title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1535 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Molecular response of canola to salt stress: insights on tolerance mechanisms link: https://peerj.com/articles/4822 last-modified: 2018-05-22 description: Canola (Brassica napus L.) is widely cultivated around the world for the production of edible oils and biodiesel fuel. Despite many canola varieties being described as ‘salt-tolerant’, plant yield and growth decline drastically with increasing salinity. Although many studies have resulted in better understanding of the many important salt-response mechanisms that control salt signaling in plants, detoxification of ions, and synthesis of protective metabolites, the engineering of salt-tolerant crops has only progressed slowly. Genetic engineering has been considered as an efficient method for improving the salt tolerance of canola but there are many unknown or little-known aspects regarding canola response to salinity stress at the cellular and molecular level. In order to develop highly salt-tolerant canola, it is essential to improve knowledge of the salt-tolerance mechanisms, especially the key components of the plant salt-response network. In this review, we focus on studies of the molecular response of canola to salinity to unravel the different pieces of the salt response puzzle. The paper includes a comprehensive review of the latest studies, particularly of proteomic and transcriptomic analysis, including the most recently identified canola tolerance components under salt stress, and suggests what researchers should focus on in future studies. creator: Reza Shokri-Gharelo creator: Pouya Motie Noparvar uri: https://doi.org/10.7717/peerj.4822 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Shokri-Gharelo and Noparvar title: Identifying potentially marker symptoms of attention-deficit/hyperactivity disorder link: https://peerj.com/articles/4820 last-modified: 2018-05-22 description: BackgroundFor the diagnosis of attention-deficit/hyperactivity disorder (ADHD), the Diagnostic and Statistical Manual of Mental Disorders (DSM-5) proposes that adherence to six symptoms in either group (inattention and hyperactivity/impulsivity) will lead to the diagnosis of one of three presentations of the disorder. Underlying this diagnostic algorithm is the assumption that the 18 symptoms have equal relevance for the diagnosis of ADHD, all are equally severe, and all have the same power to detect the presence of the disorder in all its degrees of severity, without considering the possibility of using marker symptoms. However, several studies have suggested that ADHD symptoms differ in both their power to discriminate the presence of the disorder and the degree of severity they represent. The aim of the present study was to replicate the results of previous research by evaluating the discriminative capacity and relative severity of ADHD symptoms, as well as to extend the investigation of this topic to Spanish-speaking Latin American samples.MethodsThe properties of ADHD symptoms rated by the parents of 474 Chilean children were analyzed. Symptom parameters were estimated using the graded response model.ResultsThe results suggest that symptoms of ADHD differ substantially in both the accuracy with which they reflect the presence of the disorder, and their relative severity. Symptoms “easily distracted by extraneous stimuli” and “have difficulty sustaining attention in tasks” (inattention) and “is on the go, acting as if driven by motor” (hyperactivity/impulsivity) were the most informative, and those with relatively lower severity thresholds.DiscussionThe fact that symptoms differ substantially in the probability of being observed conditionally to the trait level suggests the need to refine the diagnostic process by weighting the severity of the symptom, and even to assess the possibility of defining ADHD marker symptoms, as has been done in other disorders. creator: Víctor B. Arias creator: Igor Esnaola creator: Jairo Rodríguez-Medina uri: https://doi.org/10.7717/peerj.4820 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Arias et al. title: Effect of Reactive Black 5 azo dye on soil processes related to C and N cycling link: https://peerj.com/articles/4802 last-modified: 2018-05-22 description: Azo dyes are one of the largest classes of synthetic dyes being used in textile industries. It has been reported that 15–50% of these dyes find their way into wastewater that is often used for irrigation purpose in developing countries. The effect of azo dyes contamination on soil nitrogen (N) has been studied previously. However, how does the azo dye contamination affect soil carbon (C) cycling is unknown. Therefore, we assessed the effect of azo dye contamination (Reactive Black 5, 30 mg kg−1 dry soil), bacteria that decolorize this dye and dye + bacteria in the presence or absence of maize leaf litter on soil respiration, soil inorganic N and microbial biomass. We found that dye contamination did not induce any change in soil respiration, soil microbial biomass or soil inorganic N availability (P > 0.05). Litter evidently increased soil respiration. Our study concludes that the Reactive Black 5 azo dye (applied in low amount, i.e., 30 mg kg−1 dry soil) contamination did not modify organic matter decomposition, N mineralization and microbial biomass in a silty loam soil. creator: Khadeeja Rehman creator: Tanvir Shahzad creator: Amna Sahar creator: Sabir Hussain creator: Faisal Mahmood creator: Muhammad H. Siddique creator: Muhammad A. Siddique creator: Muhammad I. Rashid uri: https://doi.org/10.7717/peerj.4802 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Rehman et al. title: Influence of aprepitant on the pharmacodynamics and pharmacokinetics of gliclazide in rats and rabbits link: https://peerj.com/articles/4798 last-modified: 2018-05-22 description: BackgroundConcomitant drug administration is a general phenomenon in patients with chronic diseases such as diabetes mellitus. Among the currently available oral antidiabetic drugs, gliclazide is a commonly prescribed drug considering its multiple benefits in diabetic patients. Aprepitant is a commonly prescribed antiemetic drug which is mainly metabolized by CYP3A4, reported to have modest inductive and inhibitory effects on CYP2C9 and CYP3A4, respectively. Since gliclazide is metabolized by CYP2C9 (major) and CYP3A4 (minor), it is very difficult to predict the influence of aprepitant and its metabolic interaction with gliclazide. Considering the complexity associated with the combination of aprepitant and gliclazide, this study was designed to evaluate the influence of aprepitant on the pharmacodynamics (PD) and pharmacokinetics (PK) of gliclazide in animal models.MethodsThe PD interaction studies were conducted in both rodent (normal and alloxan-induced diabetic rats) and non-rodent (rabbits) animal models (n = 6) while the PK interaction study was conducted in normal rabbits (n = 6). An extrapolated human therapeutic oral dose of gliclazide, aprepitant and their combination were administered to rats and rabbits with 7 days washout between each treatment. For the multiple-dose interaction study, the same groups were administered with an interacting drug (aprepitant) for 7 days and then the combination of aprepitant and gliclazide on the 8th day. From the collected animal blood samples, blood glucose (by Glucose-Oxidase/Peroxidase method), insulin (by ELISA method) and gliclazide concentration levels (by HPLC method) were determined. Non-compartmental PK analysis was conducted by Phoenix WinNonlin software to determine the PK parameters of gliclazide. Statistical analysis was performed by student’s paired t-test.ResultsThe pharmacodynamic activity (blood glucose reduction and insulin levels) of gliclazide was significantly (p < 0.05) influenced by aprepitant in normal and diabetic condition without any convulsions in animals. There was a significant (p < 0.05) increase in concentration levels and Area Under the Curve of gliclazide while significant (p < 0.05) decrease in clearance levels of gliclazide in rabbits. The PK interaction with gliclazide is relatively more with the multiple dose treatment of aprepitant over single dose treatment.ConclusionIn combination, aprepitant significantly influenced the pharmacodynamic activity of gliclazide in animal models. Considering this, care should be taken when this combination is prescribed for the clinical benefit in diabetic patients. creator: Raghunandan Reddy Kura creator: Eswar Kumar Kilari creator: Mastan Shaik uri: https://doi.org/10.7717/peerj.4798 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Kura et al. title: Large mammal burrows in late Miocene calcic paleosols from central Argentina: paleoenvironment, taphonomy and producers link: https://peerj.com/articles/4787 last-modified: 2018-05-22 description: Large cylindrical sediment-filled structures interpreted as mammal burrows occur within the loess-paleosol sequence of the late Miocene Cerro Azul Formation of central Argentina. A total of 115 burrow fills from three localities were measured. They are typically shallowly dipping, subcylindrical, unbranched structures with rounded ends and lacking enlargements. The horizontal diameter of the burrows range between 0.15 and 1.50 m, with most of the burrows in the interval of 0.39 to 0.98 m. Geometric morphometric analysis of transverse cross-sections support their distinct subcircular and elliptical (horizontally flattened) shapes. Burrow fills are typically laminated in the lower part and massive in the upper part. The laminated intervals reflect pulses of flowing water entering the abandoned burrow during moderate rains, whereas massive intervals reflect mass flow input of dense sediment-water mixtures during heavy rains that produced sheet floods. Approximately 1% of the burrows contained fragmentary, disarticulated and weathered mammal bones that were introduced in the open burrow by currents along with other sedimentary particles. Analysis of the tetrapod burrow fossil record suggests that Miocene burrows, including those studied herein, reflect a remarkable increase in the average size of the fossorial fauna. We conclude that large late Miocene mammals dug burrows essentially as a shelter against environmental extremes and to escape predation. The simple architecture of the burrows suggests that the producers essentially foraged aboveground. Several mammal groups acquired fossorial habits in response to cold and seasonally dry climatic conditions that prevailed during the late Miocene in southern South America. The considerable range of horizontal diameters of the studied burrows can be attributed to a variety of producers, including dasypodids, the notoungulate Paedotherium minor, Glyptodontidae and Proscelidodon sp. creator: María Cristina Cardonatto creator: Ricardo Néstor Melchor uri: https://doi.org/10.7717/peerj.4787 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Cardonatto and Melchor title: Potentially inappropriate use of benzodiazepines and z-drugs in the older population—analysis of associations between long-term use and patient-related factors link: https://peerj.com/articles/4614 last-modified: 2018-05-22 description: IntroductionThe long-term use of benzodiazepines (BZD) and z-drugs in older populations is associated with a variety of sociodemographic and health-related factors. Recent studies reported that long-term BZD and z-drugs use is associated with increased age, female sex, and severe negative psychological (e.g., depression) and somatic (e.g., chronic disease) factors. The current study explores the sociodemographic and health-related factors associated with long-term BZD and z-drugs use in the elderly.MethodsWe conducted a cross-sectional survey among randomly selected patients of one health insurance plan (“AOK North-West”) with BZD and z-drugs prescriptions in the past 12 months. The sample was stratified by appropriate German prescription guidelines (yes vs. no) and age (50–65 vs. >65 years). To examine the association of selected sociodemographic and psychological variables (e.g., sex, employment status, quality of life, depression) with long-term use, a binary logistic regression analysis was conducted.ResultsIn total, data from 340 patients were analyzed. The mean age was 72.1 (SD = 14.5) years, and the most commonly used substances were zopiclon (38.1%), oxazepam (18.1%), and lorazepam (13.8%). The mean defined daily dose (DDD) was 0.73 (SD = 0.47). Insomnia was the main reason for prescribing BZD and z-drugs. The long-term use of BZD and z-drugs was significantly associated with unemployment (OR = 2.9, 95% CI [1.2–7.1]) and generally problematic medication use (OR = 0.5, 95% CI [0.2–1.0]).DiscussionUnemployment status and problematic medication use had a significant association with the patient-reported, long-term use of BZD and z-drugs. Divergent prescription patterns might suggest problematic patterns of BZD and z-drugs use. The causal connection between the identified factors and problematic BZD and z-drugs prescription is not discussed in this paper. Nevertheless, employment status and possible evidence of general problematic drug use may be a warning signal to the prescribers of BZD and z-drugs. creator: Aliaksandra Mokhar creator: Niklas Tillenburg creator: Jörg Dirmaier creator: Silke Kuhn creator: Martin Härter creator: Uwe Verthein uri: https://doi.org/10.7717/peerj.4614 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Mokhar et al. title: Impact of input data (in)accuracy on overestimation of visible area in digital viewshed models link: https://peerj.com/articles/4835 last-modified: 2018-05-21 description: Viewshed analysis is a GIS tool in standard use for more than two decades to perform numerous scientific and practical tasks. The reliability of the resulting viewshed model depends on the computational algorithm and the quality of the input digital surface model (DSM). Although many studies have dealt with improving viewshed algorithms, only a few studies have focused on the effect of the spatial accuracy of input data. Here, we compare simple binary viewshed models based on DSMs having varying levels of detail with viewshed models created using LiDAR DSM. The compared DSMs were calculated as the sums of digital terrain models (DTMs) and layers of forests and buildings with expertly assigned heights. Both elevation data and the visibility obstacle layers were prepared using digital vector maps differing in scale (1:5,000, 1:25,000, and 1:500,000) as well as using a combination of a LiDAR DTM with objects vectorized on an orthophotomap. All analyses were performed for 104 sample locations of 5 km2, covering areas from lowlands to mountains and including farmlands as well as afforested landscapes. We worked with two observer point heights, the first (1.8 m) simulating observation by a person standing on the ground and the second (80 m) as observation from high structures such as wind turbines, and with five estimates of forest heights (15, 20, 25, 30, and 35 m). At all height estimations, all of the vector-based DSMs used resulted in overestimations of visible areas considerably greater than those from the LiDAR DSM. In comparison to the effect from input data scale, the effect from object height estimation was shown to be secondary. creator: Ondřej Lagner creator: Tomáš Klouček creator: Petra Šímová uri: https://doi.org/10.7717/peerj.4835 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Lagner et al. title: On the efficiency of the genetic code after frameshift mutations link: https://peerj.com/articles/4825 last-modified: 2018-05-21 description: Statistical and biochemical studies of the standard genetic code (SGC) have found evidence that the impact of mistranslations is minimized in a way that erroneous codes are either synonymous or code for an amino acid with similar polarity as the originally coded amino acid. It could be quantified that the SGC is optimized to protect this specific chemical property as good as possible. In recent work, it has been speculated that the multilevel optimization of the genetic code stands in the wider context of overlapping codes. This work tries to follow the systematic approach on mistranslations and to extend those analyses to the general effect of frameshift mutations on the polarity conservation of amino acids. We generated one million random codes and compared their average polarity change over all triplets and the whole set of possible frameshift mutations. While the natural code—just as for the point mutations—appears to be competitively robust against frameshift mutations as well, we found that both optimizations appear to be independent of each other. For both, better codes can be found, but it becomes significantly more difficult to find candidates that optimize all of these features—just like the SGC does. We conclude that the SGC is not only very efficient in minimizing the consequences of mistranslations, but rather optimized in amino acid polarity conservation for all three effects of code alteration, namely translational errors, point and frameshift mutations. In other words, our result demonstrates that the SGC appears to be much more than just “one in a million”. creator: Regine Geyer creator: Amir Madany Mamlouk uri: https://doi.org/10.7717/peerj.4825 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Geyer and Madany Mamlouk 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.