PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Boat anchoring contributes substantially to coral reef degradation in the British Virgin Islands
items: The braincase of Mesosuchus browni (Reptilia, Archosauromorpha) with information on the inner ear and description of a pneumatic sinus
items: FunPred 3.0: improved protein function prediction using protein interaction network
items: Chemodiversity of Calophyllum inophyllum L. oil bioactive components related to their specific geographical distribution in the South Pacific region
items: Evaluation of in-vitro methods to select effective streptomycetes against toxigenic fusaria
items: Imagery ability of elite level athletes from individual vs. team and contact vs. no-contact sports
items: Aromatisation of steroids in the bivalve Mytilus trossulus
items: The use of bat houses as day roosts in macadamia orchards, South Africa
items: Crossmodal congruency effect scores decrease with repeat test exposure
items: Purification of plant-derived anti-virus mAb through optimized pH conditions for coupling between protein A and epoxy-activated beads

Boat anchoring contributes substantially to coral reef degradation in the British Virgin Islands
type: item
type: AcademicArticle
description: Community decline is often linked to anthropogenic activities. Coral reef declines, for example, have been linked to overfishing and climate change, but impacts of coastal development, pollution, and tourism have received increasing attention. Here, we isolated the impact of one little-studied aspect of recreational activity on coral reefs—damage from boat anchoring—by performing a survey of 24 sites in the British Virgin Islands (BVI) subject to varying levels of anchoring activity. The percent cover of hard corals and sea fans was reduced by a factor of ∼1.7 and ∼2.6 respectively at highly anchored sites. Hard coral colonies were 40% smaller in surface area and ∼60% less dense at sites experiencing high anchoring frequency. In addition, highly anchored sites supported only ∼60% of the species richness of little anchored sites. Frequently anchored sites were ∼60% as structurally complex and supported less than half as many fish as those rarely anchored, with 5 of 7 fish functional groups affected. Roughly 24% of BVI coral reef by area appears suitable for anchoring, suggesting that impacts associated with boat anchoring may be both locally severe and more pervasive than previously appreciated.
format: application/pdf
format: text/html
creator: Rebecca L. Flynn
creator: Graham E. Forrester
subject: Ecology
subject: Marine Biology
subject: Natural Resource Management
subject: Environmental Impacts
description: doi:10.7717/peerj.7010
publisher: PeerJ Inc.
rights: © 2019 Flynn and Forrester
abstract: Community decline is often linked to anthropogenic activities. Coral reef declines, for example, have been linked to overfishing and climate change, but impacts of coastal development, pollution, and tourism have received increasing attention. Here, we isolated the impact of one little-studied aspect of recreational activity on coral reefs—damage from boat anchoring—by performing a survey of 24 sites in the British Virgin Islands (BVI) subject to varying levels of anchoring activity. The percent cover of hard corals and sea fans was reduced by a factor of ∼1.7 and ∼2.6 respectively at highly anchored sites. Hard coral colonies were 40% smaller in surface area and ∼60% less dense at sites experiencing high anchoring frequency. In addition, highly anchored sites supported only ∼60% of the species richness of little anchored sites. Frequently anchored sites were ∼60% as structurally complex and supported less than half as many fish as those rarely anchored, with 5 of 7 fish functional groups affected. Roughly 24% of BVI coral reef by area appears suitable for anchoring, suggesting that impacts associated with boat anchoring may be both locally severe and more pervasive than previously appreciated.
bibliographic citation: Flynn et al. (2019) Boat anchoring contributes substantially to coral reef degradation in the British Virgin Islands. PeerJ 7:e7010 https://doi.org/10.7717/peerj.7010
date submitted: 2019-01-30
date accepted: 2019-04-24
issued: 2019-05-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Flynn
  given name: Rebecca L.
author list: Agent
  family name: Forrester
  given name: Graham E.
doi: 10.7717/peerj.7010
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-23
copyright: ©2019 Flynn and Forrester
attribution name: Flynn and Forrester

The braincase of Mesosuchus browni (Reptilia, Archosauromorpha) with information on the inner ear and description of a pneumatic sinus
type: item
type: AcademicArticle
description: Rhynchosauria is a group of archosauromorph reptiles abundant in terrestrial ecosystems of the Middle Triassic. Mesosuchus is one of the earliest and basalmost rhynchosaurs, playing an important role not only for the understanding of the evolution of the group as a whole, but also of archosauromorphs in general. The braincase of Mesosuchus has been previously described, albeit not in detail, and the middle and inner ears were missing. Here, we provide new information based on micro-computed tomography scanning of the best-preserved specimen of Mesosuchus, SAM-PK-6536. Contrary to what has been stated previously, the braincase of Mesosuchus is dorso-ventrally tall. The trigeminal foramen lies in a deep recess on the prootic whose flat ventral rim could indicate the articulation surface to the laterosphenoid, although no such element was found. The middle ear of Mesosuchus shows a small and deeply recessed fenestra ovalis, with the right stapes preserved in situ. It has a rather stout, imperforated and posteriorly directed shaft with a small footplate. These features suggest that the ear of Mesosuchus was well-suited for the detection of low-frequency sounds. The semicircular canals are slender and elongate and the floccular fossa is well-developed. This is indicative of a refined mechanism for gaze stabilization, which is usually related to non-sprawling postures. The most striking feature of the Mesosuchus braincase is, however, the presence of a pneumatic sinus in the basal tubera. The sinus is identified as originating from the pharyngotympanic system, implying ossified Eustachian tubes. Braincase pneumatization has not yet been a recognized feature of stem-archosaurs, but the potential presence of pneumatic foramina in an array of taxa, recognized here as such for the first time, suggests braincase sinuses could be present in many other archosauromorphs.
format: application/pdf
format: text/html
creator: Gabriela Sobral
creator: Johannes Müller
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.6798
publisher: PeerJ Inc.
rights: © 2019 Sobral and Müller
abstract: Rhynchosauria is a group of archosauromorph reptiles abundant in terrestrial ecosystems of the Middle Triassic. Mesosuchus is one of the earliest and basalmost rhynchosaurs, playing an important role not only for the understanding of the evolution of the group as a whole, but also of archosauromorphs in general. The braincase of Mesosuchus has been previously described, albeit not in detail, and the middle and inner ears were missing. Here, we provide new information based on micro-computed tomography scanning of the best-preserved specimen of Mesosuchus, SAM-PK-6536. Contrary to what has been stated previously, the braincase of Mesosuchus is dorso-ventrally tall. The trigeminal foramen lies in a deep recess on the prootic whose flat ventral rim could indicate the articulation surface to the laterosphenoid, although no such element was found. The middle ear of Mesosuchus shows a small and deeply recessed fenestra ovalis, with the right stapes preserved in situ. It has a rather stout, imperforated and posteriorly directed shaft with a small footplate. These features suggest that the ear of Mesosuchus was well-suited for the detection of low-frequency sounds. The semicircular canals are slender and elongate and the floccular fossa is well-developed. This is indicative of a refined mechanism for gaze stabilization, which is usually related to non-sprawling postures. The most striking feature of the Mesosuchus braincase is, however, the presence of a pneumatic sinus in the basal tubera. The sinus is identified as originating from the pharyngotympanic system, implying ossified Eustachian tubes. Braincase pneumatization has not yet been a recognized feature of stem-archosaurs, but the potential presence of pneumatic foramina in an array of taxa, recognized here as such for the first time, suggests braincase sinuses could be present in many other archosauromorphs.
bibliographic citation: Sobral et al. (2019) The braincase of Mesosuchus browni (Reptilia, Archosauromorpha) with information on the inner ear and description of a pneumatic sinus. PeerJ 7:e6798 https://doi.org/10.7717/peerj.6798
date submitted: 2017-09-21
date accepted: 2019-03-17
issued: 2019-05-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sobral
  given name: Gabriela
author list: Agent
  family name: Müller
  given name: Johannes
doi: 10.7717/peerj.6798
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-22
copyright: © 2019 Sobral and Müller
attribution name: Sobral and Müller

FunPred 3.0: improved protein function prediction using protein interaction network
type: item
type: AcademicArticle
description: Proteins are the most versatile macromolecules in living systems and perform crucial biological functions. In the advent of the post-genomic era, the next generation sequencing is done routinely at the population scale for a variety of species. The challenging problem is to massively determine the functions of proteins that are yet not characterized by detailed experimental studies. Identification of protein functions experimentally is a laborious and time-consuming task involving many resources. We therefore propose the automated protein function prediction methodology using in silico algorithms trained on carefully curated experimental datasets. We present the improved protein function prediction tool FunPred 3.0, an extended version of our previous methodology FunPred 2, which exploits neighborhood properties in protein–protein interaction network (PPIN) and physicochemical properties of amino acids. Our method is validated using the available functional annotations in the PPIN network of Saccharomyces cerevisiae in the latest Munich information center for protein (MIPS) dataset. The PPIN data of S. cerevisiae in MIPS dataset includes 4,554 unique proteins in 13,528 protein–protein interactions after the elimination of the self-replicating and the self-interacting protein pairs. Using the developed FunPred 3.0 tool, we are able to achieve the mean precision, the recall and the F-score values of 0.55, 0.82 and 0.66, respectively. FunPred 3.0 is then used to predict the functions of unpredicted protein pairs (incomplete and missing functional annotations) in MIPS dataset of S. cerevisiae. The method is also capable of predicting the subcellular localization of proteins along with its corresponding functions. The code and the complete prediction results are available freely at: https://github.com/SovanSaha/FunPred-3.0.git.
format: application/pdf
format: text/html
creator: Sovan Saha
creator: Piyali Chatterjee
creator: Subhadip Basu
creator: Mita Nasipuri
creator: Dariusz Plewczynski
subject: Bioinformatics
subject: Biophysics
subject: Computational Biology
subject: Genomics
description: doi:10.7717/peerj.6830
publisher: PeerJ Inc.
rights: © 2019 Saha et al.
abstract: Proteins are the most versatile macromolecules in living systems and perform crucial biological functions. In the advent of the post-genomic era, the next generation sequencing is done routinely at the population scale for a variety of species. The challenging problem is to massively determine the functions of proteins that are yet not characterized by detailed experimental studies. Identification of protein functions experimentally is a laborious and time-consuming task involving many resources. We therefore propose the automated protein function prediction methodology using in silico algorithms trained on carefully curated experimental datasets. We present the improved protein function prediction tool FunPred 3.0, an extended version of our previous methodology FunPred 2, which exploits neighborhood properties in protein–protein interaction network (PPIN) and physicochemical properties of amino acids. Our method is validated using the available functional annotations in the PPIN network of Saccharomyces cerevisiae in the latest Munich information center for protein (MIPS) dataset. The PPIN data of S. cerevisiae in MIPS dataset includes 4,554 unique proteins in 13,528 protein–protein interactions after the elimination of the self-replicating and the self-interacting protein pairs. Using the developed FunPred 3.0 tool, we are able to achieve the mean precision, the recall and the F-score values of 0.55, 0.82 and 0.66, respectively. FunPred 3.0 is then used to predict the functions of unpredicted protein pairs (incomplete and missing functional annotations) in MIPS dataset of S. cerevisiae. The method is also capable of predicting the subcellular localization of proteins along with its corresponding functions. The code and the complete prediction results are available freely at: https://github.com/SovanSaha/FunPred-3.0.git.
bibliographic citation: Saha et al. (2019) FunPred 3.0: improved protein function prediction using protein interaction network. PeerJ 7:e6830 https://doi.org/10.7717/peerj.6830
date submitted: 2018-07-20
date accepted: 2019-03-21
issued: 2019-05-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Saha
  given name: Sovan
author list: Agent
  family name: Chatterjee
  given name: Piyali
author list: Agent
  family name: Basu
  given name: Subhadip
author list: Agent
  family name: Nasipuri
  given name: Mita
author list: Agent
  family name: Plewczynski
  given name: Dariusz
doi: 10.7717/peerj.6830
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-22
copyright: © 2019 Saha et al.
attribution name: Saha et al.

Chemodiversity of Calophyllum inophyllum L. oil bioactive components related to their specific geographical distribution in the South Pacific region
type: item
type: AcademicArticle
description: Background Different parts of the tree Calophyllum inophyllum L. (nuts, leaves, roots, bark, fruits, nut oil and resin) are used as traditional medicines and cosmetics in most of the Pacific Islands. The oil efficiency as a natural cure and in traditional cosmetics has been largely described throughout the South Pacific, which led us to investigate C. inophyllum’s chemical and genetic diversity. A correlative study of the nut resin and leaf DNA from three distinct archipelagos in the South Pacific was carried out in order to identify diversity patterns in C. inophyllum across the South Pacific. Methods Calophyllum inophyllum plants were sampled from French Polynesia, New Caledonia and Fiji. We extracted tamanu oil (nut oil) resin for chemo-diversity studies and sampled leaf tissues for genetic studies. We applied an analysis method designed for small quantities (at a microscale level), and used High Performance Liquid Chromatography (HPLC) to establish the chemo-diversity of tamanu oil resin. In-house standards were co-eluted for qualitative determination. Genetic diversity was assessed using chloroplast barcoding markers (the Acetyl-CoA carboxylase (accD) gene and the psaA-ycf3 intergenic spacer region). Results Our HPLC analysis revealed 11 previously known tamanu oil constituents, with variability among plant samples. We also isolated and characterized two new neoflavonoids from tamanu oil resin namely, tamanolide E1 and E2 which are diastereoisomers. Although genetic analysis revealed low genetic variation, our multivariate analysis (PCA) of the tamanu oil resin chemical profiles revealed differentiation among geographic regions. Conclusion We showed here that chromatographic analysis using formalized in-house standards of oil resin compounds for co-elution studies against oil resin samples could identify patterns of variation among samples of C. inophyllum, and discriminate samples from different geographical origins.
format: application/pdf
format: text/html
creator: Joape Ginigini
creator: Gaël J. Lecellier
creator: Mael Nicolas
creator: Mohammed Nour
creator: Edouard Hnawia
creator: Nicolas Lebouvier
creator: Gaëtan Herbette
creator: Peter Lockhart
creator: Phila Raharivelomanana
subject: Biogeography
subject: Plant Science
subject: Biogeochemistry
description: doi:10.7717/peerj.6896
publisher: PeerJ Inc.
rights: © 2019 Ginigini et al.
abstract: Background Different parts of the tree Calophyllum inophyllum L. (nuts, leaves, roots, bark, fruits, nut oil and resin) are used as traditional medicines and cosmetics in most of the Pacific Islands. The oil efficiency as a natural cure and in traditional cosmetics has been largely described throughout the South Pacific, which led us to investigate C. inophyllum’s chemical and genetic diversity. A correlative study of the nut resin and leaf DNA from three distinct archipelagos in the South Pacific was carried out in order to identify diversity patterns in C. inophyllum across the South Pacific. Methods Calophyllum inophyllum plants were sampled from French Polynesia, New Caledonia and Fiji. We extracted tamanu oil (nut oil) resin for chemo-diversity studies and sampled leaf tissues for genetic studies. We applied an analysis method designed for small quantities (at a microscale level), and used High Performance Liquid Chromatography (HPLC) to establish the chemo-diversity of tamanu oil resin. In-house standards were co-eluted for qualitative determination. Genetic diversity was assessed using chloroplast barcoding markers (the Acetyl-CoA carboxylase (accD) gene and the psaA-ycf3 intergenic spacer region). Results Our HPLC analysis revealed 11 previously known tamanu oil constituents, with variability among plant samples. We also isolated and characterized two new neoflavonoids from tamanu oil resin namely, tamanolide E1 and E2 which are diastereoisomers. Although genetic analysis revealed low genetic variation, our multivariate analysis (PCA) of the tamanu oil resin chemical profiles revealed differentiation among geographic regions. Conclusion We showed here that chromatographic analysis using formalized in-house standards of oil resin compounds for co-elution studies against oil resin samples could identify patterns of variation among samples of C. inophyllum, and discriminate samples from different geographical origins.
bibliographic citation: Ginigini et al. (2019) Chemodiversity of Calophyllum inophyllum L. oil bioactive components related to their specific geographical distribution in the South Pacific region. PeerJ 7:e6896 https://doi.org/10.7717/peerj.6896
date submitted: 2018-10-18
date accepted: 2019-04-02
issued: 2019-05-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ginigini
  given name: Joape
author list: Agent
  family name: Lecellier
  given name: Gaël J.
author list: Agent
  family name: Nicolas
  given name: Mael
author list: Agent
  family name: Nour
  given name: Mohammed
author list: Agent
  family name: Hnawia
  given name: Edouard
author list: Agent
  family name: Lebouvier
  given name: Nicolas
author list: Agent
  family name: Herbette
  given name: Gaëtan
author list: Agent
  family name: Lockhart
  given name: Peter
author list: Agent
  family name: Raharivelomanana
  given name: Phila
doi: 10.7717/peerj.6896
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-22
copyright: © 2019 Ginigini et al.
attribution name: Ginigini et al.

Evaluation of in-vitro methods to select effective streptomycetes against toxigenic fusaria
type: item
type: AcademicArticle
description: Biocontrol microorganisms are emerging as an effective alternative to pesticides. Ideally, biocontrol agents (BCAs) for the control of fungal plant pathogens should be selected by an in vitro method that is high-throughput and is predictive of in planta efficacy, possibly considering environmental factors, and the natural diversity of the pathogen. The purpose of our study was (1) to assess the effects of Fusarium strain diversity (N = 5) and culture media (N = 6) on the identification of biological control activity of Streptomyces strains (N = 20) against Fusarium pathogens of wheat in vitro and (2) to verify the ability of our in vitro screening methods to simulate the activity in planta. Our results indicate that culture media, Fusarium strain diversity, and their interactions affect the results of an in vitro selection by dual culture assay. The results obtained on the wheat-based culture media resulted in the highest correlation score (r = 0.5) with the in planta root rot (RR) inhibition, suggesting that this in vitro method was the best predictor of in planta performance of streptomycetes against Fusarium RR of wheat assessed as extension of the necrosis on the root. Contrarily, none of the in vitro plate assays using the media tested could appropriately predict the activity of the streptomycetes against Fusarium foot rot symptoms estimated as the necrosis at the crown level. Considering overall data of correlation, the activity in planta cannot be effectively predicted by dual culture plate studies, therefore improved in vitro methods are needed to better mimic the activity of biocontrol strains in natural conditions. This work contributes to setting up laboratory standards for preliminary screening assays of Streptomyces BCAs against fungal pathogens.
format: application/pdf
format: text/html
creator: Elena Maria Colombo
creator: Cristina Pizzatti
creator: Andrea Kunova
creator: Claudio Gardana
creator: Marco Saracchi
creator: Paolo Cortesi
creator: Matias Pasquali
subject: Agricultural Science
subject: Microbiology
subject: Plant Science
description: doi:10.7717/peerj.6905
publisher: PeerJ Inc.
rights: © 2019 Colombo et al.
abstract: Biocontrol microorganisms are emerging as an effective alternative to pesticides. Ideally, biocontrol agents (BCAs) for the control of fungal plant pathogens should be selected by an in vitro method that is high-throughput and is predictive of in planta efficacy, possibly considering environmental factors, and the natural diversity of the pathogen. The purpose of our study was (1) to assess the effects of Fusarium strain diversity (N = 5) and culture media (N = 6) on the identification of biological control activity of Streptomyces strains (N = 20) against Fusarium pathogens of wheat in vitro and (2) to verify the ability of our in vitro screening methods to simulate the activity in planta. Our results indicate that culture media, Fusarium strain diversity, and their interactions affect the results of an in vitro selection by dual culture assay. The results obtained on the wheat-based culture media resulted in the highest correlation score (r = 0.5) with the in planta root rot (RR) inhibition, suggesting that this in vitro method was the best predictor of in planta performance of streptomycetes against Fusarium RR of wheat assessed as extension of the necrosis on the root. Contrarily, none of the in vitro plate assays using the media tested could appropriately predict the activity of the streptomycetes against Fusarium foot rot symptoms estimated as the necrosis at the crown level. Considering overall data of correlation, the activity in planta cannot be effectively predicted by dual culture plate studies, therefore improved in vitro methods are needed to better mimic the activity of biocontrol strains in natural conditions. This work contributes to setting up laboratory standards for preliminary screening assays of Streptomyces BCAs against fungal pathogens.
bibliographic citation: Colombo et al. (2019) Evaluation of in-vitro methods to select effective streptomycetes against toxigenic fusaria. PeerJ 7:e6905 https://doi.org/10.7717/peerj.6905
date submitted: 2018-09-24
date accepted: 2019-04-03
issued: 2019-05-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Colombo
  given name: Elena Maria
author list: Agent
  family name: Pizzatti
  given name: Cristina
author list: Agent
  family name: Kunova
  given name: Andrea
author list: Agent
  family name: Gardana
  given name: Claudio
author list: Agent
  family name: Saracchi
  given name: Marco
author list: Agent
  family name: Cortesi
  given name: Paolo
author list: Agent
  family name: Pasquali
  given name: Matias
doi: 10.7717/peerj.6905
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-22
copyright: © 2019 Colombo et al.
attribution name: Colombo et al.

Imagery ability of elite level athletes from individual vs. team and contact vs. no-contact sports
type: item
type: AcademicArticle
description: Background In the sport context, imagery has been described as the condition in which persons imagine themselves while executing skills to deal with the upcoming task or enhance performance. Systematic reviews have shown that mental imagery improves performance in motor tasks Methods The aim of the present study was to explore whether imagery vividness (i.e., the clarity or realism of the imagery experience) and controllability (i.e., the ease and accuracy with which an image can be manipulated mentally) differ by sport types (team vs. individual and contact vs. non-contact). Participants were athletes from team contact and non-contact sports (rugby and volleyball, respectively), and individual contact and non-contact sports (karate and tennis, respectively) between the ages of 20 and 33 years (M = 24.37, SD = 2.85). The participants completed the Vividness of Visual Imagery Questionnaire, the Vividness of Movement Imagery Questionnaire-2, and the Mental Image Transformation Tasks. Results A 2 ×2 × 2 (gender × 2 contact-no-contact × 2 sport type) between groups MANOVA showed differences in imagery ability by sport type. Practical indications deriving from the findings of this study can help coaches and athletes to develop mental preparation programs using sport-specific imagery.
format: application/pdf
format: text/html
creator: Donatella Di Corrado
creator: Maria Guarnera
creator: Francesca Vitali
creator: Alessandro Quartiroli
creator: Marinella Coco
subject: Kinesiology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.6940
publisher: PeerJ Inc.
rights: © 2019 Di Corrado et al.
abstract: Background In the sport context, imagery has been described as the condition in which persons imagine themselves while executing skills to deal with the upcoming task or enhance performance. Systematic reviews have shown that mental imagery improves performance in motor tasks Methods The aim of the present study was to explore whether imagery vividness (i.e., the clarity or realism of the imagery experience) and controllability (i.e., the ease and accuracy with which an image can be manipulated mentally) differ by sport types (team vs. individual and contact vs. non-contact). Participants were athletes from team contact and non-contact sports (rugby and volleyball, respectively), and individual contact and non-contact sports (karate and tennis, respectively) between the ages of 20 and 33 years (M = 24.37, SD = 2.85). The participants completed the Vividness of Visual Imagery Questionnaire, the Vividness of Movement Imagery Questionnaire-2, and the Mental Image Transformation Tasks. Results A 2 ×2 × 2 (gender × 2 contact-no-contact × 2 sport type) between groups MANOVA showed differences in imagery ability by sport type. Practical indications deriving from the findings of this study can help coaches and athletes to develop mental preparation programs using sport-specific imagery.
bibliographic citation: Di Corrado et al. (2019) Imagery ability of elite level athletes from individual vs. team and contact vs. no-contact sports. PeerJ 7:e6940 https://doi.org/10.7717/peerj.6940
date submitted: 2019-03-04
date accepted: 2019-04-11
issued: 2019-05-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Di Corrado
  given name: Donatella
author list: Agent
  family name: Guarnera
  given name: Maria
author list: Agent
  family name: Vitali
  given name: Francesca
author list: Agent
  family name: Quartiroli
  given name: Alessandro
author list: Agent
  family name: Coco
  given name: Marinella
doi: 10.7717/peerj.6940
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-22
copyright: ©2019 Di Corrado et al.
attribution name: Di Corrado et al.

Aromatisation of steroids in the bivalve Mytilus trossulus
type: item
type: AcademicArticle
description: In this study, we demonstrated the presence of the enzymatic complex able to perform aromatization (estrogen synthesis) in both, the microsomal and mitochondrial fractions of gills and gonads from Mytilus trossulus. Based on in vitro experiments, we highlighted the importance of temperature as the limiting factor of aromatisation efficiency (AE) in mussels. After testing range of temperatures (4–23 °C), the highest AE was found during incubation at 8 °C and pH 7.6 (41.66 pmol/h/mg protein in gills and 58.37 pmol/h/mg protein in gonads). The results were confirmed during field studies where the most efficient aromatisation occurred in bivalves collected in spring while the least effective in those collected in winter. During in vitro studies, AE turned out to be more intensive in female gonads than in male gonads. The process was also more intensive in mitochondrial fraction than in microsomal one (62.97 pmol/h/mg protein in male gills and 73.94 pmol/h/mg protein in female gonads). Enzymatic complex (aromatase-like enzyme) catalysing aromatisation in mussels was found to be insensitive to inhibitory effect of selective inhibitors of mammalian aromatase such as letrozole and anastrazole, suggesting its different structure from vertebrate aromatase. Further in vivo studies using 13C-labeled steroids at 8 °C temperature window confirmed that bivalves are able to uptake testosterone and androstenedione from the ambient environment and metabolise them to estrone and 17β-estradiol thus confirming endogenous estrogen’ synthesis.
format: application/pdf
format: text/html
creator: Anna Hallmann
creator: Lucyna Konieczna
creator: Justyna Swiezak
creator: Ryszard Milczarek
creator: Katarzyna Smolarz
subject: Biochemistry
subject: Marine Biology
description: doi:10.7717/peerj.6953
publisher: PeerJ Inc.
rights: © 2019 Hallmann et al.
abstract: In this study, we demonstrated the presence of the enzymatic complex able to perform aromatization (estrogen synthesis) in both, the microsomal and mitochondrial fractions of gills and gonads from Mytilus trossulus. Based on in vitro experiments, we highlighted the importance of temperature as the limiting factor of aromatisation efficiency (AE) in mussels. After testing range of temperatures (4–23 °C), the highest AE was found during incubation at 8 °C and pH 7.6 (41.66 pmol/h/mg protein in gills and 58.37 pmol/h/mg protein in gonads). The results were confirmed during field studies where the most efficient aromatisation occurred in bivalves collected in spring while the least effective in those collected in winter. During in vitro studies, AE turned out to be more intensive in female gonads than in male gonads. The process was also more intensive in mitochondrial fraction than in microsomal one (62.97 pmol/h/mg protein in male gills and 73.94 pmol/h/mg protein in female gonads). Enzymatic complex (aromatase-like enzyme) catalysing aromatisation in mussels was found to be insensitive to inhibitory effect of selective inhibitors of mammalian aromatase such as letrozole and anastrazole, suggesting its different structure from vertebrate aromatase. Further in vivo studies using 13C-labeled steroids at 8 °C temperature window confirmed that bivalves are able to uptake testosterone and androstenedione from the ambient environment and metabolise them to estrone and 17β-estradiol thus confirming endogenous estrogen’ synthesis.
bibliographic citation: Hallmann et al. (2019) Aromatisation of steroids in the bivalve Mytilus trossulus. PeerJ 7:e6953 https://doi.org/10.7717/peerj.6953
date submitted: 2019-02-16
date accepted: 2019-04-12
issued: 2019-05-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hallmann
  given name: Anna
author list: Agent
  family name: Konieczna
  given name: Lucyna
author list: Agent
  family name: Swiezak
  given name: Justyna
author list: Agent
  family name: Milczarek
  given name: Ryszard
author list: Agent
  family name: Smolarz
  given name: Katarzyna
doi: 10.7717/peerj.6953
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-22
copyright: © 2019 Hallmann et al.
attribution name: Hallmann et al.

The use of bat houses as day roosts in macadamia orchards, South Africa
type: item
type: AcademicArticle
description: The loss of roost sites is one of the major drivers of the worldwide decline in bat populations and roost site preferences, either natural or artificially provided, are not well known for African bat species specifically. In this study we focus on the preference for different artificial roost sites by insectivorous bats in macadamia orchards in northern South Africa. From June 2016 to July 2017 we monitored 31 bat houses, mounted on poles in six macadamia orchards, for presence of bats or other occupants. Twenty-one multi-chambered bat houses of three different designs were erected in sets of three. Additionally, five Rocket boxes, four bat houses in sets of two (painted black and white) and one colony bat house were erected. Bats were counted and visually identified to family or species level. From December 2016 to the end of March 2017 iButtons were installed to record and analyze temperature variation within one set of three bat houses. We related the occupancy of bat houses to the different types of houses and the environmental variables: distance to water, altitude and height of the bat houses above the ground. Overall bat house occupancy was significantly higher in the central bat house, in the set of three, and the black bat house, in the set of two. Mean temperatures differed between houses in the set of three with the central bat house having a significantly higher mean temperature than the houses flanking it. Our study might confirm previous assumptions that the microclimate of bat houses appears to be an important factor influencing occupancy. In conclusion, from the different bat houses tested in this study the designs we assume the warmest and best insulated attracted the most bats. Further research is needed on the preferred microclimate of different bat species, co-habitation within bat houses and the potential importance of altitude and distance to water. Our study provided little variation in both altitude and the distance to water.
format: application/pdf
format: text/html
creator: Sina M. Weier
creator: Valerie M.G. Linden
creator: Ingo Grass
creator: Teja Tscharntke
creator: Peter J. Taylor
subject: Agricultural Science
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.6954
publisher: PeerJ Inc.
rights: © 2019 Weier et al.
abstract: The loss of roost sites is one of the major drivers of the worldwide decline in bat populations and roost site preferences, either natural or artificially provided, are not well known for African bat species specifically. In this study we focus on the preference for different artificial roost sites by insectivorous bats in macadamia orchards in northern South Africa. From June 2016 to July 2017 we monitored 31 bat houses, mounted on poles in six macadamia orchards, for presence of bats or other occupants. Twenty-one multi-chambered bat houses of three different designs were erected in sets of three. Additionally, five Rocket boxes, four bat houses in sets of two (painted black and white) and one colony bat house were erected. Bats were counted and visually identified to family or species level. From December 2016 to the end of March 2017 iButtons were installed to record and analyze temperature variation within one set of three bat houses. We related the occupancy of bat houses to the different types of houses and the environmental variables: distance to water, altitude and height of the bat houses above the ground. Overall bat house occupancy was significantly higher in the central bat house, in the set of three, and the black bat house, in the set of two. Mean temperatures differed between houses in the set of three with the central bat house having a significantly higher mean temperature than the houses flanking it. Our study might confirm previous assumptions that the microclimate of bat houses appears to be an important factor influencing occupancy. In conclusion, from the different bat houses tested in this study the designs we assume the warmest and best insulated attracted the most bats. Further research is needed on the preferred microclimate of different bat species, co-habitation within bat houses and the potential importance of altitude and distance to water. Our study provided little variation in both altitude and the distance to water.
bibliographic citation: Weier et al. (2019) The use of bat houses as day roosts in macadamia orchards, South Africa. PeerJ 7:e6954 https://doi.org/10.7717/peerj.6954
date submitted: 2018-10-12
date accepted: 2019-04-13
issued: 2019-05-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Weier
  given name: Sina M.
author list: Agent
  family name: Linden
  given name: Valerie M.G.
author list: Agent
  family name: Grass
  given name: Ingo
author list: Agent
  family name: Tscharntke
  given name: Teja
author list: Agent
  family name: Taylor
  given name: Peter J.
doi: 10.7717/peerj.6954
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-22
copyright: ©2019 Weier et al.
attribution name: Weier et al.

Crossmodal congruency effect scores decrease with repeat test exposure
type: item
type: AcademicArticle
description: The incorporation of feedback into a person’s body schema is well established. The crossmodal congruency task (CCT) is used to objectively quantify incorporation without being susceptible to experimenter biases. This visual-tactile interference task is used to calculate the crossmodal congruency effect (CCE) score as a difference in response time between incongruent and congruent trials. Here we show that this metric is susceptible to a learning effect that causes attenuation of the CCE score due to repeated task exposure sessions. We demonstrate that this learning effect is persistent, even after a 6 month hiatus in testing. Two mitigation strategies are proposed: 1. Only use CCE scores that are taken after learning has stabilized, or 2. Use a modified CCT protocol that decreases the task exposure time. We show that the modified and shortened CCT protocol, which may be required to meet time or logistical constraints in laboratory or clinical settings, reduced the impact of the learning effect on CCT results. Importantly, the CCE scores from the modified protocol were not significantly more variable than results obtained with the original protocol. This study highlights the importance of considering exposure time to the CCT when designing experiments and suggests two mitigation strategies to improve the utility of this psychophysical assessment.
format: application/pdf
format: text/html
creator: Daniel Blustein
creator: Satinder Gill
creator: Adam Wilson
creator: Jon Sensinger
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.6976
publisher: PeerJ Inc.
rights: © 2019 Blustein et al.
abstract: The incorporation of feedback into a person’s body schema is well established. The crossmodal congruency task (CCT) is used to objectively quantify incorporation without being susceptible to experimenter biases. This visual-tactile interference task is used to calculate the crossmodal congruency effect (CCE) score as a difference in response time between incongruent and congruent trials. Here we show that this metric is susceptible to a learning effect that causes attenuation of the CCE score due to repeated task exposure sessions. We demonstrate that this learning effect is persistent, even after a 6 month hiatus in testing. Two mitigation strategies are proposed: 1. Only use CCE scores that are taken after learning has stabilized, or 2. Use a modified CCT protocol that decreases the task exposure time. We show that the modified and shortened CCT protocol, which may be required to meet time or logistical constraints in laboratory or clinical settings, reduced the impact of the learning effect on CCT results. Importantly, the CCE scores from the modified protocol were not significantly more variable than results obtained with the original protocol. This study highlights the importance of considering exposure time to the CCT when designing experiments and suggests two mitigation strategies to improve the utility of this psychophysical assessment.
bibliographic citation: Blustein et al. (2019) Crossmodal congruency effect scores decrease with repeat test exposure. PeerJ 7:e6976 https://doi.org/10.7717/peerj.6976
date submitted: 2018-09-27
date accepted: 2019-04-18
issued: 2019-05-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Blustein
  given name: Daniel
author list: Agent
  family name: Gill
  given name: Satinder
author list: Agent
  family name: Wilson
  given name: Adam
author list: Agent
  family name: Sensinger
  given name: Jon
doi: 10.7717/peerj.6976
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-22
copyright: ©2019 Blustein et al.
attribution name: Blustein et al.

Purification of plant-derived anti-virus mAb through optimized pH conditions for coupling between protein A and epoxy-activated beads
type: item
type: AcademicArticle
description: The main goal of this research was to determine optimum pH conditions for coupling between protein A and epoxy-activated Sepharose beads for purification of monoclonal antibodies (mAbs) expressed in plants. To confirm the effect of pH conditions on purification efficacy, epoxy-activated agarose beads were coupled to protein A under the pH conditions of 8.5, 9.5, 10.5, and 11.5 (8.5R, 9.5R, 10.5R, and 11.5R, respectively). A total of 300 g of fresh leaf tissue of transgenic Arabidopsis expressing human anti-rabies mAb (mAbP) SO57 were harvested to isolate the total soluble protein (TSP). An equal amount of TSP solution was applied to five resin groups including commercial protein A resin (GR) as a positive control. The modified 8.5R, 9.5R, 10.5R, and 11.5R showed delayed elution timing compared to the GR control resin. Nano-drop analysis showed that the total amount of purified mAbPSO57 mAbs from 60 g of fresh leaf mass were not significantly different among 8.5R (400 μg), 9.5R (360 μg), 10.5R (380 μg), and GR (350 μg). The 11.5R (25 μg) had the least mAbPSO57. SDS–PAGE analysis showed that the purity of mAbPSO57 was not significantly different among the five groups. Rapid fluorescent focus inhibition tests revealed that virus-neutralizing efficacies of purified mAbPSO57 from all the five different resins including the positive control resin were similar. Taken together, both pH 8.5 and 10.5 coupling conditions with high recovery rate should be optimized for purification of mAbPSO57 from transgenic Arabidopsis plant, which will eventually reduce down-stream cost required for mAb production using the plant system.
format: application/pdf
format: text/html
creator: Ilchan Song
creator: Yang Joo Kang
creator: Su-Lim Choi
creator: Dalmuri Han
creator: Deuk-Su Kim
creator: Hae Kyung Lee
creator: Joon-Chul Lee
creator: Jeanho Park
creator: Do-Sun Kim
creator: Kisung Ko
subject: Biotechnology
subject: Plant Science
subject: Infectious Diseases
description: doi:10.7717/peerj.6828
publisher: PeerJ Inc.
rights: © 2019 Song et al.
abstract: The main goal of this research was to determine optimum pH conditions for coupling between protein A and epoxy-activated Sepharose beads for purification of monoclonal antibodies (mAbs) expressed in plants. To confirm the effect of pH conditions on purification efficacy, epoxy-activated agarose beads were coupled to protein A under the pH conditions of 8.5, 9.5, 10.5, and 11.5 (8.5R, 9.5R, 10.5R, and 11.5R, respectively). A total of 300 g of fresh leaf tissue of transgenic Arabidopsis expressing human anti-rabies mAb (mAbP) SO57 were harvested to isolate the total soluble protein (TSP). An equal amount of TSP solution was applied to five resin groups including commercial protein A resin (GR) as a positive control. The modified 8.5R, 9.5R, 10.5R, and 11.5R showed delayed elution timing compared to the GR control resin. Nano-drop analysis showed that the total amount of purified mAbPSO57 mAbs from 60 g of fresh leaf mass were not significantly different among 8.5R (400 μg), 9.5R (360 μg), 10.5R (380 μg), and GR (350 μg). The 11.5R (25 μg) had the least mAbPSO57. SDS–PAGE analysis showed that the purity of mAbPSO57 was not significantly different among the five groups. Rapid fluorescent focus inhibition tests revealed that virus-neutralizing efficacies of purified mAbPSO57 from all the five different resins including the positive control resin were similar. Taken together, both pH 8.5 and 10.5 coupling conditions with high recovery rate should be optimized for purification of mAbPSO57 from transgenic Arabidopsis plant, which will eventually reduce down-stream cost required for mAb production using the plant system.
bibliographic citation: Song et al. (2019) Purification of plant-derived anti-virus mAb through optimized pH conditions for coupling between protein A and epoxy-activated beads. PeerJ 7:e6828 https://doi.org/10.7717/peerj.6828
date submitted: 2018-09-18
date accepted: 2019-03-20
issued: 2019-05-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Song
  given name: Ilchan
author list: Agent
  family name: Kang
  given name: Yang Joo
author list: Agent
  family name: Choi
  given name: Su-Lim
author list: Agent
  family name: Han
  given name: Dalmuri
author list: Agent
  family name: Kim
  given name: Deuk-Su
author list: Agent
  family name: Lee
  given name: Hae Kyung
author list: Agent
  family name: Lee
  given name: Joon-Chul
author list: Agent
  family name: Park
  given name: Jeanho
author list: Agent
  family name: Kim
  given name: Do-Sun
author list: Agent
  family name: Ko
  given name: Kisung
doi: 10.7717/peerj.6828
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-21
copyright: © 2019 Song et al.
attribution name: Song et al.

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