title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1554 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: ­Characterization of pyruvate kinase from the anoxia tolerant turtle, Trachemys scripta elegans: a potential role for enzyme methylation during metabolic rate depression link: https://peerj.com/articles/4918 last-modified: 2018-06-08 description: BackgroundPyruvate 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.MethodsTo 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.ResultsBoth 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.DiscussionAnoxia 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. creator: Amanda M.S. Mattice creator: Isabelle A. MacLean creator: Christine L. Childers creator: Kenneth B. Storey uri: https://doi.org/10.7717/peerj.4918 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Mattice et al. title: Does bathymetry drive coastal whale shark (Rhincodon typus) aggregations? link: https://peerj.com/articles/4904 last-modified: 2018-06-08 description: BackgroundThe 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.MethodsR. 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.ResultsAggregation 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.DiscussionThe 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. creator: Joshua P. Copping creator: Bryce D. Stewart creator: Colin J. McClean creator: James Hancock creator: Richard Rees uri: https://doi.org/10.7717/peerj.4904 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Copping et al. title: Actively transcribed and expressed atp8 gene in Mytilus edulis mussels link: https://peerj.com/articles/4897 last-modified: 2018-06-08 description: BackgroundAnimal 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.ResultsHere 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.ConclusionMany 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). creator: Marek Lubośny creator: Aleksandra Przyłucka creator: Beata Śmietanka creator: Sophie Breton creator: Artur Burzyński uri: https://doi.org/10.7717/peerj.4897 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Lubośny et al. title: The first tetrapod from the mid-Miocene Clarkia lagerstätte (Idaho, USA) link: https://peerj.com/articles/4880 last-modified: 2018-06-08 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. creator: Jonathan J. M. Calede creator: John D. Orcutt creator: Winifred A. Kehl creator: Bill D. Richards uri: https://doi.org/10.7717/peerj.4880 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Calede et al. title: Scan, extract, wrap, compute—a 3D method to analyse morphological shape differences link: https://peerj.com/articles/4861 last-modified: 2018-06-08 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. creator: Martin Horstmann creator: Alexander T. Topham creator: Petra Stamm creator: Sebastian Kruppert creator: John K. Colbourne creator: Ralph Tollrian creator: Linda C. Weiss uri: https://doi.org/10.7717/peerj.4861 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Horstmann et al. title: Soft-bottom fishes and spatial protection: findings from a temperate marine protected area link: https://peerj.com/articles/4653 last-modified: 2018-06-08 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. creator: Inês Sousa creator: Jorge M.S. Gonçalves creator: Joachim Claudet creator: Rui Coelho creator: Emanuel J. Gonçalves creator: Karim Erzini uri: https://doi.org/10.7717/peerj.4653 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Sousa et al. title: Effect of acute augmented feedback on between limb asymmetries and eccentric knee flexor strength during the Nordic hamstring exercise link: https://peerj.com/articles/4972 last-modified: 2018-06-07 description: BackgroundHamstring 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.MethodsUsing 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.ResultsThere 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 asymmetry for feedback or no feedback (mean difference, 5.7%; 95% CI [−2.8% to 14.3%]; P = 0.184; d = 0.41). Increases in force production under feedback were a result of increased weak limb (mean difference, 15.0 N; 95% CI [1.6–28.5 N]; P = 0.029; d = 0.22) force contribution compared to the strong limb.DiscussionThe results of this study further support the potential utility of AF in improving force production and reducing risk in athletic populations. While there are currently some financial limitations to the application of this training approach, even in high-performance sport, such an approach may improve outcomes for HSI prevention programs. Further research with more homogenous populations over greater periods of time that assess the chronic effect of such training practices on injury risk factors and injury rates are also recommended. creator: Wade J. Chalker creator: Anthony J. Shield creator: David A. Opar creator: Evelyne N. Rathbone creator: Justin W.L. Keogh uri: https://doi.org/10.7717/peerj.4972 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Chalker et al. title: High similarity in the microbiota of cold-water sponges of the Genus Mycale from two different geographical areas link: https://peerj.com/articles/4935 last-modified: 2018-06-07 description: Sponges belonging to genus Mycale are common and widely distributed across the oceans and represent a significant component of benthic communities in term of their biomass, which in many species is largely composed by bacteria. However, the microbial communities associated with Mycale species inhabiting different geographical areas have not been previously compared. Here, we provide the first detailed description of the microbiota of two Mycale species inhabiting the sub-Antarctic Magellan region (53°S) and the Western Antarctic Peninsula (62–64°S), two geographically distant areas (>1,300 km) with contrasting environmental conditions. The sponges Mycale (Aegogropila) magellanica and Mycale (Oxymycale) acerata are both abundant members of benthic communities in the Magellan region and in Antarctica, respectively. High throughput sequencing revealed a remarkable similarity in the microbiota of both sponge species, dominated by Proteobacteria and Bacteroidetes, with both species sharing more than 74% of the OTUs. In contrast, 16% and 10% of the OTUs were found only in either M. magellanica or M. acerata, respectively. Interestingly, despite slight differences in the relative abundance, the most dominant OTUs were present in both species, whereas the unique OTUs had very low abundances (less than 1% of the total abundance). These results show a significant overlap among the microbiota of both Mycale species and also suggest the existence of a low level of specificity of the most dominant symbiont groups. creator: César A. Cárdenas creator: Marcelo González-Aravena creator: Alejandro Font creator: Jon T. Hestetun creator: Eduardo Hajdu creator: Nicole Trefault creator: Maja Malmberg creator: Erik Bongcam-Rudloff uri: https://doi.org/10.7717/peerj.4935 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Cárdenas et al. title: Metal-binding polymorphism in late embryogenesis abundant protein AtLEA4-5, an intrinsically disordered protein link: https://peerj.com/articles/4930 last-modified: 2018-06-07 description: Late embryogenesis abundant (LEA) proteins accumulate in plants during adverse conditions and their main attributed function is to confer tolerance to stress. One of the deleterious effects of the adverse environment is the accumulation of metal ions to levels that generate reactive oxygen species, compromising the survival of cells. AtLEA4-5, a member of group 4 of LEAs in Arabidopsis, is an intrinsically disordered protein. It has been shown that their N-terminal region is able to undergo transitions to partially folded states and prevent the inactivation of enzymes. We have characterized metal ion binding to AtLEA4-5 by circular dichroism, electronic absorbance spectroscopy (UV–vis), electron paramagnetic resonance, dynamic light scattering, and isothermal titration calorimetry. The data shows that AtLEA4-5 contains a single binding site for Ni(II), while Zn(II) and Cu(II) have multiple binding sites and promote oligomerization. The Cu(II) interacts preferentially with histidine residues mostly located in the C-terminal region with moderate affinity and different coordination modes. These results and the lack of a stable secondary structure formation indicate that an ensemble of conformations remains accessible to the metal for binding, suggesting the formation of a fuzzy complex. Our results support the multifunctionality of LEA proteins and suggest that the C-terminal region of AtLEA4-5 could be responsible for antioxidant activity, scavenging metal ions under stress conditions while the N-terminal could function as a chaperone. creator: Leidys French-Pacheco creator: Cesar L. Cuevas-Velazquez creator: Lina Rivillas-Acevedo creator: Alejandra A. Covarrubias creator: Carlos Amero uri: https://doi.org/10.7717/peerj.4930 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 French-Pacheco et al. title: Spatial-temporal variation and impacts of drought in Xinjiang (Northwest China) during 1961–2015 link: https://peerj.com/articles/4926 last-modified: 2018-06-07 description: Observations indicate that temperature and precipitation patterns changed dramatically in Xinjiang, northwestern China, between 1961 and 2015. Dramatic changes in climatic conditions can bring about adverse effects. Specifically, meteorological drought severity based on the standardized precipitation index (SPI) and the standardized precipitation evapotranspiration index (SPEI) showed a decreasing trend in Xinjiang prior to 1997, after which the trend reversed. SPEI-based drought severity shows a much stronger change during 1997–2015 than the SPI, which is independent of the effect of evaporative demand. Meteorological drought severity has been aggravated by a significant rise in temperature (1.1 °C) over the last two decades that has not been accompanied by a corresponding increase in precipitation. As a result, the evaporative demand in Xinjiang has risen. An examination of a large spatio-temporal extent has made the aggravated drought conditions more evident. Our results indicate that increased meteorological drought severity has had a direct effect on the normalized difference vegetation index (NDVI) and river discharge. The NDVI exhibited a significant decrease during the period 1998–2013 compared to 1982–1997, a decrease that was found to be caused by increased soil moisture loss. A positive relationship was recorded between evaporative demand and the runoff coefficients of the 68 inland river catchments in northwestern China. In the future, meteorological drought severity will likely increase in arid and semiarid regions as global warming continues. creator: Junqiang Yao creator: Yong Zhao creator: Xiaojing Yu uri: https://doi.org/10.7717/peerj.4926 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Yao et al.