title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1562 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Understanding mitochondrial myopathies: a review link: https://peerj.com/articles/4790 last-modified: 2018-05-21 description: Mitochondria are small, energy-producing structures vital to the energy needs of the body. Genetic mutations cause mitochondria to fail to produce the energy needed by cells and organs which can cause severe disease and death. These genetic mutations are likely to be in the mitochondrial DNA (mtDNA), or possibly in the nuclear DNA (nDNA). The goal of this review is to assess the current understanding of mitochondrial diseases. This review focuses on the pathology, causes, risk factors, symptoms, prevalence data, symptomatic treatments, and new research aimed at possible preventions and/or treatments of mitochondrial diseases. Mitochondrial myopathies are mitochondrial diseases that cause prominent muscular symptoms such as muscle weakness and usually present with a multitude of symptoms and can affect virtually all organ systems. There is no cure for these diseases as of today. Treatment is generally supportive and emphasizes symptom management. Mitochondrial diseases occur infrequently and hence research funding levels tend to be low in comparison with more common diseases. On the positive side, quite a few genetic defects responsible for mitochondrial diseases have been identified, which are in turn being used to investigate potential treatments. Speech therapy, physical therapy, and respiratory therapy have been used in mitochondrial diseases with variable results. These therapies are not curative and at best help with maintaining a patient’s current abilities to move and function. creator: Abhimanyu S. Ahuja uri: https://doi.org/10.7717/peerj.4790 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Ahuja title: Multilocus phylogeny of the parasitic wasps in the tribe Euphorini (Hymenoptera: Braconidae) with revised generic classifications link: https://peerj.com/articles/4783 last-modified: 2018-05-21 description: BackgroundParasitic wasps in the family Braconidae are important regulators of insect pests, particularly in forest and agroecosystems. Within Braconidae, wasps in the tribe Euphorini (Euphorinae) attack economically damaging plant bugs (Miridae) that are major pests of field and vegetable crops. However, the evolutionary relationships of this tribe have been historically problematic. Most generic concepts have been based on ambiguous morphological characters which often leads to misidentification, complicating their use in biological control.MethodsUsing a combination of three genes (COI, 28S, and CAD) and 80 taxa collected worldwide, we conducted Bayesian inference using MrBayes, and maximum likelihood analyses using RAxML and IQ-Tree on individual gene trees as well as the concatenated dataset.ResultsThe monophyly of the tribe Euphorini and the two genera Peristenus and Leiophron were confirmed using maximum likelihood and Bayesian inference. The subgeneric classifications of Leiophron sensu lato were not supported, and the monotypic genus Mama was also not supported.DiscussionEuphoriella, Euphoriana, Euphorus, and Mama syn. n, have been synonymized under Leiophron. Mama mariaesyn. n was placed as a junior synonym of Leiophron reclinator. The generic concepts of Peristenus and Leiophron were refined to reflect the updated phylogeny. Further we discuss the need for revising Euphorini given the number of undescribed species within the tribe. creator: Yuanmeng Miles Zhang creator: Julia Stigenberg creator: Jacqueline Hope Meyer creator: Barbara Jo-Anne Sharanowski uri: https://doi.org/10.7717/peerj.4783 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Zhang et al. title: Intolerance of uncertainty and conditioned place preference in opioid addiction link: https://peerj.com/articles/4775 last-modified: 2018-05-21 description: Several personality factors have been implicated in vulnerability to addiction by impacting learning and decision making. One such factor is intolerance of uncertainty (IU), the tendency to perceive uncertain situations negatively and avoid them. Conditioned place preference (CPP), which compares preference for contexts paired with reward, has been used to examine the motivation for both drug and non-drug rewards. However, preference for locations associated with non-drug reward, as well as the potential influence of IU, has not been thoroughly studied in individuals with addiction. In the current study, we examined CPP using a computer-based task in a sample of addicted individuals undergoing opioid maintenance treatment and never-addicted controls. Patients were confirmed to have higher IU than controls. In the CPP task, the two groups did not differ in overall time spent in the previously-rewarded context. However, controls were more likely than patients to immediately return to this context. Contrary to our predictions, IU was not a significant predictor of preference for the previously-rewarded context, although higher IU in controls was associated with a higher number of rewards obtained in the task. No such relationship was found in patients. creator: Milen L. Radell creator: Michael Todd Allen creator: Belinda Favaloro creator: Catherine E. Myers creator: Paul Haber creator: Kirsten Morley creator: Ahmed A. Moustafa uri: https://doi.org/10.7717/peerj.4775 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Radell et al. title: Effects of long-term fertilisation on aggregates and dynamics of soil organic carbon in a semi-arid agro-ecosystem in China link: https://peerj.com/articles/4758 last-modified: 2018-05-21 description: BackgroundLong-term fertilisation has a large influence on soil physical and chemical properties in agro-ecosystems. The effects on the distribution of aggregates, however, are not fully understood. We determined the dynamic change of the distribution of aggregates and soil organic carbon (SOC) content over time in a long-term field experiment established in 1998 on the Loess Plateau of China and illustrated the relationship between them.MethodsWe determined SOC content and the distribution of aggregates in nine fertiliser treatments: manure (M); nitrogen (N); phosphorus (P); M and N; M, N, and P; M and P; N and P; bare land; and an unfertilised control. These parameters were then used for a path analysis and to analyse the fractal dimension (Dv).ResultsThe organic fertiliser increased SOC content. The proportions of 0.1–0.25 mm microaggregates and 0.25–0.5 mm macroaggregates were higher and the proportion of the 0.01–0.05 mm size class of the silt + clay fraction was lower in the treatments receiving organic fertiliser (M, MN, MNP, and MP) than that in the control, indicating that the addition of organic fertiliser promoted aggregation. The distribution of aggregates characterised by their fractal dimension (Dv), however, did not differ among the treatments.DiscussionDv was strongly correlated with the proportion of the <0.002 mm size class of the silt + clay fraction that did not differ significantly among the treatments. The change in the distribution of aggregates was strongly correlated with SOC content, which could produce organic polymer binding agents to increase the proportion of larger particles. Long-term application of organic fertiliser is thus necessary for the improvement and maintenance of soil quality in semi-arid agricultural land when residues are removed. creator: Jiaoyang Zhang creator: Caili Sun creator: Guobin Liu creator: Sha Xue uri: https://doi.org/10.7717/peerj.4758 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Zhang et al. title: Living upside down: patterns of red coral settlement in a cave link: https://peerj.com/articles/4649 last-modified: 2018-05-21 description: BackgroundLarval settlement and intra-specific interactions during the recruitment phase are crucial in determining the distribution and density of sessile marine populations. Marine caves are confined and stable habitats. As such, they provide a natural laboratory to study the settlement and recruitment processes in sessile invertebrates, including the valuable Mediterranean red coral Corallium rubrum. In the present study, the spatial and temporal variability of red coral settlers in an underwater cave was investigated by demographic and genetic approaches.MethodsSixteen PVC tiles were positioned on the walls and ceiling of the Colombara Cave, Ligurian Sea, and recovered after twenty months. A total of 372 individuals of red coral belonging to two different reproductive events were recorded. Basal diameter, height, and number of polyps were measured, and seven microsatellites loci were used to evaluate the genetic relationships among individuals and the genetic structure.ResultsSignificant differences in the colonization rate were observed both between the two temporal cohorts and between ceiling and walls. No genetic structuring was observed between cohorts. Overall, high levels of relatedness among individuals were found.ConclusionThe results show that C. rubrumindividuals on tiles are highly related at very small spatial scales, suggesting that nearby recruits are likely to be sibs. Self-recruitment and the synchronous settlement of clouds of larvae could be possible explanations for the observed pattern. creator: Federica Costantini creator: Luca Rugiu creator: Carlo Cerrano creator: Marco Abbiati uri: https://doi.org/10.7717/peerj.4649 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Costantini et al. title: I understand you feel that way, but I feel this way: the benefits of I-language and communicating perspective during conflict link: https://peerj.com/articles/4831 last-modified: 2018-05-18 description: Using hypothetical scenarios, we provided participants with potential opening statements to a conflict discussion that varied on I/you language and communicated perspective. Participants rated the likelihood that the recipient of the statement would react in a defensive manner. Using I-language and communicating perspective were both found to reduce perceptions of hostility. Statements that communicated both self- and other-perspective using I-language (e.g. ‘I understand why you might feel that way, but I feel this way, so I think the situation is unfair’) were rated as the best strategy to open a conflict discussion. Simple acts of initial language use can reduce the chances that conflict discussion will descend into a downward spiral of hostility. creator: Shane L. Rogers creator: Jill Howieson creator: Casey Neame uri: https://doi.org/10.7717/peerj.4831 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Rogers et al. title: Fitness consequences of fish circadian behavioural variation in exploited marine environments link: https://peerj.com/articles/4814 last-modified: 2018-05-18 description: The selective properties of fishing that influence behavioural traits have recently gained interest. Recent acoustic tracking experiments have revealed between-individual differences in the circadian behavioural traits of marine free-living fish; these differences are consistent across time and ecological contexts and generate different chronotypes. Here, we hypothesised that the directional selection resulting from fishing influences the wild circadian behavioural variation and affects differently to individuals in the same population differing in certain traits such as awakening time or rest onset time. We developed a spatially explicit social-ecological individual-based model (IBM) to test this hypothesis. The parametrisation of our IBM was fully based on empirical data; which represent a fishery formed by patchily distributed diurnal resident fish that are exploited by a fleet of mobile boats (mostly bottom fisheries). We ran our IBM with and without the observed circadian behavioural variation and estimated selection gradients as a quantitative measure of trait change. Our simulations revealed significant and strong selection gradients against early-riser chronotypes when compared with other behavioural and life-history traits. Significant selection gradients were consistent across a wide range of fishing effort scenarios. Our theoretical findings enhance our understanding of the selective properties of fishing by bridging the gaps among three traditionally separated fields: fisheries science, behavioural ecology and chronobiology. We derive some general predictions from our theoretical findings and outline a list of empirical research needs that are required to further understand the causes and consequences of circadian behavioural variation in marine fish. creator: Martina Martorell-Barceló creator: Andrea Campos-Candela creator: Josep Alós uri: https://doi.org/10.7717/peerj.4814 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Martorell-Barceló et al. title: A quantitative approach to determine the taxonomic identity and ontogeny of the pycnodontiform fish Pycnodus (Neopterygii, Actinopterygii) from the Eocene of Bolca Lagerstätte, Italy link: https://peerj.com/articles/4809 last-modified: 2018-05-18 description: BackgroundThe pycnodontiform fish Pycnodus is one of the representatives of the highly diverse actinopterygian fish fauna from the early Eocene Bolca Lagerstätte, representing one of the youngest and thus last occurrences of this extinct neopterygian clade. This genus has historically been used as a wastebasket taxon in regards to poorly known pycnodontiform fossils. Authors have argued over the specific status of the Bolca Lagerstätte Pycnodus in terms of how many species are contained within the genus with some arguing for multiple species and others suggesting lumping all Bolca specimens together into one species.MethodsHere, we use a quantitative approach performing biometric and geometric morphometric analyses on 52 specimens of Pycnodus in order to determine if the morphological variability within the sample might be related to inter- or intraspecific variation.ResultsThe analyses revealed that the variations of body shape, morphometric and meristic characters cannot be used to distinguish different morphotypes. On the contrary, our results show a remarkable link between shape and size, related to ontogeny.DiscussionDifferences in body shape of small (juvenile) and large (adult) individuals is probably related to different microhabitats occupation on the Bolca reef with juveniles sheltering within crevices on the reef and adults being more powerful swimmers that swim above the coral. Taxonomically, we suggest that the Bolca Pycnodus should be referred to strictly as Pycnodus apodus as this was the name given to the holotype. Additionally, an overview of species assigned to Pycnodus is given. creator: John Joseph Cawley creator: Giuseppe Marramà creator: Giorgio Carnevale creator: Jürgen Kriwet uri: https://doi.org/10.7717/peerj.4809 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Cawley et al. title: Helicobacter pylori genetic diversification in the Mongolian gerbil model link: https://peerj.com/articles/4803 last-modified: 2018-05-18 description: Helicobacter pylori requires genetic agility to infect new hosts and establish long-term colonization of changing gastric environments. In this study, we analyzed H. pylori genetic adaptation in the Mongolian gerbil model. This model is of particular interest because H. pylori-infected gerbils develop a high level of gastric inflammation and often develop gastric adenocarcinoma or gastric ulceration. We analyzed the whole genome sequences of H. pylori strains cultured from experimentally infected gerbils, in comparison to the genome sequence of the input strain. The mean annualized single nucleotide polymorphism (SNP) rate per site was 1.5e−5, which is similar to the rates detected previously in H. pylori-infected humans. Many of the mutations occurred within or upstream of genes associated with iron-related functions (fur, tonB1, fecA2, fecA3, and frpB3) or encoding outer membrane proteins (alpA, oipA, fecA2, fecA3, frpB3 and cagY). Most of the SNPs within coding regions (86%) were non-synonymous mutations. Several deletion or insertion mutations led to disruption of open reading frames, suggesting that the corresponding gene products are not required or are deleterious during chronic H. pylori colonization of the gerbil stomach. Five variants (three SNPs and two deletions) were detected in isolates from multiple animals, which suggests that these mutations conferred a selective advantage. One of the mutations (FurR88H) detected in isolates from multiple animals was previously shown to confer increased resistance to oxidative stress, and we now show that this SNP also confers a survival advantage when H. pylori is co-cultured with neutrophils. Collectively, these analyses allow the identification of mutations that are positively selected during H. pylori colonization of the gerbil model. creator: Amber C. Beckett creator: John T. Loh creator: Abha Chopra creator: Shay Leary creator: Aung Soe Lin creator: Wyatt J. McDonnell creator: Beverly R.E.A. Dixon creator: Jennifer M. Noto creator: Dawn A. Israel creator: Richard M. Peek Jr creator: Simon Mallal creator: Holly M. Scott Algood creator: Timothy L. Cover uri: https://doi.org/10.7717/peerj.4803 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Beckett et al. title: Association of epilepsy and asthma: a population-based retrospective cohort study link: https://peerj.com/articles/4792 last-modified: 2018-05-18 description: BackgroundEpidemiologic data supporting the epilepsy–asthma association are insufficient. Therefore, we examined this association in this study.MethodsBy using claims data from the National Health Insurance Research Database (Taiwan), we executed a retrospective cohort analysis. Analysis 1 entailed comparing 150,827 patients diagnosed as having incident asthma during 1996–2013 with disease-free controls who were selected randomly during the same period, frequency matched in terms of age and sex. Similarly, analysis 2 entailed comparing 25,274 patients newly diagnosed as having epilepsy with sex- and age-matched controls who were selected randomly. At the end of 2013, we evaluated in analysis 1 the epilepsy incidence and risk and evaluated in analysis 2 the asthma incidence and risk. We applied Kaplan–Meier analysis to derive plots of the proportion of asthma-free seizures.ResultsIn analysis 1, the asthma group exhibited a higher epilepsy incidence than did the control group (3.05 versus 2.26 per 1,000 person-years; adjusted hazard ratio: 1.39, 95% CI [1.33–1.45]). We also noted a greater risk of subsequent epilepsy in women and girls. In analysis 2, we determined that the asthma incidence between the control and epilepsy groups did not differ significantly; however, some age subgroups including children and individuals in their 30s had an increased risk. A negative association was found in adolescents. The Kaplan–Meier analysis revealed epilepsy to be positively associated with subsequent onset of asthma within seven years of epilepsy diagnosis.DiscussionAsthma may be associated with high epilepsy risk, and epilepsy may be associated with high asthma risk among children and individuals in their 30s. Nevertheless, people with epilepsy in other age subgroups should be aware of the possibility of developing asthma within seven years of epilepsy diagnosis. creator: Kuo-Liang Chiang creator: Fang-Chuan Kuo creator: Jen-Yu Lee creator: Chin-Yin Huang uri: https://doi.org/10.7717/peerj.4792 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Chiang et al.