title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1460 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: BioInstaller: a comprehensive R package to construct interactive and reproducible biological data analysis applications based on the R platform link: https://peerj.com/articles/5853 last-modified: 2018-10-31 description: The increase in bioinformatics resources such as tools/scripts and databases poses a great challenge for users seeking to construct interactive and reproducible biological data analysis applications. Here, we propose an open-source, comprehensive, flexible R package named BioInstaller that consists of the R functions, Shiny application, the HTTP representational state transfer application programming interfaces, and a docker image. BioInstaller can be used to collect, manage and share various types of bioinformatics resources and perform interactive and reproducible data analyses based on the extendible Shiny application with Tom’s Obvious, Minimal Language and SQLite format databases. The source code of BioInstaller is freely available at our lab website, http://bioinfo.rjh.com.cn/labs/jhuang/tools/bioinstaller, the popular package host GitHub, https://github.com/JhuangLab/BioInstaller, and the Comprehensive R Archive Network, https://CRAN.R-project.org/package=BioInstaller. In addition, a docker image can be downloaded from DockerHub (https://hub.docker.com/r/bioinstaller/bioinstaller). creator: Jianfeng Li creator: Bowen Cui creator: Yuting Dai creator: Ling Bai creator: Jinyan Huang uri: https://doi.org/10.7717/peerj.5853 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Li et al. title: Do subterranean mammals use the Earth’s magnetic field as a heading indicator to dig straight tunnels? link: https://peerj.com/articles/5819 last-modified: 2018-10-31 description: Subterranean rodents are able to dig long straight tunnels. Keeping the course of such “runways” is important in the context of optimal foraging strategies and natal or mating dispersal. These tunnels are built in the course of a long time, and in social species, by several animals. Although the ability to keep the course of digging has already been described in the 1950s, its proximate mechanism could still not be satisfactorily explained. Here, we analyzed the directional orientation of 68 burrow systems in five subterranean rodent species (Fukomys anselli, F. mechowii, Heliophobius argenteocinereus, Spalax galili, and Ctenomys talarum) on the base of detailed maps of burrow systems charted within the framework of other studies and provided to us. The directional orientation of the vast majority of all evaluated burrow systems on the individual level (94%) showed a significant deviation from a random distribution. The second order statistics (averaging mean vectors of all the studied burrow systems of a respective species) revealed significant deviations from random distribution with a prevalence of north–south (H. argenteocinereus), NNW–SSE (C. talarum), and NE–SW (Fukomys mole-rats) oriented tunnels. Burrow systems of S. galili were randomly oriented. We suggest that the Earth’s magnetic field acts as a common heading indicator, facilitating to keep the course of digging. This study provides a field test and further evidence for magnetoreception and its biological meaning in subterranean mammals. Furthermore, it lays the foundation for future field experiments. creator: Sandra Malewski creator: Sabine Begall creator: Cristian E. Schleich creator: C. Daniel Antenucci creator: Hynek Burda uri: https://doi.org/10.7717/peerj.5819 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Malewski et al. title: Cancellous bone and theropod dinosaur locomotion. Part I—an examination of cancellous bone architecture in the hindlimb bones of theropods link: https://peerj.com/articles/5778 last-modified: 2018-10-31 description: This paper is the first of a three-part series that investigates the architecture of cancellous (‘spongy’) bone in the main hindlimb bones of theropod dinosaurs, and uses cancellous bone architectural patterns to infer locomotor biomechanics in extinct non-avian species. Cancellous bone is widely known to be highly sensitive to its mechanical environment, and has previously been used to infer locomotor biomechanics in extinct tetrapod vertebrates, especially primates. Despite great promise, cancellous bone architecture has remained little utilized for investigating locomotion in many other extinct vertebrate groups, such as dinosaurs. Documentation and quantification of architectural patterns across a whole bone, and across multiple bones, can provide much information on cancellous bone architectural patterns and variation across species. Additionally, this also lends itself to analysis of the musculoskeletal biomechanical factors involved in a direct, mechanistic fashion.On this premise, computed tomographic and image analysis techniques were used to describe and analyse the three-dimensional architecture of cancellous bone in the main hindlimb bones of theropod dinosaurs for the first time. A comprehensive survey across many extant and extinct species is produced, identifying several patterns of similarity and contrast between groups. For instance, more stemward non-avian theropods (e.g. ceratosaurs and tyrannosaurids) exhibit cancellous bone architectures more comparable to that present in humans, whereas species more closely related to birds (e.g. paravians) exhibit architectural patterns bearing greater similarity to those of extant birds. Many of the observed patterns may be linked to particular aspects of locomotor biomechanics, such as the degree of hip or knee flexion during stance and gait. A further important observation is the abundance of markedly oblique trabeculae in the diaphyses of the femur and tibia of birds, which in large species produces spiralling patterns along the endosteal surface. Not only do these observations provide new insight into theropod anatomy and behaviour, they also provide the foundation for mechanistic testing of locomotor hypotheses via musculoskeletal biomechanical modelling. creator: Peter J. Bishop creator: Scott A. Hocknull creator: Christofer J. Clemente creator: John R. Hutchinson creator: Andrew A. Farke creator: Belinda R. Beck creator: Rod S. Barrett creator: David G. Lloyd uri: https://doi.org/10.7717/peerj.5778 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Bishop et al. title: Cancellous bone and theropod dinosaur locomotion. Part II—a new approach to inferring posture and locomotor biomechanics in extinct tetrapod vertebrates link: https://peerj.com/articles/5779 last-modified: 2018-10-31 description: This paper is the second of a three-part series that investigates the architecture of cancellous bone in the main hindlimb bones of theropod dinosaurs, and uses cancellous bone architectural patterns to infer locomotor biomechanics in extinct non-avian species. Cancellous bone is widely known to be highly sensitive to its mechanical environment, and therefore has the potential to provide insight into locomotor biomechanics in extinct tetrapod vertebrates such as dinosaurs. Here in Part II, a new biomechanical modelling approach is outlined, one which mechanistically links cancellous bone architectural patterns with three-dimensional musculoskeletal and finite element modelling of the hindlimb. In particular, the architecture of cancellous bone is used to derive a single ‘characteristic posture’ for a given species—one in which bone continuum-level principal stresses best align with cancellous bone fabric—and thereby clarify hindlimb locomotor biomechanics. The quasi-static approach was validated for an extant theropod, the chicken, and is shown to provide a good estimate of limb posture at around mid-stance. It also provides reasonable predictions of bone loading mechanics, especially for the proximal hindlimb, and also provides a broadly accurate assessment of muscle recruitment insofar as limb stabilization is concerned. In addition to being useful for better understanding locomotor biomechanics in extant species, the approach hence provides a new avenue by which to analyse, test and refine palaeobiomechanical hypotheses, not just for extinct theropods, but potentially many other extinct tetrapod groups as well. creator: Peter J. Bishop creator: Scott A. Hocknull creator: Christofer J. Clemente creator: John R. Hutchinson creator: Rod S. Barrett creator: David G. Lloyd uri: https://doi.org/10.7717/peerj.5779 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Bishop et al. title: Cancellous bone and theropod dinosaur locomotion. Part III—Inferring posture and locomotor biomechanics in extinct theropods, and its evolution on the line to birds link: https://peerj.com/articles/5777 last-modified: 2018-10-31 description: This paper is the last of a three-part series that investigates the architecture of cancellous bone in the main hindlimb bones of theropod dinosaurs, and uses cancellous bone architectural patterns to infer locomotor biomechanics in extinct non-avian species. Cancellous bone is highly sensitive to its prevailing mechanical environment, and may therefore help further understanding of locomotor biomechanics in extinct tetrapod vertebrates such as dinosaurs. Here in Part III, the biomechanical modelling approach derived previously was applied to two species of extinct, non-avian theropods, Daspletosaurus torosus and Troodon formosus. Observed cancellous bone architectural patterns were linked with quasi-static, three-dimensional musculoskeletal and finite element models of the hindlimb of both species, and used to derive characteristic postures that best aligned continuum-level principal stresses with cancellous bone fabric. The posture identified for Daspletosaurus was largely upright, with a subvertical femoral orientation, whilst that identified for Troodon was more crouched, but not to the degree observed in extant birds. In addition to providing new insight on posture and limb articulation, this study also tested previous hypotheses of limb bone loading mechanics and muscular control strategies in non-avian theropods, and how these aspects evolved on the line to birds. The results support the hypothesis that an upright femoral posture is correlated with bending-dominant bone loading and abduction-based muscular support of the hip, whereas a crouched femoral posture is correlated with torsion-dominant bone loading and long-axis rotation-based muscular support. Moreover, the results of this study also support the inference that hindlimb posture, bone loading mechanics and muscular support strategies evolved in a gradual fashion along the line to extant birds. creator: Peter J. Bishop creator: Scott A. Hocknull creator: Christofer J. Clemente creator: John R. Hutchinson creator: Andrew A. Farke creator: Rod S. Barrett creator: David G. Lloyd uri: https://doi.org/10.7717/peerj.5777 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Bishop et al. title: Soil respiration of a Moso bamboo forest significantly affected by gross ecosystem productivity and leaf area index in an extreme drought event link: https://peerj.com/articles/5747 last-modified: 2018-10-31 description: Moso bamboo has large potential to alleviate global warming through carbon sequestration. Since soil respiration (Rs) is a major source of CO2 emissions, we analyzed the dynamics of soil respiration (Rs) and its relation to environmental factors in a Moso bamboo (Phllostachys heterocycla cv. pubescens) forest to identify the relative importance of biotic and abiotic drivers of respiration. Annual average Rs was 44.07 t CO2 ha−1 a−1. Rs correlated significantly with soil temperature (P < 0.01), which explained 69.7% of the variation in Rs at a diurnal scale. Soil moisture was correlated significantly with Rs on a daily scale except not during winter, indicating it affected Rs. A model including both soil temperature and soil moisture explained 93.6% of seasonal variations in Rs. The relationship between Rs and soil temperature during a day showed a clear hysteresis. Rs was significantly and positively (P < 0.01) related to gross ecosystem productivity and leaf area index, demonstrating the significance of biotic factors as crucial drivers of Rs. creator: Yuli Liu creator: Guomo Zhou creator: Huaqiang Du creator: Frank Berninger creator: Fangjie Mao creator: Xuejian Li creator: Liang Chen creator: Lu Cui creator: Yangguang Li creator: Di’en Zhu uri: https://doi.org/10.7717/peerj.5747 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Liu et al. title: Testing the heat dissipation limitation hypothesis: basal metabolic rates of endotherms decrease with increasing upper and lower critical temperatures link: https://peerj.com/articles/5725 last-modified: 2018-10-31 description: Metabolic critical temperatures define the range of ambient temperatures where endotherms are able to minimize energy allocation to thermogenesis. Examining the relationship between metabolic critical temperatures and basal metabolic rates (BMR) provides a unique opportunity to gain a better understanding of how animals respond to varying ambient climatic conditions, especially in times of ongoing and projected future climate change. We make use of this opportunity by testing the heat dissipation limit (HDL) theory, which hypothesizes that the maximum amount of heat a species can dissipate constrains its energetics. Specifically, we test the theory’s implicit prediction that BMR should be lower under higher metabolic critical temperatures. We analysed the relationship of BMR with upper and lower critical temperatures for a large dataset of 146 endotherm species using regression analyses, carefully accounting for phylogenetic relationships and body mass. We show that metabolic critical temperatures are negatively related with BMR in both birds and mammals. Our results confirm the predictions of the HDL theory, suggesting that metabolic critical temperatures and basal metabolic rates respond in concert to ambient climatic conditions. This implies that heat dissipation capacities of endotherms may be an important factor to take into account in assessments of species’ vulnerability to climate change. creator: Imran Khaliq creator: Christian Hof uri: https://doi.org/10.7717/peerj.5725 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Khaliq and Hof title: Effect of operational parameters, characterization and antibacterial studies of green synthesis of silver nanoparticles using Tithonia diversifolia link: https://peerj.com/articles/5865 last-modified: 2018-10-30 description: BackgroundThere is a growing interest in the green synthesis of silver nanoparticles (AgNPs) using plant extract because the technique is cost effective, eco-friendly and environmentally benign. This is phasing out the use of toxic and hazardous chemical earlier reported. Tithonia diversifolia is a wild sunflower that grows widely in the western part of Nigeria with a proven medicinal benefit. However, several studies carried out have left doubts on the basic operational parameters needed for the green synthesis of AgNPs. The objective of this work was to carry out green synthesis of AgNPs using T. diversifolia extract via an eco-friendly route through optimization of various operational parameters, characterization, and antimicrobial studies.MethodGreen synthesis of TD-AgNPs was done via bottom-up approach through wet chemistry technique using environmentally benign T. diversifolia plant extract as both reducing and stabilizing agent. Phytochemical Screening of the TD plant extract was carried out. Experimental optimization of various operational parameters—reaction time, concentration, volume ratio, and temperature was investigated. TD-AgNPs were characterized by UV–Vis spectroscopy, FTIR Spectroscopy, SEM/energy-dispersive X-ray spectroscopy (EDX), X-ray diffraction (XRD), and transmission electron microscopy (TEM). Antimicrobial studies against multi drug resistant microorganisms (MDRM) were studied using the agar well diffusion method.ResultsThis study reveals the importance of various operational parameters in the synthesis of TD-AgNPs. Excellent surface plasmon resonance peaks (SPR) were obtained at optimum experimental factors of 90 min reaction time under room temperature at 0.001M concentration with the volume ratio of 1:9 (TD extract:Ag ion solution). The synthesis was monitored using UV–Vis and maximum wavelength obtained at 430 nm was due to SPR. The morphology and elemental constituents obtained by TEM, SEM, and EDX results revealed a spherical shape of AgNPs with prominent peak of Ag at 3.0 kV in EDX spectrum. The crystallinity nature was confirmed by XRD studies. FTIR analysis proved presence of biomolecules functioning as reducing, stabilizing, and capping agents. These biomolecules were confirmed to be flavonoid, triterpenes, and saponin from phytochemical screening. The antimicrobial studies of TD-AgNPs were tested against MDRM—Escherichia coli, Salmonella typhi, Salmonella enterica, and Bacillus subtilis.DiscussionThe variation of reaction time, temperature, concentration, and volume ratio played substantive and fundamental roles in the synthesis of TD-AgNPs. A good dispersion of small spherical size between 10 and 26 nm was confirmed by TEM and SEM. A dual action mechanism of anti-microbial effects was provided by TD-AgNPs which are bactericidal and membrane-disruption. Based on the antimicrobial activity, the synthesized TD-AgNPs could find good application in medicine, pharmaceutical, biotechnology, and food science. creator: Adewumi O. Dada creator: Adejumoke A. Inyinbor creator: Ebiega I. Idu creator: Oluwasesan M. Bello creator: Abimbola P. Oluyori creator: Tabitha A. Adelani-Akande creator: Abiodun A. Okunola creator: Olarewaju Dada uri: https://doi.org/10.7717/peerj.5865 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Dada et al. title: Habitat fragmentation is linked to cascading effects on soil functioning and CO2 emissions in Mediterranean holm-oak-forests link: https://peerj.com/articles/5857 last-modified: 2018-10-30 description: We studied key mechanisms and drivers of soil functioning by analyzing soil respiration and enzymatic activity in Mediterranean holm oak forest fragments with different influence of the agricultural matrix. For this, structural equation models (SEM) were built including data on soil abiotic (moisture, temperature, organic matter, pH, nutrients), biotic (microbial biomass, bacterial and fungal richness), and tree-structure-related (basal area) as explanatory variables of soil enzymatic activity and respiration. Our results show that increased tree growth induced by forest fragmentation in scenarios of high agricultural matrix influence triggered a cascade of causal-effect relations, affecting soil functioning. On the one hand, soil enzymatic activity was strongly stimulated by the abiotic (changes in pH and microclimate) and biotic (microbial biomass) modifications of the soil environment arising from the increased tree size and subsequent soil organic matter accumulation. Soil CO2 emissions (soil respiration), which integrate releases from all the biological activity occurring in soils (autotrophic and heterotrophic components), were mainly affected by the abiotic (moisture, temperature) modifications of the soil environment caused by trees. These results, therefore, suggest that the increasing fragmentation of forests may profoundly impact the functioning of the plant-soil-microbial system, with important effects over soil CO2 emissions and nutrient cycling at the ecosystem level. Forest fragmentation is thus revealed as a key albeit neglected factor for accurate estimations of soil carbon dynamics under global change scenarios. creator: Dulce Flores-Rentería creator: Ana Rincón creator: Teresa Morán-López creator: Ana-Maria Hereş creator: Leticia Pérez-Izquierdo creator: Fernando Valladares creator: Jorge Curiel Yuste uri: https://doi.org/10.7717/peerj.5857 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Flores-Rentería et al. title: HAHap: a read-based haplotyping method using hierarchical assembly link: https://peerj.com/articles/5852 last-modified: 2018-10-30 description: BackgroundThe need for read-based phasing arises with advances in sequencing technologies. The minimum error correction (MEC) approach is the primary trend to resolve haplotypes by reducing conflicts in a single nucleotide polymorphism-fragment matrix. However, it is frequently observed that the solution with the optimal MEC might not be the real haplotypes, due to the fact that MEC methods consider all positions together and sometimes the conflicts in noisy regions might mislead the selection of corrections. To tackle this problem, we present a hierarchical assembly-based method designed to progressively resolve local conflicts.ResultsThis study presents HAHap, a new phasing algorithm based on hierarchical assembly. HAHap leverages high-confident variant pairs to build haplotypes progressively. The phasing results by HAHap on both real and simulated data, compared to other MEC-based methods, revealed better phasing error rates for constructing haplotypes using short reads from whole-genome sequencing. We compared the number of error corrections (ECs) on real data with other methods, and it reveals the ability of HAHap to predict haplotypes with a lower number of ECs. We also used simulated data to investigate the behavior of HAHap under different sequencing conditions, highlighting the applicability of HAHap in certain situations. creator: Yu-Yu Lin creator: Ping Chun Wu creator: Pei-Lung Chen creator: Yen-Jen Oyang creator: Chien-Yu Chen uri: https://doi.org/10.7717/peerj.5852 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Lin et al.