title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=1818
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Engineering a light-controlled F1 ATPase using structure-based protein design
link: https://peerj.com/articles/2286
last-modified: 2016-07-28
description: The F1 sub-complex of ATP synthase is a biological nanomotor that converts the free energy of ATP hydrolysis into mechanical work with an astonishing efficiency of up to 100% (Kinosita et al., 2000). To probe the principal mechanics of the machine, I re-engineered the active site of E.coli F1 ATPase with a structure-based protein design approach: by incorporation of a site-specific, photoswitchable crosslinker, whose end-to-end distance can be modulated by illumination with light of two different wavelengths, a dynamic constraint was imposed on the inter-atomic distances of the α and β subunits. Crosslinking reduced the ATP hydrolysis activity of four designs tested in vitro and in one case created a synthetic ATPase whose activity can be reversibly modulated by subsequent illumination with near UV and blue light. The work is a first step into the direction of the long-term goal to design nanoscaled machines based on biological parts that can be precisely controlled by light.
creator: Daniel Hoersch
uri: https://doi.org/10.7717/peerj.2286
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2016 Hoersch

title: Site fidelity, size, and morphology may differ by tidal position for an intertidal fish, Bathygobius cocosensis (Perciformes-Gobiidae), in Eastern Australia
link: https://peerj.com/articles/2263
last-modified: 2016-07-28
description: The intertidal zone is a transitional environment that undergoes daily environmental fluctuations as tides rise and fall. Relatively few fish species are adapted to endure the physiological pressures of this environment. This study focused on Bathygobius cocosensis (Gobiidae), a common intertidal fish in New South Wales, Australia. We investigated whether shore height impacted site fidelity, survival probability, fish size, and morphological traits with respect to tidal height. Mark-recapture methods were used over a five month period to determine if individuals in high shore pools had greater site fidelity; fish in high tide pools were more than twice as likely to be recaptured in their original pool than fish from low tide pools. High pool individuals were, on average, smaller with larger eyes and longer snouts relative to their size as compared to low pool individuals. We discuss several mechanisms that could cause the observed pattern in morphological variation. Ultimately, this study suggests that within species behaviour and morphology differ by tidal position for an intertidal fish.
creator: Lucie A. Malard
creator: Katrina McGuigan
creator: Cynthia Riginos
uri: https://doi.org/10.7717/peerj.2263
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2016 Malard et al.

title: Three-dimensional geometrical changes of the human tibialis anterior muscle and its central aponeurosis measured with three-dimensional ultrasound during isometric contractions
link: https://peerj.com/articles/2260
last-modified: 2016-07-28
description: Background. Muscles not only shorten during contraction to perform mechanical work, but they also bulge radially because of the isovolumetric constraint on muscle fibres. Muscle bulging may have important implications for muscle performance, however quantifying three-dimensional (3D) muscle shape changes in human muscle is problematic because of difficulties with sustaining contractions for the duration of an in vivo scan. Although two-dimensional ultrasound imaging is useful for measuring local muscle deformations, assumptions must be made about global muscle shape changes, which could lead to errors in fully understanding the mechanical behaviour of muscle and its surrounding connective tissues, such as aponeurosis. Therefore, the aims of this investigation were (a) to determine the intra-session reliability of a novel 3D ultrasound (3DUS) imaging method for measuring in vivo human muscle and aponeurosis deformations and (b) to examine how contraction intensity influences in vivo human muscle and aponeurosis strains during isometric contractions.Methods. Participants (n = 12) were seated in a reclined position with their left knee extended and ankle at 90° and performed isometric dorsiflexion contractions up to 50% of maximal voluntary contraction. 3DUS scans of the tibialis anterior (TA) muscle belly were performed during the contractions and at rest to assess muscle volume, muscle length, muscle cross-sectional area, muscle thickness and width, fascicle length and pennation angle, and central aponeurosis width and length. The 3DUS scan involved synchronous B-mode ultrasound imaging and 3D motion capture of the position and orientation of the ultrasound transducer, while successive cross-sectional slices were captured by sweeping the transducer along the muscle.Results. 3DUS was shown to be highly reliable across measures of muscle volume, muscle length, fascicle length and central aponeurosis length (ICC ≥ 0.98, CV < 1%). The TA remained isovolumetric across contraction conditions and progressively shortened along its line of action as contraction intensity increased. This caused the muscle to bulge centrally, predominantly in thickness, while muscle fascicles shortened and pennation angle increased as a function of contraction intensity. This resulted in central aponeurosis strains in both the transverse and longitudinal directions increasing with contraction intensity.Discussion. 3DUS is a reliable and viable method for quantifying multidirectional muscle and aponeurosis strains during isometric contractions within the same session. Contracting muscle fibres do work in directions along and orthogonal to the muscle’s line of action and central aponeurosis length and width appear to be a function of muscle fascicle shortening and transverse expansion of the muscle fibres, which is dependent on contraction intensity. How factors other than muscle force change the elastic mechanical behaviour of the aponeurosis requires further investigation.
creator: Brent J. Raiteri
creator: Andrew G. Cresswell
creator: Glen A. Lichtwark
uri: https://doi.org/10.7717/peerj.2260
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2016 Raiteri et al.

title: Perception of the risk of adverse reactions to analgesics: differences between medical students and residents
link: https://peerj.com/articles/2255
last-modified: 2016-07-28
description: Background. Medications are not exempt from adverse drug reactions (ADR) and how the physician perceives the risk of prescription drugs could influence their availability to report ADR and their prescription behavior.Methods. We assess the perception of risk and the perception of ADR associated with COX2-Inbitors, paracetamol, NSAIDs, and morphine in medical students and residents of northeast of Mexico.Results. The analgesic with the highest risk perception in both group of students was morphine, while the drug with the least risk perceived was paracetamol. Addiction and gastrointestinal bleeding were the ADR with the highest score for morphine and NSAIDs respectively.Discussion. Our findings show that medical students give higher risk scores than residents toward risk due to analgesics. Continuing training and informing physicians about ADRs is necessary since the lack of training is known to induce inadequate use of drugs.
creator: Sandra Castillo-Guzman
creator: Omar González-Santiago
creator: Ismael A. Delgado-Leal
creator: Gerardo E. Lozano-Luévano
creator: Misael J. Reyes-Rodríguez
creator: César V. Elizondo-Solis
creator: Teresa A. Nava-Obregón
creator: Dionicio Palacios-Ríos
uri: https://doi.org/10.7717/peerj.2255
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2016 Castillo-Guzman et al.

title: A simple grid implementation with Berkeley Open Infrastructure for Network Computing using BLAST as a model
link: https://peerj.com/articles/2248
last-modified: 2016-07-28
description: Development of high-throughput technologies, such as Next-generation sequencing, allows thousands of experiments to be performed simultaneously while reducing resource requirement. Consequently, a massive amount of experiment data is now rapidly generated. Nevertheless, the data are not readily usable or meaningful until they are further analysed and interpreted. Due to the size of the data, a high performance computer (HPC) is required for the analysis and interpretation. However, the HPC is expensive and difficult to access. Other means were developed to allow researchers to acquire the power of HPC without a need to purchase and maintain one such as cloud computing services and grid computing system. In this study, we implemented grid computing in a computer training center environment using Berkeley Open Infrastructure for Network Computing (BOINC) as a job distributor and data manager combining all desktop computers to virtualize the HPC. Fifty desktop computers were used for setting up a grid system during the off-hours. In order to test the performance of the grid system, we adapted the Basic Local Alignment Search Tools (BLAST) to the BOINC system. Sequencing results from Illumina platform were aligned to the human genome database by BLAST on the grid system. The result and processing time were compared to those from a single desktop computer and HPC. The estimated durations of BLAST analysis for 4 million sequence reads on a desktop PC, HPC and the grid system were 568, 24 and 5 days, respectively. Thus, the grid implementation of BLAST by BOINC is an efficient alternative to the HPC for sequence alignment. The grid implementation by BOINC also helped tap unused computing resources during the off-hours and could be easily modified for other available bioinformatics software.
creator: Watthanai Pinthong
creator: Panya Muangruen
creator: Prapat Suriyaphol
creator: Dumrong Mairiang
uri: https://doi.org/10.7717/peerj.2248
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2016 Pinthong et al.

title: The potential effects of climate change on amphibian distribution, range fragmentation and turnover in China
link: https://peerj.com/articles/2185
last-modified: 2016-07-28
description: Many studies predict that climate change will cause species movement and turnover, but few have considered the effect of climate change on range fragmentation for current species and/or populations. We used MaxEnt to predict suitable habitat, fragmentation and turnover for 134 amphibian species in China under 40 future climate change scenarios spanning four pathways (RCP2.6, RCP4.5, RCP6 and RCP8.5) and two time periods (the 2050s and 2070s). Our results show that climate change may cause a major shift in spatial patterns of amphibian diversity. Amphibians in China would lose 20% of their original ranges on average; the distribution outside current ranges would increase by 15%. Suitable habitats for over 90% of species will be located in the north of their current range, for over 95% of species in higher altitudes (from currently 137–4,124 m to 286–4,396 m in the 2050s or 314–4,448 m in the 2070s), and for over 75% of species in the west of their current range. Also, our results predict two different general responses to the climate change: some species contract their ranges while moving westwards, southwards and to higher altitudes, while others expand their ranges. Finally, our analyses indicate that range dynamics and fragmentation are related, which means that the effects of climate change on Chinese amphibians might be two-folded.
creator: Ren-Yan Duan
creator: Xiao-Quan Kong
creator: Min-Yi Huang
creator: Sara Varela
creator: Xiang Ji
uri: https://doi.org/10.7717/peerj.2185
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2016 Duan et al.

title: What are the probable predictors of urinary incontinence during pregnancy?
link: https://peerj.com/articles/2283
last-modified: 2016-07-27
description: Objectives. The frequency, predisposing factors and impact of urinary incontinence (UI) on quality of life (QoL) during pregnancy were investigated.Materials and Method. A preliminary cross-sectional survey was studied among pregnant women between January and July of 2014. A total of 132 pregnant women were recruited using a questionnaire form for sociodemographic features, the Turkish version of the International Consultation on Incontinence-Short Form (ICIQ-SF), for the characteristics of UI and Wagner’s Quality of Life scale to assess impact on QoL. p < 0.05 was set significant.Results.Urinary incontinence was present in 56 out of 132 pregnant women (42.4%, UI-present group): mean age, 26.7 ± 5.4y(p = 0.780); median height, 160 cm (min–max: 153–176, p = 0.037); median BMI, 28.7 kg/m2(min–max: 22.4–50.0, p = 0.881); urine leakage occurred per week once (n = 18, 32.1%), twice or thrice (n = 8, 14.3%); per day few times (n = 14, 25%), once (n = 5, 8.9%) and always (n = 8, 14.3%) with mainly a small amount of urine leakage (n = 33, 58.9%) or a moderate (n = 4, 7.1%). There were statistically significant relationships between QoL scores and frequency of UI (p = 0.002) or amount of leakage (p = 0.002). Impact on QoL scores ranged from mild (n = 33, 58.9%), moderate (n = 4, 7.1%) to severe (n = 4, 7.1%) levels in daily life. UI impacted the daily life activities of women by making them less likely to undertake activities outside their homes (23.2%), by affecting their working performance and friendships (8.9%), their daily home activities (7.1%), their general health status (12.5%), their sexual relations (12.5%), by making them more nervous or anxious (10.7%) and by the need to wear pads or protectors (25%). ANOVA, Tukey, and Tamhane tests as the minimal important difference model yielded significant relevance between statistical analyses and clinical outcomes by using standard deviations (p = 0.001, 0.001 and 0.005 respectively). The following features favored the occurence of UI: Age (OR = 0.845, 95% CI [0.268–2.669]), being a housewife (OR = 1.800, 95% CI [0.850–3.810]), anemia (OR = 0.939, 95% CI [0.464–1.901]), parity (OR = 0.519, 95% CI [0.325–0.829]), miscarriage (OR = 1.219, 95% CI [0.588–2.825]) and living in rural areas (OR = 1.800, 95% CI [0.887–3.653]). Height (p = 0, 037), educational status (0.016), miscarriage (0.002), parity (0.006) and place of living (0.020) were significant factors.Conclusions.Many pregnant women are suffering from UI, which warrants a significant public health consideration in the region. Age, height, being a housewife or graduation level higher than primary school, living in rural, parity, miscarriage, and anemia were the factors in favor of the onset of UI. The authors plan a health promotion program in the region according to the results in order to provide information to health caregivers, especially family physicians, and to educate women about the predictors of UI and pelvic floor exercises for primary prevention and secondary relief of UI during and after pregnancy and provide some hygienic supplies to the poor in this aspect.
creator: Nejat Demircan
creator: Ülkü Özmen
creator: Fürüzan Köktürk
creator: Hamdi Küçük
creator: Şevket Ata
creator: Müge Harma
creator: İnan İlker Arıkan
uri: https://doi.org/10.7717/peerj.2283
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2016 Demircan et al.

title: Further evidence of Chelonid herpesvirus 5 (ChHV5) latency: high levels of ChHV5 DNA detected in clinically healthy marine turtles
link: https://peerj.com/articles/2274
last-modified: 2016-07-27
description: The Chelonid herpesvirus 5 (ChHV5) has been consistently associated with fibropapillomatosis (FP), a transmissible neoplastic disease of marine turtles. Whether ChHV5 plays a causal role remains debated, partly because while FP tumours have been clearly documented to contain high concentrations of ChHV5 DNA, recent PCR-based studies have demonstrated that large proportions of asymptomatic marine turtles are also carriers of ChHV5. We used a real-time PCR assay to quantify the levels of ChHV5 Glycoprotein B (gB) DNA in both tumour and non-tumour skin tissues, from clinically affected and healthy turtles drawn from distant ocean basins across four species. In agreement with previous studies, higher ratios of viral to host DNA were consistently observed in tumour versus non-tumour tissues in turtles with FP. Unexpectedly however, the levels of ChHV5 gB DNA in clinically healthy turtles were significantly higher than in non-tumour tissues from FP positive turtles. Thus, a large proportion of clinically healthy sea turtle populations worldwide across species carry ChHV5 gB DNA presumably through persistent latent infections. ChHV5 appears to be ubiquitous regardless of the animals’ clinical conditions. Hence, these results support the theory that ChHV5 is a near ubiquitous virus with latency characteristics requiring co-factors, possibly environmental or immune related, to induce FP.
creator: Alonzo Alfaro-Núñez
creator: Anders Miki Bojesen
creator: Mads F. Bertelsen
creator: Nathan Wales
creator: George H. Balazs
creator: M. Thomas P. Gilbert
uri: https://doi.org/10.7717/peerj.2274
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2016 Alfaro-Núñez et al.

title: Medium-sized exotic prey create novel food webs: the case of predators and scavengers consuming lagomorphs
link: https://peerj.com/articles/2273
last-modified: 2016-07-27
description: Food web interactions are key to community structure. The introduction of species can be seen as an uncontrolled experiment of the addition of species. Introduced species lead to multiple changes, frequently threatening the native biodiversity. However, little is known about their direct effect on the upper level of the food web. In this study we review empirical data on the predator–prey relationship between the introduced lagomorphs and their consumers, and use meta-analytical tools to quantify the strength of their interactions. We expect that exotic lagomorphs will destabilize food webs, affect ecological processes and compromise the conservation of the invaded regions. We found 156 studies on the diet of 43 species of predators that consume lagomorphs as exotic preys in South America and Oceania. We found an average exotic lagomorphs-predator link of 20% which indicates a strong interaction, given that the average for the strongest links with native prey (when lagomorphs are not included in the predator diet) is about 24%. Additionally, this last link decreases to 17% when lagomorphs are present. When lagomorphs arrive in a new environment they may become the most important resource for predators, producing an unstable equilibrium in the novel food web. Any disruption of this interaction could have catastrophic consequences for the native diversity by directly impacting predators or indirectly impacting native preys by apparent competition. Eradication or any change in their abundances should be carefully considered in conservation actions since those will have great impacts on predator populations and ultimately in the whole communities.
creator: Facundo Barbar
creator: Fernando Hiraldo
creator: Sergio A. Lambertucci
uri: https://doi.org/10.7717/peerj.2273
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2016 Barbar et al.

title: Competition-function tradeoffs in ectomycorrhizal fungi
link: https://peerj.com/articles/2270
last-modified: 2016-07-27
description: Background. The extent to which ectomycorrhizal fungi mediate primary production, carbon storage, and nutrient remineralization in terrestrial ecosystems depends upon fungal community composition. However, the factors that govern community composition at the root system scale are not well understood. Here, we explore a potential tradeoff between ectomycorrhizal fungal competitive ability and enzymatic function.Methods. We grew Pinus muricata (Bishop Pine) seedlings in association with ectomycorrhizal fungi from three different genera in a fully factorial experimental design. We measured seedling growth responses, ectomycorrhizal abundance, and the root tip activity of five different extracellular enzymes involved in the mobilization of carbon and phosphorus.Results. We found an inverse relationship between competitiveness, quantified based on relative colonization levels, and enzymatic activity. Specifically, Thelephora terrestris, the dominant fungus, had the lowest enzyme activity levels, while Suillus pungens, the least dominant fungus, had the highest.Discussion. Our results identify a tradeoff between competition and function in ectomycorrhizal fungi, perhaps mediated by the competing energetic demands associated with competitive interactions and enzymatic production. These data suggest that mechanisms such as active partner maintenance by host trees may be important to maintaining “high-quality” ectomycorrhizal fungal partners in natural systems.
creator: Holly V. Moeller
creator: Kabir G. Peay
uri: https://doi.org/10.7717/peerj.2270
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2016 Moeller and Peay