PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Hemiparasitic plants increase alpine plant richness and evenness but reduce arbuscular mycorrhizal fungal colonization in dominant plant species
items: Mapping the distribution of scale-rayed wrasse Acantholabrus palloni in Swedish Skagerrak using angling records
items: Trait-based predation suitability offers insight into effects of changing prey communities
items: Experimental food supplementation increases reproductive effort in the Variable Antshrike in subtropical Brazil
items: Sociality genes are associated with human-directed social behaviour in golden and Labrador retriever dogs
items: Canadian packaged gluten-free foods are less nutritious than their regular gluten-containing counterparts
items: Structural and functional analysis of the roles of the HCV 5′ NCR miR122-dependent long-range association and SLVI in genome translation and replication
items: Effects of mixed reality head-mounted glasses during 90 minutes of mental and manual tasks on cognitive and physiological functions
items: Host anemone size as a determinant of social group size and structure in the orange clownfish (Amphiprion percula)
items: Unimodal head-width distribution of the European eel (Anguilla anguilla L.) from the Zeeschelde does not support disruptive selection

Hemiparasitic plants increase alpine plant richness and evenness but reduce arbuscular mycorrhizal fungal colonization in dominant plant species
type: item
type: AcademicArticle
description: Hemiparasitic plants increase plant biodiversity by reducing the abundance of dominant plant species, allowing for the establishment of subordinate species. Hemiparasites reduce host resources by directly removing nutrients from hosts, competing for light and space, and may indirectly reduce host resources by disrupting plant associations with symbiotic root fungi, like arbuscular mycorrhizal fungi and dark-septate endophytes. Here, we explored how a generalist hemiparasite, Castilleja, influences plant richness, evenness, community composition, and mycorrhizal colonization patterns across a ∼1,000 m elevational gradient in the North American Rocky Mountains. We hypothesized that the presence of Castilleja would be associated with increased plant richness and evenness, shaping plant community composition, and would reduce mycorrhizal colonization within dominant plant taxa. However, the magnitude of the effects would be contingent upon climate contexts, that is, elevation. Overall, we found that the presence of Castilleja was associated with an 11% increase in plant richness and a 5% increase in plant evenness, regardless of elevation. However, we found that the presence of Castilleja influenced plant composition at only two of the five sites and at the remaining three of five sites, plot pairing was the only predictor that influenced composition. Additionally, we found that the presence of Castilleja reduced mycorrhizal fungal colonization within dominant plant species by ∼20%, regardless of elevation. Taken together, our results suggest that hemiparasites regulate plant diversity, evenness, and interactions with mycorrhizal fungi independent of abiotic and biotic contexts occurring at the site, although overall effect on community composition is likely driven by site-level factors.
format: application/pdf
format: text/html
creator: Michael McKibben
creator: Jeremiah A. Henning
subject: Ecology
description: doi:10.7717/peerj.5682
publisher: PeerJ Inc.
rights: © 2018 McKibben and Henning
abstract: Hemiparasitic plants increase plant biodiversity by reducing the abundance of dominant plant species, allowing for the establishment of subordinate species. Hemiparasites reduce host resources by directly removing nutrients from hosts, competing for light and space, and may indirectly reduce host resources by disrupting plant associations with symbiotic root fungi, like arbuscular mycorrhizal fungi and dark-septate endophytes. Here, we explored how a generalist hemiparasite, Castilleja, influences plant richness, evenness, community composition, and mycorrhizal colonization patterns across a ∼1,000 m elevational gradient in the North American Rocky Mountains. We hypothesized that the presence of Castilleja would be associated with increased plant richness and evenness, shaping plant community composition, and would reduce mycorrhizal colonization within dominant plant taxa. However, the magnitude of the effects would be contingent upon climate contexts, that is, elevation. Overall, we found that the presence of Castilleja was associated with an 11% increase in plant richness and a 5% increase in plant evenness, regardless of elevation. However, we found that the presence of Castilleja influenced plant composition at only two of the five sites and at the remaining three of five sites, plot pairing was the only predictor that influenced composition. Additionally, we found that the presence of Castilleja reduced mycorrhizal fungal colonization within dominant plant species by ∼20%, regardless of elevation. Taken together, our results suggest that hemiparasites regulate plant diversity, evenness, and interactions with mycorrhizal fungi independent of abiotic and biotic contexts occurring at the site, although overall effect on community composition is likely driven by site-level factors.
bibliographic citation: McKibben et al. (2018) Hemiparasitic plants increase alpine plant richness and evenness but reduce arbuscular mycorrhizal fungal colonization in dominant plant species. PeerJ 6:e5682 https://doi.org/10.7717/peerj.5682
date submitted: 2018-06-05
date accepted: 2018-08-30
issued: 2018-11-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: McKibben
  given name: Michael
author list: Agent
  family name: Henning
  given name: Jeremiah A.
doi: 10.7717/peerj.5682
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-07
copyright: © 2018 McKibben and Henning
attribution name: McKibben and Henning

Mapping the distribution of scale-rayed wrasse Acantholabrus palloni in Swedish Skagerrak using angling records
type: item
type: AcademicArticle
description: In this paper, we map the distribution of scale-rayed wrasse Acantholabrus palloni in eastern Skagerrak based on a combination of verified and personally communicated angling records. Long thought to be occasional vagrants outside its known range in the eastern Atlantic Ocean and Mediterranean Sea, we ask if this rare and understudied labrid has expanded its range and become established in Swedish waters. A recent surge in verified angling records in the Swedish Anglers Association’s specimen database Storfiskregistret provides information to suggest that this species should no longer be considered an occasional guest, but rather a species established in the Swedish parts of Skagerrak. These records are supported by additional personal communications with anglers. The species is currently well spread geographically along the Swedish Skagerrak coast, with many locations providing repeated captures of adult fish over multiple years. The typical Swedish catch sites are rocky reefs located between the general 40- and 80-m depth curves, likely influenced by currents bringing higher-salinity water from the North Sea. The present study show that angling records can provide an important, but underutilized, resource for mapping the distribution of data-deficient fish species.
format: application/pdf
format: text/html
creator: Joacim Näslund
creator: Markus Lundgren
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Conservation Biology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.5900
publisher: PeerJ Inc.
rights: © 2018 Näslund and Lundgren
abstract: In this paper, we map the distribution of scale-rayed wrasse Acantholabrus palloni in eastern Skagerrak based on a combination of verified and personally communicated angling records. Long thought to be occasional vagrants outside its known range in the eastern Atlantic Ocean and Mediterranean Sea, we ask if this rare and understudied labrid has expanded its range and become established in Swedish waters. A recent surge in verified angling records in the Swedish Anglers Association’s specimen database Storfiskregistret provides information to suggest that this species should no longer be considered an occasional guest, but rather a species established in the Swedish parts of Skagerrak. These records are supported by additional personal communications with anglers. The species is currently well spread geographically along the Swedish Skagerrak coast, with many locations providing repeated captures of adult fish over multiple years. The typical Swedish catch sites are rocky reefs located between the general 40- and 80-m depth curves, likely influenced by currents bringing higher-salinity water from the North Sea. The present study show that angling records can provide an important, but underutilized, resource for mapping the distribution of data-deficient fish species.
bibliographic citation: Näslund et al. (2018) Mapping the distribution of scale-rayed wrasse Acantholabrus palloni in Swedish Skagerrak using angling records. PeerJ 6:e5900 https://doi.org/10.7717/peerj.5900
date submitted: 2018-03-02
date accepted: 2018-10-02
issued: 2018-11-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Näslund
  given name: Joacim
author list: Agent
  family name: Lundgren
  given name: Markus
doi: 10.7717/peerj.5900
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-06
copyright: © 2018 Näslund and Lundgren
attribution name: Näslund and Lundgren

Trait-based predation suitability offers insight into effects of changing prey communities
type: item
type: AcademicArticle
description: Increasing environmental pressures and human impacts are reshaping community structures and species interactions throughout all trophic levels. The morphological and behavioural characteristics of species communities contain key ecological information on why prey species appear attractive to predators but are rarely applied when exploring predator-prey (PP) relationships. Expanding our knowledge on how changing prey communities can alter the food resource suitability (RS) for predators is vital for understanding PP dynamics in changing ecosystems. Detailed predator diet data are commonly restricted to commercially important species and often not available over long temporal scales. To find out whether structural changes of prey communities impact the food RS for predator communities over space and time, we apply a novel framework to describe and interpret changes in predator diet-suitability based on predation-relevant traits of prey. We use information on described feeding links from the literature to compile the prey spectrum for each predator and subsequently translate the prey-species into a prey-trait spectrum. For each predator, we then calculate a frequency-based prey-trait affinity score and relate it to the available food resource pool, the community weighted means of prey traits, resulting in a prey-suitability measure. We aim to reveal whether a described multi-decadal change in the community structure of zoobenthos had an impact on the food suitability for the benthic-feeding fish in a coastal system of the Baltic Sea. We assess the direction of change in resource quality from the perspective of benthic-feeding fish and describe predator-specific responses to examine which species are likely to profit or be disadvantaged by changes in their prey spectrum. Furthermore, we test the relationship between functional diversity of prey communities and food suitability for predators, and whether predation linkage-structures are affected through prey community-ch…
format: application/pdf
format: text/html
creator: Benjamin Weigel
creator: Erik Bonsdorff
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.5899
publisher: PeerJ Inc.
rights: © 2018 Weigel and Bonsdorff
abstract: Increasing environmental pressures and human impacts are reshaping community structures and species interactions throughout all trophic levels. The morphological and behavioural characteristics of species communities contain key ecological information on why prey species appear attractive to predators but are rarely applied when exploring predator-prey (PP) relationships. Expanding our knowledge on how changing prey communities can alter the food resource suitability (RS) for predators is vital for understanding PP dynamics in changing ecosystems. Detailed predator diet data are commonly restricted to commercially important species and often not available over long temporal scales. To find out whether structural changes of prey communities impact the food RS for predator communities over space and time, we apply a novel framework to describe and interpret changes in predator diet-suitability based on predation-relevant traits of prey. We use information on described feeding links from the literature to compile the prey spectrum for each predator and subsequently translate the prey-species into a prey-trait spectrum. For each predator, we then calculate a frequency-based prey-trait affinity score and relate it to the available food resource pool, the community weighted means of prey traits, resulting in a prey-suitability measure. We aim to reveal whether a described multi-decadal change in the community structure of zoobenthos had an impact on the food suitability for the benthic-feeding fish in a coastal system of the Baltic Sea. We assess the direction of change in resource quality from the perspective of benthic-feeding fish and describe predator-specific responses to examine which species are likely to profit or be disadvantaged by changes in their prey spectrum. Furthermore, we test the relationship between functional diversity of prey communities and food suitability for predators, and whether predation linkage-structures are affected through prey community-ch…
bibliographic citation: Weigel et al. (2018) Trait-based predation suitability offers insight into effects of changing prey communities. PeerJ 6:e5899 https://doi.org/10.7717/peerj.5899
date submitted: 2018-07-04
date accepted: 2018-10-07
issued: 2018-11-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Weigel
  given name: Benjamin
author list: Agent
  family name: Bonsdorff
  given name: Erik
doi: 10.7717/peerj.5899
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-06
copyright: © 2018 Weigel and Bonsdorff
attribution name: Weigel and Bonsdorff

Experimental food supplementation increases reproductive effort in the Variable Antshrike in subtropical Brazil
type: item
type: AcademicArticle
description: Food limitation may interact with nest predation and influence nesting patterns, such as breeding season length and renesting intervals. If so, reproductive effort should change with food availability. Thus, when food is limited, birds should have fewer attempts and shorter seasons than when food is not limiting. Here we experimentally test that increased food availability results in increased reproductive effort in a fragmented landscape in the Variable Antshrike (Thamnophilus caerulescens) in southern Brazil. We followed nesting pairs in a naturally fragmented habitat and experimentally supplemented food for half of those pairs. Birds were seen, but evidence of nesting was never found in two small fragments, even though these fragments were larger than individual territories. Pairs with supplemented food were more likely to increase clutch size from two to three eggs and tended to renest sooner (20 d on average) than control pairs. Also, fragment size was associated with breeding patterns, although fragment replicates were unavailable. Nest duration, nest success and breeding season length were all greater, while renesting intervals were shorter, in the largest fragments. Simulations showed that only the largest fragments were able to have a net production of young. Food availability clearly influenced reproductive effort and as a consequence, because of the interaction with predation risk, forest fragments of varying sizes will have complex reproductive dynamics.
format: application/pdf
format: text/html
creator: James J. Roper
creator: André M.X. Lima
creator: Angélica M.K. Uejima
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.5898
publisher: PeerJ Inc.
rights: © 2018 Roper et al.
abstract: Food limitation may interact with nest predation and influence nesting patterns, such as breeding season length and renesting intervals. If so, reproductive effort should change with food availability. Thus, when food is limited, birds should have fewer attempts and shorter seasons than when food is not limiting. Here we experimentally test that increased food availability results in increased reproductive effort in a fragmented landscape in the Variable Antshrike (Thamnophilus caerulescens) in southern Brazil. We followed nesting pairs in a naturally fragmented habitat and experimentally supplemented food for half of those pairs. Birds were seen, but evidence of nesting was never found in two small fragments, even though these fragments were larger than individual territories. Pairs with supplemented food were more likely to increase clutch size from two to three eggs and tended to renest sooner (20 d on average) than control pairs. Also, fragment size was associated with breeding patterns, although fragment replicates were unavailable. Nest duration, nest success and breeding season length were all greater, while renesting intervals were shorter, in the largest fragments. Simulations showed that only the largest fragments were able to have a net production of young. Food availability clearly influenced reproductive effort and as a consequence, because of the interaction with predation risk, forest fragments of varying sizes will have complex reproductive dynamics.
bibliographic citation: Roper et al. (2018) Experimental food supplementation increases reproductive effort in the Variable Antshrike in subtropical Brazil. PeerJ 6:e5898 https://doi.org/10.7717/peerj.5898
date submitted: 2014-12-10
date accepted: 2018-10-06
issued: 2018-11-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Roper
  given name: James J.
author list: Agent
  family name: Lima
  given name: André M.X.
author list: Agent
  family name: Uejima
  given name: Angélica M.K.
doi: 10.7717/peerj.5898
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-06
copyright: ©2018 Roper et al.
attribution name: Roper et al.

Sociality genes are associated with human-directed social behaviour in golden and Labrador retriever dogs
type: item
type: AcademicArticle
description: Background Dogs have human-directed social skills that allow them to communicate and cooperate with humans. We have previously identified two loci on chromosome 26 associated with human contact-seeking behaviors during an unsolvable problem task in laboratory beagles (Persson et al., 2016). The aim of the present study was to verify the single nucleotide polymorphisms (SNPs) in additional dog breeds. We also studied how the allele frequencies have changed during domestication and recent selection. Methods Dogs of two breeds, 61 golden retrievers and 100 Labrador retrievers, were phenotyped and genotyped, and 19 wolves were genotyped. The Labrador retrievers were divided into common and field type by pedigree data to make it possible to study the effects of recent selection. All dogs were tested in an unsolvable problem task where human-directed social behaviors were scored. DNA from dogs (buccal swabs) and wolves (blood or brain tissue) was analyzed for genotype on two of the previously identified SNP markers, BICF2G630798942 (SNP1) and BICF2S23712114 (SNP2), by pyrosequencing. Results There was genetic variation for SNP1 in both dog breeds whereas the wolves were fixed for this polymorphism, and for SNP2 there was variation in both dogs and wolves. For both SNPs, Labrador retriever types differed significantly in allele frequencies. We found associations between SNPs and human-directed social behavior in both dog breeds. In golden retrievers, SNP1 was associated with physical contact variables, for example, with the duration of physical contact with the owner (F2,56 = 4.389, p = 0.017). SNP2 was associated with several behavioral variables in both breeds, among others owner gazing frequency in both golden retrievers (F2,55 = 6.330, p = 0.003) and Labradors (F1,93 = 5.209, p = 0.025). Discussion Our results verify the association between the previously identified SNPs and human-directed social behavior scored in an unsolvable problem task. Differences in allele freq…
format: application/pdf
format: text/html
creator: Mia E. Persson
creator: Ann-Sofie Sundman
creator: Lise-Lotte Halldén
creator: Agaia J. Trottier
creator: Per Jensen
subject: Animal Behavior
subject: Genetics
subject: Zoology
description: doi:10.7717/peerj.5889
publisher: PeerJ Inc.
rights: © 2018 Persson et al.
abstract: Background Dogs have human-directed social skills that allow them to communicate and cooperate with humans. We have previously identified two loci on chromosome 26 associated with human contact-seeking behaviors during an unsolvable problem task in laboratory beagles (Persson et al., 2016). The aim of the present study was to verify the single nucleotide polymorphisms (SNPs) in additional dog breeds. We also studied how the allele frequencies have changed during domestication and recent selection. Methods Dogs of two breeds, 61 golden retrievers and 100 Labrador retrievers, were phenotyped and genotyped, and 19 wolves were genotyped. The Labrador retrievers were divided into common and field type by pedigree data to make it possible to study the effects of recent selection. All dogs were tested in an unsolvable problem task where human-directed social behaviors were scored. DNA from dogs (buccal swabs) and wolves (blood or brain tissue) was analyzed for genotype on two of the previously identified SNP markers, BICF2G630798942 (SNP1) and BICF2S23712114 (SNP2), by pyrosequencing. Results There was genetic variation for SNP1 in both dog breeds whereas the wolves were fixed for this polymorphism, and for SNP2 there was variation in both dogs and wolves. For both SNPs, Labrador retriever types differed significantly in allele frequencies. We found associations between SNPs and human-directed social behavior in both dog breeds. In golden retrievers, SNP1 was associated with physical contact variables, for example, with the duration of physical contact with the owner (F2,56 = 4.389, p = 0.017). SNP2 was associated with several behavioral variables in both breeds, among others owner gazing frequency in both golden retrievers (F2,55 = 6.330, p = 0.003) and Labradors (F1,93 = 5.209, p = 0.025). Discussion Our results verify the association between the previously identified SNPs and human-directed social behavior scored in an unsolvable problem task. Differences in allele freq…
bibliographic citation: Persson et al. (2018) Sociality genes are associated with human-directed social behaviour in golden and Labrador retriever dogs. PeerJ 6:e5889 https://doi.org/10.7717/peerj.5889
date submitted: 2018-06-26
date accepted: 2018-10-08
issued: 2018-11-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Persson
  given name: Mia E.
author list: Agent
  family name: Sundman
  given name: Ann-Sofie
author list: Agent
  family name: Halldén
  given name: Lise-Lotte
author list: Agent
  family name: Trottier
  given name: Agaia J.
author list: Agent
  family name: Jensen
  given name: Per
doi: 10.7717/peerj.5889
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-06
copyright: © 2018 Persson et al.
attribution name: Persson et al.

Canadian packaged gluten-free foods are less nutritious than their regular gluten-containing counterparts
type: item
type: AcademicArticle
description: Background A strict gluten-free (GF) diet is required for the management of celiac disease (CD). The nutritional adequacy of this diet has been questioned due to the elimination of wheat, an important vehicle for micronutrient fortification and source of fibre. While novel and/or reformulated packaged GF products have rapidly entered the marketplace, providing alternatives to wheat-based staples, it is unknown whether these new products are nutritionally comparable. Methods From a database of 3,851 foods collected across 21 grocery stores in Eastern Canada, we compared the nutrient content of 398 unique GF items with 445 gluten-containing (GC) equivalents. Wilcoxon rank tests were conducted on listed nutrient content (g, mg, µg) per 100 g of product and the nutrient contribution of iron, folate and fibre were evaluated using Health Canada’s nutrient claim regulations. Results GF staples (cereals, breads, flours, pastas) contained 1.3 times more fat and less iron (by 55%), folate (by 44%) and protein (by 36%), than GC counterparts (P < 0.0001). On average, GF pastas had only 37% of the fibre in GC pastas (P < 0.0001). Notably, GF and GC flours were equivalent in nutrient content. Despite GF and GC flours having similar nutritional content, the vast majority of the processed GF foods fell short in key nutrients. Discussion Packaged GF foods in Canada are generally less nutritious than their GC counterparts, suggesting that GF diets should not be promoted to those who do not require it. The use of nutrient-dense GF flours in homemade foods may improve nutrient intakes on the GF diet.
format: application/pdf
format: text/html
creator: Jennifer A. Jamieson
creator: Mary Weir
creator: Laura Gougeon
subject: Food Science and Technology
subject: Gastroenterology and Hepatology
subject: Nutrition
description: doi:10.7717/peerj.5875
publisher: PeerJ Inc.
rights: © 2018 Jamieson et al.
abstract: Background A strict gluten-free (GF) diet is required for the management of celiac disease (CD). The nutritional adequacy of this diet has been questioned due to the elimination of wheat, an important vehicle for micronutrient fortification and source of fibre. While novel and/or reformulated packaged GF products have rapidly entered the marketplace, providing alternatives to wheat-based staples, it is unknown whether these new products are nutritionally comparable. Methods From a database of 3,851 foods collected across 21 grocery stores in Eastern Canada, we compared the nutrient content of 398 unique GF items with 445 gluten-containing (GC) equivalents. Wilcoxon rank tests were conducted on listed nutrient content (g, mg, µg) per 100 g of product and the nutrient contribution of iron, folate and fibre were evaluated using Health Canada’s nutrient claim regulations. Results GF staples (cereals, breads, flours, pastas) contained 1.3 times more fat and less iron (by 55%), folate (by 44%) and protein (by 36%), than GC counterparts (P < 0.0001). On average, GF pastas had only 37% of the fibre in GC pastas (P < 0.0001). Notably, GF and GC flours were equivalent in nutrient content. Despite GF and GC flours having similar nutritional content, the vast majority of the processed GF foods fell short in key nutrients. Discussion Packaged GF foods in Canada are generally less nutritious than their GC counterparts, suggesting that GF diets should not be promoted to those who do not require it. The use of nutrient-dense GF flours in homemade foods may improve nutrient intakes on the GF diet.
bibliographic citation: Jamieson et al. (2018) Canadian packaged gluten-free foods are less nutritious than their regular gluten-containing counterparts. PeerJ 6:e5875 https://doi.org/10.7717/peerj.5875
date submitted: 2018-06-11
date accepted: 2018-10-04
issued: 2018-11-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jamieson
  given name: Jennifer A.
author list: Agent
  family name: Weir
  given name: Mary
author list: Agent
  family name: Gougeon
  given name: Laura
doi: 10.7717/peerj.5875
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-06
copyright: ©2018 Jamieson et al.
attribution name: Jamieson et al.

Structural and functional analysis of the roles of the HCV 5′ NCR miR122-dependent long-range association and SLVI in genome translation and replication
type: item
type: AcademicArticle
description: The hepatitis C virus RNA genome possesses a variety of conserved structural elements, in both coding and non-coding regions, that are important for viral replication. These elements are known or predicted to modulate key life cycle events, such as translation and genome replication, some involving conformational changes induced by long-range RNA–RNA interactions. One such element is SLVI, a stem-loop (SL) structure located towards the 5′ end of the core protein-coding region. This element forms an alternative RNA–RNA interaction with complementary sequences in the 5′ untranslated regions that are independently involved in the binding of the cellular microRNA 122 (miR122). The switch between ‘open’ and ‘closed’ structures involving SLVI has previously been proposed to modulate translation, with lower translation efficiency associated with the ‘closed’ conformation. In the current study, we have used selective 2′-hydroxyl acylation analysed by primer extension to validate this RNA–RNA interaction in the absence and presence of miR122. We show that the long-range association (LRA) only forms in the absence of miR122, or otherwise requires the blocking of miR122 binding combined with substantial disruption of SLVI. Using site-directed mutations introduced to promote open or closed conformations of the LRA we demonstrate no correlation between the conformation and the translation phenotype. In addition, we observed no influence on virus replication compared to unmodified genomes. The presence of SLVI is well-documented to suppress translation, but these studies demonstrate that this is not due to its contribution to the LRA. We conclude that, although there are roles for SLVI in translation, the LRA is not a riboswitch regulating the translation and replication phenotypes of the virus.
format: application/pdf
format: text/html
creator: Kirsten Bentley
creator: Jonathan P. Cook
creator: Andrew K. Tuplin
creator: David J. Evans
subject: Microbiology
subject: Molecular Biology
subject: Virology
description: doi:10.7717/peerj.5870
publisher: PeerJ Inc.
rights: © 2018 Bentley et al.
abstract: The hepatitis C virus RNA genome possesses a variety of conserved structural elements, in both coding and non-coding regions, that are important for viral replication. These elements are known or predicted to modulate key life cycle events, such as translation and genome replication, some involving conformational changes induced by long-range RNA–RNA interactions. One such element is SLVI, a stem-loop (SL) structure located towards the 5′ end of the core protein-coding region. This element forms an alternative RNA–RNA interaction with complementary sequences in the 5′ untranslated regions that are independently involved in the binding of the cellular microRNA 122 (miR122). The switch between ‘open’ and ‘closed’ structures involving SLVI has previously been proposed to modulate translation, with lower translation efficiency associated with the ‘closed’ conformation. In the current study, we have used selective 2′-hydroxyl acylation analysed by primer extension to validate this RNA–RNA interaction in the absence and presence of miR122. We show that the long-range association (LRA) only forms in the absence of miR122, or otherwise requires the blocking of miR122 binding combined with substantial disruption of SLVI. Using site-directed mutations introduced to promote open or closed conformations of the LRA we demonstrate no correlation between the conformation and the translation phenotype. In addition, we observed no influence on virus replication compared to unmodified genomes. The presence of SLVI is well-documented to suppress translation, but these studies demonstrate that this is not due to its contribution to the LRA. We conclude that, although there are roles for SLVI in translation, the LRA is not a riboswitch regulating the translation and replication phenotypes of the virus.
bibliographic citation: Bentley et al. (2018) Structural and functional analysis of the roles of the HCV 5′ NCR miR122-dependent long-range association and SLVI in genome translation and replication. PeerJ 6:e5870 https://doi.org/10.7717/peerj.5870
date submitted: 2018-07-20
date accepted: 2018-09-30
issued: 2018-11-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bentley
  given name: Kirsten
author list: Agent
  family name: Cook
  given name: Jonathan P.
author list: Agent
  family name: Tuplin
  given name: Andrew K.
author list: Agent
  family name: Evans
  given name: David J.
doi: 10.7717/peerj.5870
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-06
copyright: © 2018 Bentley et al.
attribution name: Bentley et al.

Effects of mixed reality head-mounted glasses during 90 minutes of mental and manual tasks on cognitive and physiological functions
type: item
type: AcademicArticle
description: Background We evaluated the effects of a mixed reality (MR) head-mounted deviceon some cognitiveand physiological functions during 90 min tasks in an attempt to determine their safety for workers. Methods A total of 12 volunteers performed 90-min intellectual and manual tasks with and without MR glasses. Balance, Stroop, and memory tests were conducted before, during and after these tasks. Heart rate and electromyographic activity of some muscles were recorded. A survey was used to determine subjective fatigue, pain, or discomfort. Results Balance, heart rate, rate of perceived exertion, memory, and attention were unaffected by wearing MR glasses. Electromyographic activity increased with MR glasses for deltoid, biceps brachii, and soleus muscles. Few subjects reported discomfort, pain, or visual fatigue with MR glasses. Some participants reported they lost the notion of time and reality. Discussion Accordingly, we concluded that the MR glasses under investigation (Hololens) can be used safely. An appropriate setup and familiarization are needed to optimize use.
format: application/pdf
format: text/html
creator: Carole Cometti
creator: Christos Païzis
creator: Audrey Casteleira
creator: Guillaume Pons
creator: Nicolas Babault
subject: Bioengineering
subject: Neuroscience
subject: Global Health
subject: Public Health
subject: Human-Computer Interaction
description: doi:10.7717/peerj.5847
publisher: PeerJ Inc.
rights: © 2018 Cometti et al.
abstract: Background We evaluated the effects of a mixed reality (MR) head-mounted deviceon some cognitiveand physiological functions during 90 min tasks in an attempt to determine their safety for workers. Methods A total of 12 volunteers performed 90-min intellectual and manual tasks with and without MR glasses. Balance, Stroop, and memory tests were conducted before, during and after these tasks. Heart rate and electromyographic activity of some muscles were recorded. A survey was used to determine subjective fatigue, pain, or discomfort. Results Balance, heart rate, rate of perceived exertion, memory, and attention were unaffected by wearing MR glasses. Electromyographic activity increased with MR glasses for deltoid, biceps brachii, and soleus muscles. Few subjects reported discomfort, pain, or visual fatigue with MR glasses. Some participants reported they lost the notion of time and reality. Discussion Accordingly, we concluded that the MR glasses under investigation (Hololens) can be used safely. An appropriate setup and familiarization are needed to optimize use.
bibliographic citation: Cometti et al. (2018) Effects of mixed reality head-mounted glasses during 90 minutes of mental and manual tasks on cognitive and physiological functions. PeerJ 6:e5847 https://doi.org/10.7717/peerj.5847
date submitted: 2018-06-06
date accepted: 2018-09-30
issued: 2018-11-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cometti
  given name: Carole
author list: Agent
  family name: Païzis
  given name: Christos
author list: Agent
  family name: Casteleira
  given name: Audrey
author list: Agent
  family name: Pons
  given name: Guillaume
author list: Agent
  family name: Babault
  given name: Nicolas
doi: 10.7717/peerj.5847
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-06
copyright: © 2018 Cometti et al.
attribution name: Cometti et al.

Host anemone size as a determinant of social group size and structure in the orange clownfish (Amphiprion percula)
type: item
type: AcademicArticle
description: The size and structure of social groups of animals can be governed by a range of ecological factors and behavioral interactions. In small, highly site-attached coral reef fishes, group size is often constrained by the size of the habitat patch they are restricted to. However, group size may also be influenced by changes in abundance along important environmental gradients, such as depth or distance offshore. In addition, the body size and sex structure within social groups can be determined by the size of the habitat patch and the dominance relationships among group members. Here we examined the roles of ecological factors and behavioral interactions in governing group size and structure in the orange clownfish, Amphiprion percula, on inshore reefs in Kimbe Bay, Papua New Guinea. We quantified relationships between ecological variables (anemone size, depth, and distance from shore) and social group variables (group size, and total body length of the three largest individuals (ranks 1, 2, and 3)). Anemone size explained the greatest amount of variation in group variables, with strong, positive relationships between anemone surface area and group size, and total length of individuals ranked 1, 2, and 3. Group structure was also weakly correlated with increasing depth and distance from shore, most likely through the indirect effects of these environmental gradients on anemone size. Variation in group size and the lengths of ranks 2 and 3 were all closely related to the length of rank 1. Path analysis indicated that anemone size has a strong direct effect on the length of rank 1. In turn, the length of rank 1 directly affects the size of the subordinate individuals and indirectly affects the group size through its influence on subordinates. Hence, anemone size directly and indirectly controls social group size and structure in this space-limited fish species. It is also likely that anemonefish have feedback effects on anemone size, although this could not be differentia…
format: application/pdf
format: text/html
creator: Juliette Chausson
creator: Maya Srinivasan
creator: Geoffrey P. Jones
subject: Animal Behavior
subject: Ecology
subject: Marine Biology
subject: Environmental Impacts
description: doi:10.7717/peerj.5841
publisher: PeerJ Inc.
rights: © 2018 Chausson et al.
abstract: The size and structure of social groups of animals can be governed by a range of ecological factors and behavioral interactions. In small, highly site-attached coral reef fishes, group size is often constrained by the size of the habitat patch they are restricted to. However, group size may also be influenced by changes in abundance along important environmental gradients, such as depth or distance offshore. In addition, the body size and sex structure within social groups can be determined by the size of the habitat patch and the dominance relationships among group members. Here we examined the roles of ecological factors and behavioral interactions in governing group size and structure in the orange clownfish, Amphiprion percula, on inshore reefs in Kimbe Bay, Papua New Guinea. We quantified relationships between ecological variables (anemone size, depth, and distance from shore) and social group variables (group size, and total body length of the three largest individuals (ranks 1, 2, and 3)). Anemone size explained the greatest amount of variation in group variables, with strong, positive relationships between anemone surface area and group size, and total length of individuals ranked 1, 2, and 3. Group structure was also weakly correlated with increasing depth and distance from shore, most likely through the indirect effects of these environmental gradients on anemone size. Variation in group size and the lengths of ranks 2 and 3 were all closely related to the length of rank 1. Path analysis indicated that anemone size has a strong direct effect on the length of rank 1. In turn, the length of rank 1 directly affects the size of the subordinate individuals and indirectly affects the group size through its influence on subordinates. Hence, anemone size directly and indirectly controls social group size and structure in this space-limited fish species. It is also likely that anemonefish have feedback effects on anemone size, although this could not be differentia…
bibliographic citation: Chausson et al. (2018) Host anemone size as a determinant of social group size and structure in the orange clownfish (Amphiprion percula). PeerJ 6:e5841 https://doi.org/10.7717/peerj.5841
date submitted: 2018-07-03
date accepted: 2018-09-27
issued: 2018-11-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chausson
  given name: Juliette
author list: Agent
  family name: Srinivasan
  given name: Maya
author list: Agent
  family name: Jones
  given name: Geoffrey P.
doi: 10.7717/peerj.5841
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-06
copyright: © 2018 Chausson et al.
attribution name: Chausson et al.

Unimodal head-width distribution of the European eel (Anguilla anguilla L.) from the Zeeschelde does not support disruptive selection
type: item
type: AcademicArticle
description: Since the early 20th century, European eels (Anguilla anguilla L.) have been dichotomously classified into ‘narrow’ and ‘broad’ heads. These morphs are mainly considered the result of a differential food choice, with narrow heads feeding primarily on small/soft prey and broad heads on large/hard prey. Yet, such a classification implies that head-width variation follows a bimodal distribution, leading to the assumption of disruptive selection. We investigated the head morphology of 272 eels, caught over three consecutive years (2015–2017) at a single location in the Zeeschelde (Belgium). Based on our results, BIC favored a unimodal distribution, while AIC provided equal support for a unimodal and a bimodal distribution. Notably, visualization of the distributions revealed a strong overlap between the two normal distributions under the bimodal model, likely explaining the ambiguity under AIC. Consequently, it is more likely that head-width variation followed a unimodal distribution, indicating there are no disruptive selection pressures for bimodality in the Zeeschelde. As such, eels could not be divided in two distinct head-width groups. Instead, their head widths showed a continuum of narrow to broad with a normal distribution. This pattern was consistent across all maturation stages studied here.
format: application/pdf
format: text/html
creator: Pieterjan Verhelst
creator: Jens De Meyer
creator: Jan Reubens
creator: Johan Coeck
creator: Peter Goethals
creator: Tom Moens
creator: Ans Mouton
subject: Animal Behavior
subject: Developmental Biology
description: doi:10.7717/peerj.5773
publisher: PeerJ Inc.
rights: © 2018 Verhelst et al.
abstract: Since the early 20th century, European eels (Anguilla anguilla L.) have been dichotomously classified into ‘narrow’ and ‘broad’ heads. These morphs are mainly considered the result of a differential food choice, with narrow heads feeding primarily on small/soft prey and broad heads on large/hard prey. Yet, such a classification implies that head-width variation follows a bimodal distribution, leading to the assumption of disruptive selection. We investigated the head morphology of 272 eels, caught over three consecutive years (2015–2017) at a single location in the Zeeschelde (Belgium). Based on our results, BIC favored a unimodal distribution, while AIC provided equal support for a unimodal and a bimodal distribution. Notably, visualization of the distributions revealed a strong overlap between the two normal distributions under the bimodal model, likely explaining the ambiguity under AIC. Consequently, it is more likely that head-width variation followed a unimodal distribution, indicating there are no disruptive selection pressures for bimodality in the Zeeschelde. As such, eels could not be divided in two distinct head-width groups. Instead, their head widths showed a continuum of narrow to broad with a normal distribution. This pattern was consistent across all maturation stages studied here.
bibliographic citation: Verhelst et al. (2018) Unimodal head-width distribution of the European eel (Anguilla anguilla L.) from the Zeeschelde does not support disruptive selection. PeerJ 6:e5773 https://doi.org/10.7717/peerj.5773
date submitted: 2018-06-09
date accepted: 2018-09-17
issued: 2018-11-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Verhelst
  given name: Pieterjan
author list: Agent
  family name: De Meyer
  given name: Jens
author list: Agent
  family name: Reubens
  given name: Jan
author list: Agent
  family name: Coeck
  given name: Johan
author list: Agent
  family name: Goethals
  given name: Peter
author list: Agent
  family name: Moens
  given name: Tom
author list: Agent
  family name: Mouton
  given name: Ans
doi: 10.7717/peerj.5773
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-06
copyright: ©2018 Verhelst et al.
attribution name: Verhelst et al.

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