PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: A new therocephalian (Gorynychus masyutinae gen. et sp. nov.) from the Permian Kotelnich locality, Kirov Region, Russia
items: Literature-based latitudinal distribution and possible range shifts of two US east coast dune grass species (Uniola paniculata and Ammophila breviligulata)
items: MipLAAO, a new L-amino acid oxidase from the redtail coral snake Micrurus mipartitus
items: ­Characterization of pyruvate kinase from the anoxia tolerant turtle, Trachemys scripta elegans: a potential role for enzyme methylation during metabolic rate depression
items: Does bathymetry drive coastal whale shark (Rhincodon typus) aggregations?
items: Actively transcribed and expressed atp8 gene in Mytilus edulis mussels
items: The first tetrapod from the mid-Miocene Clarkia lagerstätte (Idaho, USA)
items: Scan, extract, wrap, compute—a 3D method to analyse morphological shape differences
items: Soft-bottom fishes and spatial protection: findings from a temperate marine protected area
items: Effect of acute augmented feedback on between limb asymmetries and eccentric knee flexor strength during the Nordic hamstring exercise

A new therocephalian (Gorynychus masyutinae gen. et sp. nov.) from the Permian Kotelnich locality, Kirov Region, Russia
type: item
type: AcademicArticle
description: A new therocephalian taxon (Gorynychus masyutinae gen. et sp. nov.) is described based on a nearly complete skull and partial postcranium from the Permian Kotelnich locality of Russia. Gorynychus displays an unusual mixture of primitive (“pristerosaurian”) and derived (eutherocephalian) characters. Primitive features of Gorynychus include extensive dentition on the palatal boss and transverse process of the pterygoid, paired vomers, and a prominent dentary angle; derived features include the absence of the postfrontal. Gorynychus can be distinguished from all other therocephalians by its autapomorphic dental morphology, with roughly denticulated incisors and postcanines. Phylogenetic analysis recovers Gorynychus as a non-lycosuchid, non-scylacosaurid therocephalian situated as sister-taxon to Eutherocephalia. The identification of Gorynychus as the largest predator from Kotelnich indicates that therocephalians acted as apex predators in middle–late Permian transition ecosystems in Russia, corroborating a pattern observed in South African faunas. However, other aspects of the Kotelnich fauna, and Permian Russian tetrapod faunas in general, differ markedly from those of South Africa and suggest that Karoo faunas are not necessarily representative of global patterns.
format: application/pdf
format: text/html
creator: Christian F. Kammerer
creator: Vladimir Masyutin
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.4933
publisher: PeerJ Inc.
rights: © 2018 Kammerer and Masyutin
abstract: A new therocephalian taxon (Gorynychus masyutinae gen. et sp. nov.) is described based on a nearly complete skull and partial postcranium from the Permian Kotelnich locality of Russia. Gorynychus displays an unusual mixture of primitive (“pristerosaurian”) and derived (eutherocephalian) characters. Primitive features of Gorynychus include extensive dentition on the palatal boss and transverse process of the pterygoid, paired vomers, and a prominent dentary angle; derived features include the absence of the postfrontal. Gorynychus can be distinguished from all other therocephalians by its autapomorphic dental morphology, with roughly denticulated incisors and postcanines. Phylogenetic analysis recovers Gorynychus as a non-lycosuchid, non-scylacosaurid therocephalian situated as sister-taxon to Eutherocephalia. The identification of Gorynychus as the largest predator from Kotelnich indicates that therocephalians acted as apex predators in middle–late Permian transition ecosystems in Russia, corroborating a pattern observed in South African faunas. However, other aspects of the Kotelnich fauna, and Permian Russian tetrapod faunas in general, differ markedly from those of South Africa and suggest that Karoo faunas are not necessarily representative of global patterns.
bibliographic citation: Kammerer et al. (2018) A new therocephalian (Gorynychus masyutinae gen. et sp. nov.) from the Permian Kotelnich locality, Kirov Region, Russia. PeerJ 6:e4933 https://doi.org/10.7717/peerj.4933
date submitted: 2018-03-15
date accepted: 2018-05-17
issued: 2018-06-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kammerer
  given name: Christian F.
author list: Agent
  family name: Masyutin
  given name: Vladimir
doi: 10.7717/peerj.4933
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-08
copyright: © 2018 Kammerer and Masyutin
attribution name: Kammerer and Masyutin

Literature-based latitudinal distribution and possible range shifts of two US east coast dune grass species (Uniola paniculata and Ammophila breviligulata)
type: item
type: AcademicArticle
description: Previous work on the US Atlantic coast has generally shown that coastal foredunes are dominated by two dune grass species, Ammophila breviligulata (American beachgrass) and Uniola paniculata (sea oats). From Virginia northward, A. breviligulata dominates, while U. paniculata is the dominant grass south of Virginia. Previous work suggests that these grasses influence the shape of coastal foredunes in species-specific ways, and that they respond differently to environmental stressors; thus, it is important to know which species dominates a given dune system. The range boundaries of these two species remains unclear given the lack of comprehensive surveys. In an attempt to determine these boundaries, we conducted a literature survey of 98 studies that either stated the range limits and/or included field-based studies/observations of the two grass species. We then produced an interactive map that summarizes the locations of the surveyed papers and books. The literature review suggests that the current southern range limit for A. breviligulata is Cape Fear, NC, and the northern range limit for U. paniculata is Assateague Island, on the Maryland and Virginia border. Our data suggest a northward expansion of U. paniculata, possibly associated with warming trends observed near the northern range limit in Painter, VA. In contrast, the data regarding a range shift for A. breviligulata remain inconclusive. We also compare our literature-based map with geolocated records from the Global Biodiversity Information Facility and iNaturalist research grade crowd-sourced observations. We intend for our literature-based map to aid coastal researchers who are interested in the dynamics of these two species and the potential for their ranges to shift as a result of climate change.
format: application/pdf
format: text/html
creator: Evan B. Goldstein
creator: Elsemarie V. Mullins
creator: Laura J. Moore
creator: Reuben G. Biel
creator: Joseph K. Brown
creator: Sally D. Hacker
creator: Katya R. Jay
creator: Rebecca S. Mostow
creator: Peter Ruggiero
creator: Julie C. Zinnert
subject: Biosphere Interactions
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.4932
publisher: PeerJ Inc.
rights: © 2018 Goldstein et al.
abstract: Previous work on the US Atlantic coast has generally shown that coastal foredunes are dominated by two dune grass species, Ammophila breviligulata (American beachgrass) and Uniola paniculata (sea oats). From Virginia northward, A. breviligulata dominates, while U. paniculata is the dominant grass south of Virginia. Previous work suggests that these grasses influence the shape of coastal foredunes in species-specific ways, and that they respond differently to environmental stressors; thus, it is important to know which species dominates a given dune system. The range boundaries of these two species remains unclear given the lack of comprehensive surveys. In an attempt to determine these boundaries, we conducted a literature survey of 98 studies that either stated the range limits and/or included field-based studies/observations of the two grass species. We then produced an interactive map that summarizes the locations of the surveyed papers and books. The literature review suggests that the current southern range limit for A. breviligulata is Cape Fear, NC, and the northern range limit for U. paniculata is Assateague Island, on the Maryland and Virginia border. Our data suggest a northward expansion of U. paniculata, possibly associated with warming trends observed near the northern range limit in Painter, VA. In contrast, the data regarding a range shift for A. breviligulata remain inconclusive. We also compare our literature-based map with geolocated records from the Global Biodiversity Information Facility and iNaturalist research grade crowd-sourced observations. We intend for our literature-based map to aid coastal researchers who are interested in the dynamics of these two species and the potential for their ranges to shift as a result of climate change.
bibliographic citation: Goldstein et al. (2018) Literature-based latitudinal distribution and possible range shifts of two US east coast dune grass species (Uniola paniculata and Ammophila breviligulata). PeerJ 6:e4932 https://doi.org/10.7717/peerj.4932
date submitted: 2018-02-07
date accepted: 2018-05-18
issued: 2018-06-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Goldstein
  given name: Evan B.
author list: Agent
  family name: Mullins
  given name: Elsemarie V.
author list: Agent
  family name: Moore
  given name: Laura J.
author list: Agent
  family name: Biel
  given name: Reuben G.
author list: Agent
  family name: Brown
  given name: Joseph K.
author list: Agent
  family name: Hacker
  given name: Sally D.
author list: Agent
  family name: Jay
  given name: Katya R.
author list: Agent
  family name: Mostow
  given name: Rebecca S.
author list: Agent
  family name: Ruggiero
  given name: Peter
author list: Agent
  family name: Zinnert
  given name: Julie C.
doi: 10.7717/peerj.4932
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-08
copyright: © 2018 Goldstein et al.
attribution name: Goldstein et al.

MipLAAO, a new L-amino acid oxidase from the redtail coral snake Micrurus mipartitus
type: item
type: AcademicArticle
description: L-amino acid oxidases (LAAOs) are ubiquitous enzymes in nature. Bioactivities described for these enzymes include apoptosis induction, edema formation, induction or inhibition of platelet aggregation, as well as antiviral, antiparasite, and antibacterial actions. With over 80 species, Micrurus snakes are the representatives of the Elapidae family in the New World. Although LAAOs in Micrurus venoms have been predicted by venom gland transcriptomic studies and detected in proteomic studies, no enzymes of this kind have been previously purified from their venoms. Earlier proteomic studies revealed that the venom of M. mipartitus from Colombia contains ∼4% of LAAO. This enzyme, here named MipLAAO, was isolated and biochemically and functionally characterized. The enzyme is found in monomeric form, with an isotope-averaged molecular mass of 59,100.6 Da, as determined by MALDI-TOF. Its oxidase activity shows substrate preference for hydrophobic amino acids, being optimal at pH 8.0. By nucleotide sequencing of venom gland cDNA of mRNA transcripts obtained from a single snake, six isoforms of MipLAAO with minor variations among them were retrieved. The deduced sequences present a mature chain of 483 amino acids, with a predicted pI of 8.9, and theoretical masses between 55,010.9 and 55,121.0 Da. The difference with experimentally observed mass is likely due to glycosylation, in agreement with the finding of three putative N-glycosylation sites in its amino acid sequence. A phylogenetic analysis of MmipLAAO placed this new enzyme within the clade of homologous proteins from elapid snakes, characterized by the conserved Serine at position 223, in contrast to LAAOs from viperids. MmipLAAO showed a potent bactericidal effect on S. aureus (MIC: 2 µg/mL), but not on E. coli. The former activity could be of interest to future studies assessing its potential as antimicrobial agent.
format: application/pdf
format: text/html
creator: Paola Rey-Suárez
creator: Cristian Acosta
creator: Uday Torres
creator: Mónica Saldarriaga-Córdoba
creator: Bruno Lomonte
creator: Vitelbina Núñez
subject: Biochemistry
subject: Biotechnology
subject: Microbiology
subject: Toxicology
description: doi:10.7717/peerj.4924
publisher: PeerJ Inc.
rights: © 2018 Rey-Suárez et al.
abstract: L-amino acid oxidases (LAAOs) are ubiquitous enzymes in nature. Bioactivities described for these enzymes include apoptosis induction, edema formation, induction or inhibition of platelet aggregation, as well as antiviral, antiparasite, and antibacterial actions. With over 80 species, Micrurus snakes are the representatives of the Elapidae family in the New World. Although LAAOs in Micrurus venoms have been predicted by venom gland transcriptomic studies and detected in proteomic studies, no enzymes of this kind have been previously purified from their venoms. Earlier proteomic studies revealed that the venom of M. mipartitus from Colombia contains ∼4% of LAAO. This enzyme, here named MipLAAO, was isolated and biochemically and functionally characterized. The enzyme is found in monomeric form, with an isotope-averaged molecular mass of 59,100.6 Da, as determined by MALDI-TOF. Its oxidase activity shows substrate preference for hydrophobic amino acids, being optimal at pH 8.0. By nucleotide sequencing of venom gland cDNA of mRNA transcripts obtained from a single snake, six isoforms of MipLAAO with minor variations among them were retrieved. The deduced sequences present a mature chain of 483 amino acids, with a predicted pI of 8.9, and theoretical masses between 55,010.9 and 55,121.0 Da. The difference with experimentally observed mass is likely due to glycosylation, in agreement with the finding of three putative N-glycosylation sites in its amino acid sequence. A phylogenetic analysis of MmipLAAO placed this new enzyme within the clade of homologous proteins from elapid snakes, characterized by the conserved Serine at position 223, in contrast to LAAOs from viperids. MmipLAAO showed a potent bactericidal effect on S. aureus (MIC: 2 µg/mL), but not on E. coli. The former activity could be of interest to future studies assessing its potential as antimicrobial agent.
bibliographic citation: Rey-Suárez et al. (2018) MipLAAO, a new L-amino acid oxidase from the redtail coral snake Micrurus mipartitus. PeerJ 6:e4924 https://doi.org/10.7717/peerj.4924
date submitted: 2018-03-16
date accepted: 2018-05-17
issued: 2018-06-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rey-Suárez
  given name: Paola
author list: Agent
  family name: Acosta
  given name: Cristian
author list: Agent
  family name: Torres
  given name: Uday
author list: Agent
  family name: Saldarriaga-Córdoba
  given name: Mónica
author list: Agent
  family name: Lomonte
  given name: Bruno
author list: Agent
  family name: Núñez
  given name: Vitelbina
doi: 10.7717/peerj.4924
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-08
copyright: ©2018 Rey-Suárez et al.
attribution name: Rey-Suárez et al.

­Characterization of pyruvate kinase from the anoxia tolerant turtle, Trachemys scripta elegans: a potential role for enzyme methylation during metabolic rate depression
type: item
type: AcademicArticle
description: Background Pyruvate kinase (PK) is responsible for the final reaction in glycolysis. As PK is a glycolytic control point, the analysis of PK posttranslational modifications (PTM) and kinetic changes reveals a key piece of the reorganization of energy metabolism in an anoxia tolerant vertebrate. Methods To explore PK regulation, the enzyme was isolated from red skeletal muscle and liver of aerobic and 20-hr anoxia-exposed red eared-slider turtles (Trachemys scripta elegans). Kinetic analysis and immunoblotting were used to assess enzyme function and the corresponding covalent modifications to the enzymes structure during anoxia. Results Both muscle and liver isoforms showed decreased affinity for phosphoenolpyruvate substrate during anoxia, and muscle PK also had a lower affinity for ADP. I50 values for the inhibitors ATP and lactate were lower for PK from both tissues after anoxic exposure while I50 L-alanine was only reduced in the liver. Both isozymes showed significant increases in threonine phosphorylation (by 42% in muscle and 60% in liver) and lysine methylation (by 43% in muscle and 70% in liver) during anoxia which have been linked to suppression of PK activity in other organisms. Liver PK also showed a 26% decrease in tyrosine phosphorylation under anoxia. Discussion Anoxia responsive changes in turtle muscle and liver PK coordinate with an overall reduced activity state. This reduced affinity for the forward glycolytic reaction is likely a key component of the overall metabolic rate depression that supports long term survival in anoxia tolerant turtles. The coinciding methyl- and phospho- PTM alterations present the mechanism for tissue specific enzyme modification during anoxia.
format: application/pdf
format: text/html
creator: Amanda M.S. Mattice
creator: Isabelle A. MacLean
creator: Christine L. Childers
creator: Kenneth B. Storey
subject: Biochemistry
subject: Molecular Biology
description: doi:10.7717/peerj.4918
publisher: PeerJ Inc.
rights: © 2018 Mattice et al.
abstract: Background Pyruvate kinase (PK) is responsible for the final reaction in glycolysis. As PK is a glycolytic control point, the analysis of PK posttranslational modifications (PTM) and kinetic changes reveals a key piece of the reorganization of energy metabolism in an anoxia tolerant vertebrate. Methods To explore PK regulation, the enzyme was isolated from red skeletal muscle and liver of aerobic and 20-hr anoxia-exposed red eared-slider turtles (Trachemys scripta elegans). Kinetic analysis and immunoblotting were used to assess enzyme function and the corresponding covalent modifications to the enzymes structure during anoxia. Results Both muscle and liver isoforms showed decreased affinity for phosphoenolpyruvate substrate during anoxia, and muscle PK also had a lower affinity for ADP. I50 values for the inhibitors ATP and lactate were lower for PK from both tissues after anoxic exposure while I50 L-alanine was only reduced in the liver. Both isozymes showed significant increases in threonine phosphorylation (by 42% in muscle and 60% in liver) and lysine methylation (by 43% in muscle and 70% in liver) during anoxia which have been linked to suppression of PK activity in other organisms. Liver PK also showed a 26% decrease in tyrosine phosphorylation under anoxia. Discussion Anoxia responsive changes in turtle muscle and liver PK coordinate with an overall reduced activity state. This reduced affinity for the forward glycolytic reaction is likely a key component of the overall metabolic rate depression that supports long term survival in anoxia tolerant turtles. The coinciding methyl- and phospho- PTM alterations present the mechanism for tissue specific enzyme modification during anoxia.
bibliographic citation: Mattice et al. (2018) ­Characterization of pyruvate kinase from the anoxia tolerant turtle, Trachemys scripta elegans: a potential role for enzyme methylation during metabolic rate depression. PeerJ 6:e4918 https://doi.org/10.7717/peerj.4918
date submitted: 2018-03-15
date accepted: 2018-05-16
issued: 2018-06-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mattice
  given name: Amanda M.S.
author list: Agent
  family name: MacLean
  given name: Isabelle A.
author list: Agent
  family name: Childers
  given name: Christine L.
author list: Agent
  family name: Storey
  given name: Kenneth B.
doi: 10.7717/peerj.4918
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-08
copyright: ©2018 Mattice et al.
attribution name: Mattice et al.

Does bathymetry drive coastal whale shark (Rhincodon typus) aggregations?
type: item
type: AcademicArticle
description: Background The whale shark (Rhincodon typus) is known to aggregate in a number of coastal locations globally, however what causes these aggregations to form where they do is largely unknown. This study examines whether bathymetry is an important driver of coastal aggregation locations for R. typus through bathymetry’s effect on primary productivity and prey availability. This is a global study taking into account all coastal areas within R. typus’ range. Methods R. typus aggregation locations were identified through an extensive literature review. Global bathymetric data were compared at R. typus aggregation locations and a large random selection of non-aggregation areas. Generalised linear models were used to assess which bathymetric characteristic had the biggest influence on aggregation presence. Results Aggregation sites were significantly shallower than non-aggregation sites and in closer proximity to deep water (the mesopelagic zone) by two orders of magnitude. Slope at aggregation sites was significantly steeper than non-aggregation sites. These three bathymetric variables were shown to have the biggest association with aggregation sites, with up to 88% of deviation explained by the GLMs. Discussion The three key bathymetric characteristics similar at the aggregation sites are known to induce upwelling events, increase primary productivity and consequently attract numerous other filter feeding species. The location of aggregation sites in these key areas can be attributed to this increased prey availability, thought to be the main reason R. typus aggregations occur, extensively outlined in the literature. The proximity of aggregations to shallow areas such as reefs could also be an important factor why whale sharks thermoregulate after deep dives to feed. These findings increase our understanding of whale shark behaviour and may help guide the identification and conservation of further aggregation sites.
format: application/pdf
format: text/html
creator: Joshua P. Copping
creator: Bryce D. Stewart
creator: Colin J. McClean
creator: James Hancock
creator: Richard Rees
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Conservation Biology
subject: Marine Biology
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.4904
publisher: PeerJ Inc.
rights: © 2018 Copping et al.
abstract: Background The whale shark (Rhincodon typus) is known to aggregate in a number of coastal locations globally, however what causes these aggregations to form where they do is largely unknown. This study examines whether bathymetry is an important driver of coastal aggregation locations for R. typus through bathymetry’s effect on primary productivity and prey availability. This is a global study taking into account all coastal areas within R. typus’ range. Methods R. typus aggregation locations were identified through an extensive literature review. Global bathymetric data were compared at R. typus aggregation locations and a large random selection of non-aggregation areas. Generalised linear models were used to assess which bathymetric characteristic had the biggest influence on aggregation presence. Results Aggregation sites were significantly shallower than non-aggregation sites and in closer proximity to deep water (the mesopelagic zone) by two orders of magnitude. Slope at aggregation sites was significantly steeper than non-aggregation sites. These three bathymetric variables were shown to have the biggest association with aggregation sites, with up to 88% of deviation explained by the GLMs. Discussion The three key bathymetric characteristics similar at the aggregation sites are known to induce upwelling events, increase primary productivity and consequently attract numerous other filter feeding species. The location of aggregation sites in these key areas can be attributed to this increased prey availability, thought to be the main reason R. typus aggregations occur, extensively outlined in the literature. The proximity of aggregations to shallow areas such as reefs could also be an important factor why whale sharks thermoregulate after deep dives to feed. These findings increase our understanding of whale shark behaviour and may help guide the identification and conservation of further aggregation sites.
bibliographic citation: Copping et al. (2018) Does bathymetry drive coastal whale shark (Rhincodon typus) aggregations?. PeerJ 6:e4904 https://doi.org/10.7717/peerj.4904
date submitted: 2018-02-10
date accepted: 2018-05-13
issued: 2018-06-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Copping
  given name: Joshua P.
author list: Agent
  family name: Stewart
  given name: Bryce D.
author list: Agent
  family name: McClean
  given name: Colin J.
author list: Agent
  family name: Hancock
  given name: James
author list: Agent
  family name: Rees
  given name: Richard
doi: 10.7717/peerj.4904
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-08
copyright: ©2018 Copping et al.
attribution name: Copping et al.

Actively transcribed and expressed atp8 gene in Mytilus edulis mussels
type: item
type: AcademicArticle
description: Background Animal mitochondrial genomes typically encode 37 genes: 13 proteins, 22 tRNAs and two rRNAs. However, many species represent exceptions to that rule. Bivalvia along with Nematoda and Platyhelminthes are often suspected to fully or partially lack the ATP synthase subunit 8 (atp8) gene. This raises the question as to whether they are really lacking this gene or is this maybe an annotation problem? Among bivalves, Mytilus edulis has been inferred to lack an ATP8 gene since the characterization of its mitochondrial genome in 1992. Even though recent bioinformatic analyses suggested that atp8 is present in Mytilus spp., due to high divergence in predicted amino acid sequences, the existence of a functional atp8 gene in this group remains controversial. Results Here we demonstrate that M. edulis mitochondrial open reading frames suggested to be atp8 (in male and female mtDNAs) are actively translated proteins. We also provide evidence that both proteins are an integral part of the ATP synthase complex based on in-gel detection of ATP synthase activity and two-dimensional Blue-Native and SDS polyacrylamide electrophoresis. Conclusion Many organisms (e.g., Bivalvia along with Nematoda and Platyhelminthes) are considered to be lacking certain mitochondrial genes often only based on poor similarity between protein coding gene sequences in genetically closed species. In some situations, this may lead to the inference that the ATP8 gene is absent, when it is in fact present, but highly divergent. This shows how important complementary role protein-based approaches, such as those in the present study, can provide to bioinformatic, genomic studies (i.e., ability to confirm the presence of a gene).
format: application/pdf
format: text/html
creator: Marek Lubośny
creator: Aleksandra Przyłucka
creator: Beata Śmietanka
creator: Sophie Breton
creator: Artur Burzyński
subject: Genetics
subject: Marine Biology
subject: Molecular Biology
description: doi:10.7717/peerj.4897
publisher: PeerJ Inc.
rights: © 2018 Lubośny et al.
abstract: Background Animal mitochondrial genomes typically encode 37 genes: 13 proteins, 22 tRNAs and two rRNAs. However, many species represent exceptions to that rule. Bivalvia along with Nematoda and Platyhelminthes are often suspected to fully or partially lack the ATP synthase subunit 8 (atp8) gene. This raises the question as to whether they are really lacking this gene or is this maybe an annotation problem? Among bivalves, Mytilus edulis has been inferred to lack an ATP8 gene since the characterization of its mitochondrial genome in 1992. Even though recent bioinformatic analyses suggested that atp8 is present in Mytilus spp., due to high divergence in predicted amino acid sequences, the existence of a functional atp8 gene in this group remains controversial. Results Here we demonstrate that M. edulis mitochondrial open reading frames suggested to be atp8 (in male and female mtDNAs) are actively translated proteins. We also provide evidence that both proteins are an integral part of the ATP synthase complex based on in-gel detection of ATP synthase activity and two-dimensional Blue-Native and SDS polyacrylamide electrophoresis. Conclusion Many organisms (e.g., Bivalvia along with Nematoda and Platyhelminthes) are considered to be lacking certain mitochondrial genes often only based on poor similarity between protein coding gene sequences in genetically closed species. In some situations, this may lead to the inference that the ATP8 gene is absent, when it is in fact present, but highly divergent. This shows how important complementary role protein-based approaches, such as those in the present study, can provide to bioinformatic, genomic studies (i.e., ability to confirm the presence of a gene).
bibliographic citation: Lubośny et al. (2018) Actively transcribed and expressed atp8 gene in Mytilus edulis mussels. PeerJ 6:e4897 https://doi.org/10.7717/peerj.4897
date submitted: 2018-02-14
date accepted: 2018-05-11
issued: 2018-06-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lubośny
  given name: Marek
author list: Agent
  family name: Przyłucka
  given name: Aleksandra
author list: Agent
  family name: Śmietanka
  given name: Beata
author list: Agent
  family name: Breton
  given name: Sophie
author list: Agent
  family name: Burzyński
  given name: Artur
doi: 10.7717/peerj.4897
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-08
copyright: ©2018 Lubośny et al.
attribution name: Lubośny et al.

The first tetrapod from the mid-Miocene Clarkia lagerstätte (Idaho, USA)
type: item
type: AcademicArticle
description: The Clarkia lagerstätte (Latah Formation) of Idaho is well known for its beautifully preserved plant fossils as well as a fauna of insects and fish. Here we present the first known tetrapod fossil from these deposits. This specimen, recovered from the lower anoxic zone of the beds, is preserved as a carbonaceous film of a partial skeleton associated with a partial lower incisor and some tooth fragments. The morphology of the teeth indicates that the first tetrapod reported from Clarkia is a rodent. Its skeletal morphology as well as its bunodont and brachydont dentition suggests that it is a member of the squirrel family (Sciuridae). It is a large specimen that cannot be assigned to a known genus. Instead, it appears to represent the first occurrence of a new taxon with particularly gracile postcranial morphology likely indicative of an arboreal ecology. This new specimen is a rare glimpse into the poorly known arboreal mammal fossil record of the Neogene. It supports a greater taxonomic and ecological diversity of Miocene Sciuridae than previously recognized and offers new lines of inquiry in the paleoecological research enabled by the unique preservation conditions of the Clarkia biota.
format: application/pdf
format: text/html
creator: Jonathan J. M. Calede
creator: John D. Orcutt
creator: Winifred A. Kehl
creator: Bill D. Richards
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.4880
publisher: PeerJ Inc.
rights: © 2018 Calede et al.
abstract: The Clarkia lagerstätte (Latah Formation) of Idaho is well known for its beautifully preserved plant fossils as well as a fauna of insects and fish. Here we present the first known tetrapod fossil from these deposits. This specimen, recovered from the lower anoxic zone of the beds, is preserved as a carbonaceous film of a partial skeleton associated with a partial lower incisor and some tooth fragments. The morphology of the teeth indicates that the first tetrapod reported from Clarkia is a rodent. Its skeletal morphology as well as its bunodont and brachydont dentition suggests that it is a member of the squirrel family (Sciuridae). It is a large specimen that cannot be assigned to a known genus. Instead, it appears to represent the first occurrence of a new taxon with particularly gracile postcranial morphology likely indicative of an arboreal ecology. This new specimen is a rare glimpse into the poorly known arboreal mammal fossil record of the Neogene. It supports a greater taxonomic and ecological diversity of Miocene Sciuridae than previously recognized and offers new lines of inquiry in the paleoecological research enabled by the unique preservation conditions of the Clarkia biota.
bibliographic citation: Calede et al. (2018) The first tetrapod from the mid-Miocene Clarkia lagerstätte (Idaho, USA). PeerJ 6:e4880 https://doi.org/10.7717/peerj.4880
date submitted: 2018-02-01
date accepted: 2018-05-10
issued: 2018-06-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Calede
  given name: Jonathan J. M.
author list: Agent
  family name: Orcutt
  given name: John D.
author list: Agent
  family name: Kehl
  given name: Winifred A.
author list: Agent
  family name: Richards
  given name: Bill D.
doi: 10.7717/peerj.4880
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-08
copyright: © 2018 Calede et al.
attribution name: Calede et al.

Scan, extract, wrap, compute—a 3D method to analyse morphological shape differences
type: item
type: AcademicArticle
description: Quantitative analysis of shape and form is critical in many biological disciplines, as context-dependent morphotypes reflect changes in gene expression and physiology, e.g., in comparisons of environment-dependent phenotypes, forward/reverse genetic assays or shape development during ontogenesis. 3D-shape rendering methods produce models with arbitrarily numbered, and therefore non-comparable, mesh points. However, this prevents direct comparisons. We introduce a workflow that allows the generation of comparable 3D models based on several specimens. Translocations between points of modelled morphotypes are plotted as heat maps and statistically tested. With this workflow, we are able to detect, model and investigate the significance of shape and form alterations in all spatial dimensions, demonstrated with different morphotypes of the pond-dwelling microcrustacean Daphnia. Furthermore, it allows the detection even of inconspicuous morphological features that can be exported to programs for subsequent analysis, e.g., streamline- or finite-element analysis.
format: application/pdf
format: text/html
creator: Martin Horstmann
creator: Alexander T. Topham
creator: Petra Stamm
creator: Sebastian Kruppert
creator: John K. Colbourne
creator: Ralph Tollrian
creator: Linda C. Weiss
subject: Computational Biology
subject: Ecology
subject: Computational Science
description: doi:10.7717/peerj.4861
publisher: PeerJ Inc.
rights: © 2018 Horstmann et al.
abstract: Quantitative analysis of shape and form is critical in many biological disciplines, as context-dependent morphotypes reflect changes in gene expression and physiology, e.g., in comparisons of environment-dependent phenotypes, forward/reverse genetic assays or shape development during ontogenesis. 3D-shape rendering methods produce models with arbitrarily numbered, and therefore non-comparable, mesh points. However, this prevents direct comparisons. We introduce a workflow that allows the generation of comparable 3D models based on several specimens. Translocations between points of modelled morphotypes are plotted as heat maps and statistically tested. With this workflow, we are able to detect, model and investigate the significance of shape and form alterations in all spatial dimensions, demonstrated with different morphotypes of the pond-dwelling microcrustacean Daphnia. Furthermore, it allows the detection even of inconspicuous morphological features that can be exported to programs for subsequent analysis, e.g., streamline- or finite-element analysis.
bibliographic citation: Horstmann et al. (2018) Scan, extract, wrap, compute—a 3D method to analyse morphological shape differences. PeerJ 6:e4861 https://doi.org/10.7717/peerj.4861
date submitted: 2017-06-30
date accepted: 2018-05-07
issued: 2018-06-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Horstmann
  given name: Martin
author list: Agent
  family name: Topham
  given name: Alexander T.
author list: Agent
  family name: Stamm
  given name: Petra
author list: Agent
  family name: Kruppert
  given name: Sebastian
author list: Agent
  family name: Colbourne
  given name: John K.
author list: Agent
  family name: Tollrian
  given name: Ralph
author list: Agent
  family name: Weiss
  given name: Linda C.
doi: 10.7717/peerj.4861
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-08
copyright: ©2018 Horstmann et al.
attribution name: Horstmann et al.

Soft-bottom fishes and spatial protection: findings from a temperate marine protected area
type: item
type: AcademicArticle
description: Numerous studies over the last decades have focused on marine protected areas (MPAs) and their effects on fish communities. However, there is a knowledge gap regarding how species that live associated with soft-substrates (e.g., sand, mud) respond to spatial protection. We analyzed abundance, biomass and total lengths of the soft-bottom fishes in a multiple-use MPA in the north-eastern Atlantic, the Luiz Saldanha Marine Park (Portugal), during and after the implementation of its management plan. Data were collected by experimental fishing in areas with three different levels of protection, during the implementation period and for three years after full implementation of the MPA. Univariate analysis detected significant biomass increases between the two periods. Fish assemblages were mainly structured by depth and substrate, followed by protection level. Community composition analyses revealed significant differences between protection levels and between the two periods. Species exhibited a broad variation in their response to protection, and we hypothesize that factors such as species habitat preferences, body size and late maturity might be underlying determinants. Overall, this study provides some evidence of protection effectiveness in soft-bottom fish communities, supported by the significant increase in biomass in the protected areas and the positive trends of some species.
format: application/pdf
format: text/html
creator: Inês Sousa
creator: Jorge M.S. Gonçalves
creator: Joachim Claudet
creator: Rui Coelho
creator: Emanuel J. Gonçalves
creator: Karim Erzini
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
subject: Natural Resource Management
description: doi:10.7717/peerj.4653
publisher: PeerJ Inc.
rights: © 2018 Sousa et al.
abstract: Numerous studies over the last decades have focused on marine protected areas (MPAs) and their effects on fish communities. However, there is a knowledge gap regarding how species that live associated with soft-substrates (e.g., sand, mud) respond to spatial protection. We analyzed abundance, biomass and total lengths of the soft-bottom fishes in a multiple-use MPA in the north-eastern Atlantic, the Luiz Saldanha Marine Park (Portugal), during and after the implementation of its management plan. Data were collected by experimental fishing in areas with three different levels of protection, during the implementation period and for three years after full implementation of the MPA. Univariate analysis detected significant biomass increases between the two periods. Fish assemblages were mainly structured by depth and substrate, followed by protection level. Community composition analyses revealed significant differences between protection levels and between the two periods. Species exhibited a broad variation in their response to protection, and we hypothesize that factors such as species habitat preferences, body size and late maturity might be underlying determinants. Overall, this study provides some evidence of protection effectiveness in soft-bottom fish communities, supported by the significant increase in biomass in the protected areas and the positive trends of some species.
bibliographic citation: Sousa et al. (2018) Soft-bottom fishes and spatial protection: findings from a temperate marine protected area. PeerJ 6:e4653 https://doi.org/10.7717/peerj.4653
date submitted: 2017-07-15
date accepted: 2018-03-30
issued: 2018-06-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sousa
  given name: Inês
author list: Agent
  family name: Gonçalves
  given name: Jorge M.S.
author list: Agent
  family name: Claudet
  given name: Joachim
author list: Agent
  family name: Coelho
  given name: Rui
author list: Agent
  family name: Gonçalves
  given name: Emanuel J.
author list: Agent
  family name: Erzini
  given name: Karim
doi: 10.7717/peerj.4653
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-08
copyright: ©2018 Sousa et al.
attribution name: Sousa et al.

Effect of acute augmented feedback on between limb asymmetries and eccentric knee flexor strength during the Nordic hamstring exercise
type: item
type: AcademicArticle
description: Background Hamstring strain injuries (HSI) are one of the most prevalent and serious injuries affecting athletes, particularly those in team ball sports or track and field. Recent evidence demonstrates that eccentric knee flexor weakness and between limb asymmetries are possible risk factors for HSIs. While eccentric hamstring resistance training, e.g. the Nordic hamstring exercise (NHE) significantly increases eccentric hamstring strength and reduces HSI risk, little research has examined whether between limb asymmetries can be reduced with training. As augmented feedback (AF) can produce significant acute and chronic increases in muscular strength and reduce injury risk, one way to address the limitation in the eccentric hamstring training literature may be to provide athletes real-time visual AF of their NHE force outputs with the goal to minimise the between limb asymmetry. Methods Using a cross over study design, 44 injury free, male cricket players from two skill levels performed two NHE sessions on a testing device. The two NHE sessions were identical with the exception of AF, with the two groups randomised to perform the sessions with and without visual feedback of each limb’s force production in real-time. When performing the NHE with visual AF, the participants were provided with the following instructions to ‘reduce limb asymmetries as much as possible using the real-time visual force outputs displayed in front them’. Between limb asymmetries and mean peak force outputs were compared between the two feedback conditions (FB1 and FB2) using independent t-tests to ensure there was no carryover effect, and to determine any period and treatment effects. The magnitude of the differences in the force outputs were also examined using Cohen d effect size. Results There was a significant increase in mean peak force production when feedback was provided (mean difference, 21.7 N; 95% CI [0.2–42.3 N]; P = 0.048; d = 0.61) and no significant difference in between limb …
format: application/pdf
format: text/html
creator: Wade J. Chalker
creator: Anthony J. Shield
creator: David A. Opar
creator: Evelyne N. Rathbone
creator: Justin W.L. Keogh
subject: Anatomy and Physiology
subject: Kinesiology
description: doi:10.7717/peerj.4972
publisher: PeerJ Inc.
rights: © 2018 Chalker et al.
abstract: Background Hamstring strain injuries (HSI) are one of the most prevalent and serious injuries affecting athletes, particularly those in team ball sports or track and field. Recent evidence demonstrates that eccentric knee flexor weakness and between limb asymmetries are possible risk factors for HSIs. While eccentric hamstring resistance training, e.g. the Nordic hamstring exercise (NHE) significantly increases eccentric hamstring strength and reduces HSI risk, little research has examined whether between limb asymmetries can be reduced with training. As augmented feedback (AF) can produce significant acute and chronic increases in muscular strength and reduce injury risk, one way to address the limitation in the eccentric hamstring training literature may be to provide athletes real-time visual AF of their NHE force outputs with the goal to minimise the between limb asymmetry. Methods Using a cross over study design, 44 injury free, male cricket players from two skill levels performed two NHE sessions on a testing device. The two NHE sessions were identical with the exception of AF, with the two groups randomised to perform the sessions with and without visual feedback of each limb’s force production in real-time. When performing the NHE with visual AF, the participants were provided with the following instructions to ‘reduce limb asymmetries as much as possible using the real-time visual force outputs displayed in front them’. Between limb asymmetries and mean peak force outputs were compared between the two feedback conditions (FB1 and FB2) using independent t-tests to ensure there was no carryover effect, and to determine any period and treatment effects. The magnitude of the differences in the force outputs were also examined using Cohen d effect size. Results There was a significant increase in mean peak force production when feedback was provided (mean difference, 21.7 N; 95% CI [0.2–42.3 N]; P = 0.048; d = 0.61) and no significant difference in between limb …
bibliographic citation: Chalker et al. (2018) Effect of acute augmented feedback on between limb asymmetries and eccentric knee flexor strength during the Nordic hamstring exercise. PeerJ 6:e4972 https://doi.org/10.7717/peerj.4972
date submitted: 2018-03-02
date accepted: 2018-05-24
issued: 2018-06-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chalker
  given name: Wade J.
author list: Agent
  family name: Shield
  given name: Anthony J.
author list: Agent
  family name: Opar
  given name: David A.
author list: Agent
  family name: Rathbone
  given name: Evelyne N.
author list: Agent
  family name: Keogh
  given name: Justin W.L.
doi: 10.7717/peerj.4972
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-07
copyright: © 2018 Chalker et al.
attribution name: Chalker et al.

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