes distance, a measure of wing shape asymmetry. We found colony dependent differences in both wing size and shape asymmetry. Additionally, we found a negative association between wing shape asymmetry and road proximity at the three km buffer, and associations between wing shape asymmetry and road proximity, anthropogenic land cover and vegetation cover at the 500 m buffer. Whilst we were unable to account for additional variables that may influence asymmetry including temperature, pesticide presence, and parasitism our results demonstrate the potential usefulness of wing shape asymmetry for assessing the impact of certain landscape traits associated with urbanization. Furthermore, they highlight important spatial scale considerations that warrant investigation in future phenotypic studies assessing urbanization impact.
format: application/pdf
format: text/html
creator: Ryan J. Leonard
creator: Katie K.Y. Wat
creator: Clare McArthur
creator: Dieter F. Hochuli
subject: Ecology
subject: Entomology
subject: Environmental Impacts
description: doi:10.7717/peerj.5940
publisher: PeerJ Inc.
rights: © 2018 Leonard et al.
abstract: Changes in the mean and variance of phenotypic traits like wing and head morphology are frequently used as indicators of environmental stress experienced during development and may serve as a convenient index of urbanization exposure. To test this claim, we collected adult western honey bee (Apis mellifera Linnaeus 1758, Hymenoptera, Apidae) workers from colonies located across an urbanization gradient, and quantified associations between the symmetries of both wing size and wing shape, and several landscape traits associated with urbanization. Landscape traits were assessed at two spatial scales (three km and 500 m) and included vegetation and anthropogenic land cover, total road length, road proximity and, population and dwelling density. We then used geometric morphometric techniques to determine two wing asymmetry scores—centroid size, a measure of wing size asymmetry and Procrustes distance, a measure of wing shape asymmetry. We found colony dependent differences in both wing size and shape asymmetry. Additionally, we found a negative association between wing shape asymmetry and road proximity at the three km buffer, and associations between wing shape asymmetry and road proximity, anthropogenic land cover and vegetation cover at the 500 m buffer. Whilst we were unable to account for additional variables that may influence asymmetry including temperature, pesticide presence, and parasitism our results demonstrate the potential usefulness of wing shape asymmetry for assessing the impact of certain landscape traits associated with urbanization. Furthermore, they highlight important spatial scale considerations that warrant investigation in future phenotypic studies assessing urbanization impact.
bibliographic citation: Leonard et al. (2018) Urbanisation and wing asymmetry in the western honey bee (Apis mellifera, Linnaeus 1758) at multiple scales. PeerJ 6:e5940 https://doi.org/10.7717/peerj.5940
date submitted: 2018-04-10
date accepted: 2018-10-16
issued: 2018-12-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Leonard
  given name: Ryan J.
author list: Agent
  family name: Wat
  given name: Katie K.Y.
author list: Agent
  family name: McArthur
  given name: Clare
author list: Agent
  family name: Hochuli
  given name: Dieter F.
doi: 10.7717/peerj.5940
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-03
copyright: © 2018 Leonard et al.
attribution name: Leonard et al.

Characterization of bacterioplankton communities and quantification of organic carbon pools off the Galapagos Archipelago under contrasting environmental conditions
type: item
type: AcademicArticle
description: Bacteria play a crucial role in the marine carbon cycle, contributing to the production and degradation of organic carbon. Here, we investigated organic carbon pools, aggregate formation, and bacterioplankton communities in three contrasting oceanographic settings in the Galapagos Archipelago. We studied a submarine CO2 vent at Roca Redonda (RoR), an upwelling site at Bolivar Channel (BoC) subjected to a weak El Niño event at the time of sampling in October 2014, as well as a site without volcanic or upwelling influence at Cowley Islet (CoI). We recorded physico-chemical parameters, and quantified particulate and dissolved organic carbon, transparent exopolymeric particles, and the potential of the water to form larger marine aggregates. Free-living and particle-attached bacterial communities were assessed via 16S rRNA gene sequencing. Both RoR and BoC exhibited temperatures elevated by 1–1.5 °C compared to CoI. RoR further experienced reduced pH between 6.8 and 7.4. We observed pronounced differences in organic carbon pools at each of the three sites, with highest dissolved organic carbon concentrations at BoC and RoR, and highest particulate organic carbon concentrations and aggregate formation at BoC. Bacterioplankton communities at BoC were dominated by opportunistic copiotrophic taxa, such as Alteromonas and Roseobacter, known to thrive in phytoplankton blooms, as opposed to oligotrophic taxa dominating at CoI, such as members of the SAR11 clade. Therefore, we propose that bacterial communities were mainly influenced by the availability of organic carbon at the investigated sites. Our study provides a comprehensive characterization of organic carbon pools and bacterioplankton communities, highlighting the high heterogeneity of various components of the marine carbon cycle around the Galapagos Archipelago.
format: application/pdf
format: text/html
creator: Nataly Carolina Guevara Campoverde
creator: Christiane Hassenrück
creator: Pier Luigi Buttigieg
creator: Astrid Gärdes
subject: Ecology
subject: Marine Biology
subject: Microbiology
description: doi:10.7717/peerj.5984
publisher: PeerJ Inc.
rights: © 2018 Guevara Campoverde et al.
abstract: Bacteria play a crucial role in the marine carbon cycle, contributing to the production and degradation of organic carbon. Here, we investigated organic carbon pools, aggregate formation, and bacterioplankton communities in three contrasting oceanographic settings in the Galapagos Archipelago. We studied a submarine CO2 vent at Roca Redonda (RoR), an upwelling site at Bolivar Channel (BoC) subjected to a weak El Niño event at the time of sampling in October 2014, as well as a site without volcanic or upwelling influence at Cowley Islet (CoI). We recorded physico-chemical parameters, and quantified particulate and dissolved organic carbon, transparent exopolymeric particles, and the potential of the water to form larger marine aggregates. Free-living and particle-attached bacterial communities were assessed via 16S rRNA gene sequencing. Both RoR and BoC exhibited temperatures elevated by 1–1.5 °C compared to CoI. RoR further experienced reduced pH between 6.8 and 7.4. We observed pronounced differences in organic carbon pools at each of the three sites, with highest dissolved organic carbon concentrations at BoC and RoR, and highest particulate organic carbon concentrations and aggregate formation at BoC. Bacterioplankton communities at BoC were dominated by opportunistic copiotrophic taxa, such as Alteromonas and Roseobacter, known to thrive in phytoplankton blooms, as opposed to oligotrophic taxa dominating at CoI, such as members of the SAR11 clade. Therefore, we propose that bacterial communities were mainly influenced by the availability of organic carbon at the investigated sites. Our study provides a comprehensive characterization of organic carbon pools and bacterioplankton communities, highlighting the high heterogeneity of various components of the marine carbon cycle around the Galapagos Archipelago.
bibliographic citation: Guevara Campoverde et al. (2018) Characterization of bacterioplankton communities and quantification of organic carbon pools off the Galapagos Archipelago under contrasting environmental conditions. PeerJ 6:e5984 https://doi.org/10.7717/peerj.5984
date submitted: 2018-06-09
date accepted: 2018-10-22
issued: 2018-12-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guevara Campoverde
  given name: Nataly Carolina
author list: Agent
  family name: Hassenrück
  given name: Christiane
author list: Agent
  family name: Buttigieg
  given name: Pier Luigi
author list: Agent
  family name: Gärdes
  given name: Astrid
doi: 10.7717/peerj.5984
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-03
copyright: ©2018 Guevara Campoverde et al.
attribution name: Guevara Campoverde et al.

The proportion of core species in a community varies with spatial scale and environmental heterogeneity
type: item
type: AcademicArticle
description: Ecological communities are composed of a combination of core species that maintain local viable populations and transient species that occur infrequently due to dispersal from surrounding regions. Preliminary work indicates that while core and transient species are both commonly observed in community surveys of a wide range of taxonomic groups, their relative prevalence varies substantially from one community to another depending upon the spatial scale at which the community was characterized and its environmental context. We used a geographically extensive dataset of 968 bird community time series to quantitatively describe how the proportion of core species in a community varies with spatial scale and environmental heterogeneity. We found that the proportion of core species in an assemblage increased with spatial scale in a positive decelerating fashion with a concomitant decrease in the proportion of transient species. Variation in the shape of this scaling relationship between sites was related to regional environmental heterogeneity, with lower proportions of core species at a given scale associated with high environmental heterogeneity. Understanding this influence of scale and environmental heterogeneity on the proportion of core species may help resolve discrepancies between studies of biotic interactions, resource availability, and mass effects conducted at different scales, because the importance of these and other ecological processes are expected to differ substantially between core and transient species.
format: application/pdf
format: text/html
creator: Molly F. Jenkins
creator: Ethan P. White
creator: Allen H. Hurlbert
subject: Computational Biology
subject: Ecology
description: doi:10.7717/peerj.6019
publisher: PeerJ Inc.
rights: © 2018 Jenkins et al.
abstract: Ecological communities are composed of a combination of core species that maintain local viable populations and transient species that occur infrequently due to dispersal from surrounding regions. Preliminary work indicates that while core and transient species are both commonly observed in community surveys of a wide range of taxonomic groups, their relative prevalence varies substantially from one community to another depending upon the spatial scale at which the community was characterized and its environmental context. We used a geographically extensive dataset of 968 bird community time series to quantitatively describe how the proportion of core species in a community varies with spatial scale and environmental heterogeneity. We found that the proportion of core species in an assemblage increased with spatial scale in a positive decelerating fashion with a concomitant decrease in the proportion of transient species. Variation in the shape of this scaling relationship between sites was related to regional environmental heterogeneity, with lower proportions of core species at a given scale associated with high environmental heterogeneity. Understanding this influence of scale and environmental heterogeneity on the proportion of core species may help resolve discrepancies between studies of biotic interactions, resource availability, and mass effects conducted at different scales, because the importance of these and other ecological processes are expected to differ substantially between core and transient species.
bibliographic citation: Jenkins et al. (2018) The proportion of core species in a community varies with spatial scale and environmental heterogeneity. PeerJ 6:e6019 https://doi.org/10.7717/peerj.6019
date submitted: 2018-08-27
date accepted: 2018-10-28
issued: 2018-11-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jenkins
  given name: Molly F.
author list: Agent
  family name: White
  given name: Ethan P.
author list: Agent
  family name: Hurlbert
  given name: Allen H.
doi: 10.7717/peerj.6019
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-30
copyright: ©2018 Jenkins et al.
attribution name: Jenkins et al.

Between extreme simplification and ideal optimization: antennal sensilla morphology of miniaturized Megaphragma wasps (Hymenoptera: Trichogrammatidae)
type: item
type: AcademicArticle
description: One of the major trends in the evolution of parasitoid wasps is miniaturization, which has produced the smallest known insects. Megaphragma spp. (Hymenoptera: Trichogrammatidae) are smaller than some unicellular organisms, with an adult body length of the smallest only 170 µm. Their parasitoid lifestyle depends on retention of a high level of sensory reception comparable to that in parasitoid wasps that may have antennae hundreds of times larger. Antennal sensilla of males and females of Megaphragma amalphitanum and M. caribea and females of the parthenogenetic M. mymaripenne are described, including sensillum size, external morphology, and distribution. Eight different morphological types of sensilla were discovered, two of them appearing exclusively on female antennae. Two of the types, sensilla styloconica and aporous placoid sensilla, have not been described previously. Regression analyses were performed to detect and evaluate possible miniaturization trends by comparing available data for species of larger parasitoid wasps. The number of antennal sensilla was found to decrease with the body size; M. amalphitanum males have only 39 sensilla per antenna. The number of antennal sensilla types and sizes of the sensilla, however, show little to no correlation with the body size. Our findings on the effects of miniaturization on the antennal sensilla of Megaphragma provide material for discussion on the limits to the reduction of insect antenna.
format: application/pdf
format: text/html
creator: Anna V. Diakova
creator: Anastasia A. Makarova
creator: Alexey A. Polilov
subject: Entomology
subject: Zoology
description: doi:10.7717/peerj.6005
publisher: PeerJ Inc.
rights: © 2018 Diakova et al.
abstract: One of the major trends in the evolution of parasitoid wasps is miniaturization, which has produced the smallest known insects. Megaphragma spp. (Hymenoptera: Trichogrammatidae) are smaller than some unicellular organisms, with an adult body length of the smallest only 170 µm. Their parasitoid lifestyle depends on retention of a high level of sensory reception comparable to that in parasitoid wasps that may have antennae hundreds of times larger. Antennal sensilla of males and females of Megaphragma amalphitanum and M. caribea and females of the parthenogenetic M. mymaripenne are described, including sensillum size, external morphology, and distribution. Eight different morphological types of sensilla were discovered, two of them appearing exclusively on female antennae. Two of the types, sensilla styloconica and aporous placoid sensilla, have not been described previously. Regression analyses were performed to detect and evaluate possible miniaturization trends by comparing available data for species of larger parasitoid wasps. The number of antennal sensilla was found to decrease with the body size; M. amalphitanum males have only 39 sensilla per antenna. The number of antennal sensilla types and sizes of the sensilla, however, show little to no correlation with the body size. Our findings on the effects of miniaturization on the antennal sensilla of Megaphragma provide material for discussion on the limits to the reduction of insect antenna.
bibliographic citation: Diakova et al. (2018) Between extreme simplification and ideal optimization: antennal sensilla morphology of miniaturized Megaphragma wasps (Hymenoptera: Trichogrammatidae). PeerJ 6:e6005 https://doi.org/10.7717/peerj.6005
date submitted: 2018-08-31
date accepted: 2018-10-26
issued: 2018-11-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Diakova
  given name: Anna V.
author list: Agent
  family name: Makarova
  given name: Anastasia A.
author list: Agent
  family name: Polilov
  given name: Alexey A.
doi: 10.7717/peerj.6005
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-30
copyright: ©2018 Diakova et al.
attribution name: Diakova et al.

Analyses of long non-coding RNA and mRNA profiling in the spleen of diarrheic piglets caused by Clostridium perfringens type C
type: item
type: AcademicArticle
description: Background Clostridium perfringens (C. perfringens) type C is the most common bacteria causing piglet diarrheal disease and it greatly affects the economy of the global pig industry. The spleen is an important immune organ in mammals; it plays an irreplaceable role in resisting and eradicating pathogenic microorganisms. Based on different immune capacity in piglets, individuals display the resistance and susceptibility to diarrhea caused by C. perfringens type C. Recently, long non-coding RNA (lncRNA) and mRNA have been found to be involved in host immune and inflammatory responses to pathogenic infections. However, little is known about spleen transcriptome information in piglet diarrhea caused by C. perfringens type C. Methods Hence, we infected 7-day-old piglets with C. perfringens type C to lead to diarrhea. Then, we investigated lncRNA and mRNA expression profiles in spleens of piglets, including control (SC), susceptible (SS), and resistant (SR) groups. Results As a result, 2,056 novel lncRNAs and 2,417 differentially expressed genes were found. These lncRNAs shared the same characteristics of fewer exons and shorter length. Bioinformatics analysis identified that two lncRNAs (ALDBSSCT0000006918 and ALDBSSCT0000007366) may be involved in five immune/inflammation-related pathways (such as Toll-like receptor signaling pathway, MAPK signaling pathway, and Jak-STAT signaling pathway), which were associated with resistance and susceptibility to C. perfringens type C infection. This study contributes to the understanding of potential mechanisms involved in the immune response of piglets infected with C. perfringens type C.
format: application/pdf
format: text/html
creator: Zunqiang Yan
creator: Xiaoyu Huang
creator: Wenyang Sun
creator: Qiaoli Yang
creator: Hairen Shi
creator: Tiantuan Jiang
creator: Shenggui Li
creator: Pengfei Wang
creator: Shuangbao Gun
subject: Genomics
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.5997
publisher: PeerJ Inc.
rights: © 2018 Yan et al.
abstract: Background Clostridium perfringens (C. perfringens) type C is the most common bacteria causing piglet diarrheal disease and it greatly affects the economy of the global pig industry. The spleen is an important immune organ in mammals; it plays an irreplaceable role in resisting and eradicating pathogenic microorganisms. Based on different immune capacity in piglets, individuals display the resistance and susceptibility to diarrhea caused by C. perfringens type C. Recently, long non-coding RNA (lncRNA) and mRNA have been found to be involved in host immune and inflammatory responses to pathogenic infections. However, little is known about spleen transcriptome information in piglet diarrhea caused by C. perfringens type C. Methods Hence, we infected 7-day-old piglets with C. perfringens type C to lead to diarrhea. Then, we investigated lncRNA and mRNA expression profiles in spleens of piglets, including control (SC), susceptible (SS), and resistant (SR) groups. Results As a result, 2,056 novel lncRNAs and 2,417 differentially expressed genes were found. These lncRNAs shared the same characteristics of fewer exons and shorter length. Bioinformatics analysis identified that two lncRNAs (ALDBSSCT0000006918 and ALDBSSCT0000007366) may be involved in five immune/inflammation-related pathways (such as Toll-like receptor signaling pathway, MAPK signaling pathway, and Jak-STAT signaling pathway), which were associated with resistance and susceptibility to C. perfringens type C infection. This study contributes to the understanding of potential mechanisms involved in the immune response of piglets infected with C. perfringens type C.
bibliographic citation: Yan et al. (2018) Analyses of long non-coding RNA and mRNA profiling in the spleen of diarrheic piglets caused by Clostridium perfringens type C. PeerJ 6:e5997 https://doi.org/10.7717/peerj.5997
date submitted: 2018-05-08
date accepted: 2018-10-24
issued: 2018-11-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yan
  given name: Zunqiang
author list: Agent
  family name: Huang
  given name: Xiaoyu
author list: Agent
  family name: Sun
  given name: Wenyang
author list: Agent
  family name: Yang
  given name: Qiaoli
author list: Agent
  family name: Shi
  given name: Hairen
author list: Agent
  family name: Jiang
  given name: Tiantuan
author list: Agent
  family name: Li
  given name: Shenggui
author list: Agent
  family name: Wang
  given name: Pengfei
author list: Agent
  family name: Gun
  given name: Shuangbao
doi: 10.7717/peerj.5997
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-30
copyright: © 2018 Yan et al.
attribution name: Yan et al.

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359