title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=1224
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Heterologous expression, purification and biochemical characterization of a glutamate racemase (MurI) from Streptococcus mutans UA159
link: https://peerj.com/articles/8300
last-modified: 2019-12-20
description: BackgroundGlutamate racemase (MurI) is a cofactor-independent enzyme that is essential to the bacterial peptidoglycan biosynthesis pathway and has therefore been considered an attractive target for the development of antimicrobial drugs. While in our previous study the essentiality of the murI gene was shown in Streptococcus mutans, the primary aetiologic agent of human dental caries, studies on S. mutans MurI have not yet provided definitive results. This study aimed to produce and characterize the biochemical properties of the MurI from the S. mutans UA159 genome.MethodsStructure characterization prediction and multiple sequence alignment were performed by bioinformatic analysis. Recombinant His6-tagged S. mutans MurI was overexpressed in the expression vector pColdII and further purified using a Ni2+ affinity chromatography method. Protein solubility, purity and aggregation state were analyzed by SDS–PAGE, Western blotting, native PAGE and SEC-HPLC. Kinetic parameters were assessed by a circular dichroism (CD) assay. Kinetic constants were calculated based on the curve fit for the Michaelis–Menten equation. The effects of temperature and pH on enzymatic activity were determined by a series of coupled enzyme reaction mixtures.ResultsThe glutamate racemase gene from S. mutans UA159 was amplified by PCR, cloned and expressed in Escherichia coli BL21 (DE3). The 264-amino-acid protein, as a mixture of dimeric and monomeric enzymes, was purified to electrophoretic homogeneity. In the CD assay, S. mutans MurI displayed unique kinetic parameters (Km, d-Glu→l-Glu = 0.3631 ± 0.3205 mM, Vmax, d-Glu→l-Glu = 0.1963 ± 0.0361 mM min−1, kcat, d-Glu→l-Glu = 0.0306 ± 0.0065 s−1, kcat/Km,d-Glu→l-Glu = 0.0844 ± 0.0128 s−1 mM−1, with d-glutamate as substrate; Km, l-Glu→d-Glu = 0.8077 ± 0.5081 mM, Vmax, l-Glu→d-Glu = 0.2421 ± 0.0418 mM min−1, kcat,l-Glu→d-Glu = 0.0378 ± 0.0056 s−1, kcat/Km,l-Glu→d-Glu = 0.0468 ± 0.0176 s−1 mM−1, with l-glutamate as substrate). S. mutans MurI possessed an assay temperature optimum of 37.5 °C and its optimum pH was 8.0.ConclusionThe findings of this study provide insight into the structure and biochemical traits of the glutamate racemase in S. mutans and supply a conceivable guideline for employing glutamate racemase in anti-caries drug design.
creator: Xiangzhu Wang
creator: Chanchan Chen
creator: Ting Shen
creator: Jiangying Zhang
uri: https://doi.org/10.7717/peerj.8300
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2019 Wang et al.

title: Effect of induced hyperopia on fall risk and Fourier transformation of postural sway
link: https://peerj.com/articles/8329
last-modified: 2019-12-20
description: Background and PurposeFall accidents are a social challenge in Korea and elsewhere. Most previous studies have focused on the effects of reduced visual acuity due to myopia on falls and body balance. The objective of this study was to investigate whether uncorrected hyperopia was a major risk factor for falls and to establish whether the risk of falls was absolutely correlated with visual acuity.MethodsFifty-one young subjects with a mean age of 22.75 ± 2.13 years were enrolled in this study. To induce hyperopic and myopic refractive errors, spherical lenses of ±1.0–6.0 D (1.0 D stepwise) were used. Under each induced condition, fall risk index and sway power were assessed via Fourier transformation of postural sway using a TETRAX system.ResultsThe fall risk index for eyes-closed was significantly greater than that of eyes-open with full correction (t = −5.876, p < 0.05). The fall risk index increased significantly from hyperopia induced with −4.0 D lenses (with visual acuity of 0.69 ± 0.32) compared to eyes-open with full correction (F = 3.213, p < 0.05). However, there was no significant change in the induced myopia conditions, despite a drastic decline in decimal visual acuity. Sway power increased significantly in the low-to-medium frequency band derived from the peripheral vestibular system when hyperopia was induced. A significant difference was detected in hyperopia induced with −6.0 D lenses compared to eyes-open with full correction (F = 4.981, p = 0.017).ConclusionAn uncorrected hyperopia rather than myopia may increase the risk of falls, although eyes may show normal visual acuity due to the inherent accommodation mechanism. Our findings suggest that the corrected state of refractive errors is more important than the level of visual acuity as the criteria for appropriate visual input, which contributes to stable posture. Therefore, clinicians should consider the refractive condition, especially the characteristics of hyperopia, when analyzing body balance, and appropriate correction of uncorrected hyperopia to prevent falls.
creator: Byeong-Yeon Moon
creator: Jae Hyeok Choi
creator: Dong-Sik Yu
creator: Sang-Yeob Kim
uri: https://doi.org/10.7717/peerj.8329
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2019 Moon et al.

title: Crowdsourcing visual perception experiments: a case of contrast threshold
link: https://peerj.com/articles/8339
last-modified: 2019-12-20
description: Crowdsourcing has commonly been used for psychological research but not for studies on sensory perception. A reason is that in online experiments, one cannot ensure that the rigorous settings required for the experimental environment are replicated. The present study examined the suitability of online experiments on basic visual perception, particularly the contrast threshold. We conducted similar visual experiments in the laboratory and online, employing three experimental conditions. The first was a laboratory experiment, where a small sample of participants (n = 24; laboratory condition) completed a task with 10 iterations. The other two conditions were online experiments: participants were either presented with a task without repetition of trials (n = 285; online non-repetition condition) or one with 10 iterations (n = 166; online repetition condition). The results showed significant equivalence in the contrast thresholds between the laboratory and online repetition conditions, although a substantial amount of data needed to be excluded from the analyses in the latter condition. The contrast threshold was significantly higher in the online non-repetition condition compared with the laboratory and online repetition conditions. To make crowdsourcing more suitable for investigating the contrast threshold, ways to reduce data wastage need to be formulated.
creator: Kyoshiro Sasaki
creator: Yuki Yamada
uri: https://doi.org/10.7717/peerj.8339
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2019 Sasaki and Yamada

title: Hole in One: an element reduction approach to modeling bone porosity in finite element analysis
link: https://peerj.com/articles/8112
last-modified: 2019-12-19
description: Finite element analysis has been an increasingly widely applied biomechanical modeling method in many different science and engineering fields over the last decade. In the biological sciences, there are many examples of FEA in areas such as paleontology and functional morphology. Despite this common use, the modeling of trabecular bone remains a key issue because their highly complex and porous geometries are difficult to replicate in the solid mesh format required for many simulations. A common practice is to assign uniform model material properties to whole or portions of models that represent trabecular bone. In this study we aimed to demonstrate that a physical, element reduction approach constitutes a valid protocol for addressing this problem in addition to the wholesale mathematical approach. We tested a customized script for element reduction modeling on five exemplar trabecular geometry models of carnivoran temporomandibular joints, and compared stress and strain energy results of both physical and mathematical trabecular modeling to models incorporating actual trabecular geometry. Simulation results indicate that that the physical, element reduction approach generally outperformed the mathematical approach: physical changes in the internal structure of experimental cylindrical models had a major influence on the recorded stress values throughout the model, and more closely approximates values obtained in models containing actual trabecular geometry than solid models with modified trabecular material properties. In models with both physical and mathematical adjustments for bone porosity, the physical changes exhibit more weight than material properties changes in approximating values of control models. Therefore, we conclude that maintaining or mimicking the internal porosity of a trabecular structure is a more effective method of approximating trabecular bone behavior in finite element models than modifying material properties.
creator: Beatriz L. Santaella
creator: Z. Jack Tseng
uri: https://doi.org/10.7717/peerj.8112
license: https://creativecommons.org/licenses/by-nc/4.0
rights: ©2019 Santaella and Tseng

title: Functioning of autobiographical memory specificity and self-defining memories in people with cancer diagnosis
link: https://peerj.com/articles/8126
last-modified: 2019-12-19
description: ObjectivesCognitive and emotional disturbances have been associated with the diagnosis and treatment of cancer. Autobiographical memory is one of the specific cognitive processes affected during this disease. The current study had two main aims: (1) to compare the functioning of autobiographical memory specificity and its related variables (executive functioning, depression and perceived stress) in a group of persons with cancer and a control group; and (2) to analyze whether the experience of cancer evolved into a self-defining memory in the sample of participants diagnosed with this disease.MethodThe study sample comprised 62 participants, 31 in the group with a cancer diagnosis and 31 in the control group. Autobiographical memory specificity, executive functions, depression, stress and self-defining memory were evaluated in the current study.ResultsDepressive symptomatology and reduced executive functioning, but not perceived stress levels, are related and are predictors of autobiographical memory specificity. In addition, the identified characteristics of the self-defining memories were associated with the cancer experience as a threat to physical integrity and an awareness of the meaning of life.ConclusionThis emerging research line is especially important in view of its possible impacts on patients’ well-being, due to the importance of psychological processes in cancer disease.
creator: Marta Nieto
creator: Beatriz Navarro-Bravo
creator: Beatriz Moreno
creator: Alberto Ocana
creator: Juan Pedro Serrano
creator: Clotilde Boix Gras
creator: Jorge Ricarte
creator: Luz Fernández-Aguilar
creator: Laura Ros
creator: Jose Miguel Latorre
uri: https://doi.org/10.7717/peerj.8126
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2019 Nieto et al.

title: Comparative analysis of bacterial communities associated with healthy and diseased corals in the Indonesian sea
link: https://peerj.com/articles/8137
last-modified: 2019-12-19
description: Coral reef ecosystems are impacted by climate change and human activities, such as increasing coastal development, overfishing, sewage and other pollutant discharge, and consequent eutrophication, which triggers increasing incidents of diseases and deterioration of corals worldwide. In this study, bacterial communities associated with four species of corals: Acropora aspera, Acropora formosa, Cyphastrea sp., and Isopora sp. in the healthy and disease stages with different diseases were compared using tagged 16S rRNA sequencing. In total, 59 bacterial phyla, 190 orders, and 307 genera were assigned in coral metagenomes where Proteobacteria and Firmicutes were pre-dominated followed by Bacteroidetes together with Actinobacteria, Fusobacteria, and Lentisphaerae as minor taxa. Principal Coordinates Analysis (PCoA) showed separated clustering of bacterial diversity in healthy and infected groups for individual coral species. Fusibacter was found as the major bacterial genus across all corals. The lower number of Fusibacter was found in A. aspera infected with white band disease and Isopora sp. with white plaque disease, but marked increases of Vibrio and Acrobacter, respectively, were observed. This was in contrast to A. formosa infected by a black band and Cyphastrea sp. infected by yellow blotch diseases which showed an increasing abundance of Fusibacter but a decrease in WH1-8 bacteria. Overall, infection was shown to result in disturbance in the complexity and structure of the associated bacterial microbiomes which can be relevant to the pathogenicity of the microbes associated with infected corals.
creator: Wuttichai Mhuantong
creator: Handung Nuryadi
creator: Agus Trianto
creator: Agus Sabdono
creator: Sithichoke Tangphatsornruang
creator: Lily Eurwilaichitr
creator: Pattanop Kanokratana
creator: Verawat Champreda
uri: https://doi.org/10.7717/peerj.8137
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2019 Mhuantong et al.

title: Simulating more realistic predation threat using attack playbacks
link: https://peerj.com/articles/8149
last-modified: 2019-12-19
description: Use of virtual proxies of live animals are rapidly gaining ground in studies of animal behaviour. Such proxies help to reduce the number of live experimental animals needed to stimulate the behaviour of experimental individuals and to increase standardisation. However, using too simplistic proxies may fail to induce a desired effect and/or lead to quick habituation. For instance, in a predation context, prey often employ multimodal cues to detect predators or use specific aspects of predator behaviour to assess threat. In a live interaction, predator and prey often show behaviours directed towards each other, which are absent in virtual proxies. Here we compared the effectiveness of chemical and visual predator cues in the cooperatively breeding cichlid Neolamprologus pulcher, a species in which predation pressure has been the evolutionary driver of its sociality. We created playbacks of predators simulating an attack and tested their effectiveness in comparison to a playback showing regular activity and to a live predator. We further compared the effectiveness of predator odour and conspecific skin extracts on behaviours directed towards a predator playback. Regular playbacks of calmly swimming predators were less effective than live predators in stimulating a focal individual’s aggression and attention. However, playbacks mimicking an attacking predator induced responses much like a live predator. Chemical cues did not affect predator directed behaviour.
creator: Mukta Watve
creator: Sebastian Prati
creator: Barbara Taborsky
uri: https://doi.org/10.7717/peerj.8149
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2019 Watve et al.

title: Heatstroke-induced hepatocyte exosomes promote liver injury by activating the NOD-like receptor signaling pathway in mice
link: https://peerj.com/articles/8216
last-modified: 2019-12-19
description: BackgroundLiver injury is a common and important clinical issue of severe heat stress (HS), which has toxic effects and promotes subsequent multiple organ failure. The pathogenesis of HS-induced liver injury has not been fully elucidated. Passively injured hepatocytes also drive liver injury. Exosomes, extracellular vesicles secreted by hepatocytes as “danger signals,” mediate the intercellular transportation of diverse functional protein cargoes and modulate the biological processes of target cells. However, whether hepatocyte exosomes are involved in HS-induced liver injury has not been reported. The purpose of the current study was to clarify the release of hepatocyte exosomes under HS conditions and to explore their role in mediating HS-induced liver injury.MethodsHS was induced in hepatocytes or mice by hyperthermic treatment at 43.0 °C for 1 h. Exosomes from control and HS-exposed hepatocytes were isolated by standard differential ultracentrifugation. The hepatocyte exosomes were characterized, and the differentially expressed proteins of the control and HS exosomes were identified by isobaric tags for relative and absolute quantitation (iTRAQ) mass spectrometry and subjected to Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis. Recipient hepatocytes were treated with control or HS exosomes, whereas in vivo, the exosomes were infused into mice. The internalization of HS hepatocyte exosomes by hepatocytes or the liver was tracked. The effect of HS exosomes on the activation of the NOD-like receptor signaling pathway and liver injury was demonstrated in vitro and in vivo.ResultsHS induced an increase in the release of exosomes from hepatocytes, which were internalized by recipient liver cells in vitro and taken up by the liver in vivo. HS significantly changed the proteomic profiles of hepatocyte exosomes based on the iTRAQ analysis. The KEGG pathway analysis revealed the enrichment of proteins associated with injury and inflammatory signaling pathways, especially the NOD-like receptor signaling pathway, the activity of which was upregulated. Subsequently, the capacity of HS hepatocyte exosomes to activate the NOD-like receptor signaling pathway was verified and found to aggrevate liver damage and inflammation in vitro and in vivo.ConclusionsThis study is the first preliminary study to demonstrate the induction of acute liver injury by hepatic exosomes in the setting of severe HS and reveals potentially related pathways. These results provide a basis for future research and the identification of new targets for clinical intervention.
creator: Yue Li
creator: Xintao Zhu
creator: Ming Zhang
creator: Huasheng Tong
creator: Lei Su
uri: https://doi.org/10.7717/peerj.8216
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2019 Li et al.

title: Bacterial microbiota composition of Ixodes ricinus ticks: the role of environmental variation, tick characteristics and microbial interactions
link: https://peerj.com/articles/8217
last-modified: 2019-12-19
description: Ecological factors, host characteristics and/or interactions among microbes may all shape the occurrence of microbes and the structure of microbial communities within organisms. In the past, disentangling these factors and determining their relative importance in shaping within-host microbiota communities has been hampered by analytical limitations to account for (dis)similar environmental preferences (‘environmental filtering’). Here we used a joint species distribution modelling (JSDM) approach to characterize the bacterial microbiota of one of the most important disease vectors in Europe, the sheep tick Ixodes ricinus, along ecological gradients in the Swiss Alps. Although our study captured extensive environmental variation along elevational clines, the explanatory power of such large-scale ecological factors was comparably weak, suggesting that tick-specific traits and behaviours, microhabitat and -climate experienced by ticks, and interactions among microbes play an important role in shaping tick microbial communities. Indeed, when accounting for shared environmental preferences, evidence for significant patterns of positive or negative co-occurrence among microbes was found, which is indicative of competition or facilitation processes. Signals of facilitation were observed primarily among human pathogens, leading to co-infection within ticks, whereas signals of competition were observed between the tick endosymbiont Spiroplasma and human pathogens. These findings highlight the important role of small-scale ecological variation and microbe-microbe interactions in shaping tick microbial communities and the dynamics of tick-borne disease.
creator: Tuomas Aivelo
creator: Anna Norberg
creator: Barbara Tschirren
uri: https://doi.org/10.7717/peerj.8217
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2019 Aivelo et al.

title: The effect of pupil size and peripheral brightness on detection and discrimination performance
link: https://peerj.com/articles/8220
last-modified: 2019-12-19
description: It is easier to read dark text on a bright background (positive polarity) than to read bright text on a dark background (negative polarity). This positive-polarity advantage is often linked to pupil size: A bright background induces small pupils, which in turn increases visual acuity. Here we report that pupil size, when manipulated through peripheral brightness, has qualitatively different effects on discrimination of fine stimuli in central vision and detection of faint stimuli in peripheral vision. Small pupils are associated with improved discrimination performance, consistent with the positive-polarity advantage, but only for very small stimuli that are at the threshold of visual acuity. In contrast, large pupils are associated with improved detection performance. These results are likely due to two pupil-size related factors: Small pupils increase visual acuity, which improves discrimination of fine stimuli; and large pupils increase light influx, which improves detection of faint stimuli. Light scatter is likely also a contributing factor: When a display is bright, light scatter creates a diffuse veil of retinal illumination that reduces perceived image contrast, thus impairing detection performance. We further found that pupil size was larger during the detection task than during the discrimination task, even though both tasks were equally difficult and similar in visual input; this suggests that the pupil may automatically assume an optimal size for the current task. Our results may explain why pupils dilate in response to arousal: This may reflect an increased emphasis on detection of unpredictable danger, which is crucially important in many situations that are characterized by high levels of arousal. Finally, we discuss the implications of our results for the ergonomics of display design.
creator: Sebastiaan Mathôt
creator: Yavor Ivanov
uri: https://doi.org/10.7717/peerj.8220
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2019 Mathôt and Ivanov