title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1413 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: The running kinematics of free-roaming giraffes, measured using a low cost unmanned aerial vehicle (UAV) link: https://peerj.com/articles/6312 last-modified: 2019-02-12 description: The study of animal locomotion can be logistically challenging, especially in the case of large or unhandleable animals in uncontrolled environments. Here we demonstrate the utility of a low cost unmanned aerial vehicle (UAV) in measuring two-dimensional running kinematics from free-roaming giraffes (Giraffa camelopardalis giraffa) in the Free State Province, South Africa. We collected 120 Hz video of running giraffes, and calibrated each video frame using metatarsal length as a constant object of scale. We tested a number of methods to measure metatarsal length. The method with the least variation used close range photography and a trigonometric equation to spatially calibrate the still image, and derive metatarsal length. In the absence of this option, a spatially calibrated surface model of the study terrain was used to estimate topographical dimensions in video footage of interest. Data for the terrain models were collected using the same equipment, during the same study period. We subsequently validated the accuracy of the UAV method by comparing similar speed measurements of a human subject running on a treadmill, with treadmill speed. At 8 m focal distance we observed an error of 8% between the two measures of speed. This error was greater at a shorter focal distance, and when the subject was not in the central field of view. We recommend that future users maximise the camera focal distance, and keep the subject in the central field of view. The studied giraffes used a grounded rotary gallop with a speed range of 3.4–6.9 ms−1 (never cantering, trotting or pacing), and lower duty factors when compared with other cursorial quadrupeds. As this pattern might result in adverse increases in peak vertical limb forces with speed, it was notable to find that contralateral limbs became more in-phase with speed. Considering the latter pattern and the modest maximal speed of giraffes, we speculate that tissue safety factors are maintained within tolerable bounds this way. Furthermore, the angular kinematics of the neck were frequently isolated from the pitching of the body during running; this may be a result of the large mass of the head and neck. Further field experiments and biomechanical models are needed to robustly test these speculations. creator: Christopher K. Basu creator: Francois Deacon creator: John R. Hutchinson creator: Alan M. Wilson uri: https://doi.org/10.7717/peerj.6312 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Basu et al. title: Responses of Phaseolus calcaltus to lime and biochar application in an acid soil link: https://peerj.com/articles/6346 last-modified: 2019-02-12 description: IntroductionRice bean (Phaseolus calcaltus), as an annual summer legume, is always subjected to acid soils in tropical to subtropical regions, limiting its growth and nodulation. However, little is known about its responses to lime and biochar addition, the two in improving soil fertility in acid soils.Materials and MethodsIn the current study, a pot experiment was conducted using rice bean on a sandy yellow soil (Orthic Acrisol) with a pH of 5.5. The experiment included three lime rates (0, 0.75 and 1.5 g kg−1) and three biochar rates (0, 5 and 10 g kg−1). The biochar was produced from aboveground parts of Solanum tuberosum using a home-made device with temperature of pyrolysis about 500 °C.Results and DiscussionThe results indicated that both lime and biochar could reduce soil exchange Al concentration, increase soil pH and the contents of soil microbial biomass carbon and microbial biomass nitrogen, and enhance urease and dehydrogenase activities, benefiting P. calcaltus growth and nodulation in acid soils. Lime application did decrease the concentrations of soil available phosphorus (AP) and alkali dispelled nitrogen (AN), whereas biochar application increased the concentrations of soil AP, AN and available potassium (AK). However, sole biochar application could not achieve as much yield increase as lime application did. High lime rate (1.5 g lime kg−1) incorporated with low biochar rate (5 g biochar kg−1) could obtain higher shoot biomass, nutrient uptake, and nodule number when compared with high lime rate and high biochar rate.ConclusionLime incorporated with biochar application could achieve optimum improvement for P. calcaltus growing in acid soils when compared with sole lime or biochar addition. creator: Luhua Yao creator: Xiangyu Yu creator: Lei Huang creator: Xuefeng Zhang creator: Dengke Wang creator: Xiao Zhao creator: Yang Li creator: Zhibin He creator: Lin Kang creator: Xiaoting Li creator: Dan Liu creator: Qianlin Xiao creator: Yanjun Guo uri: https://doi.org/10.7717/peerj.6346 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Yao et al. title: Nation-scale primary prevention to reduce newly incident adolescent drug use: the issue of lag time link: https://peerj.com/articles/6356 last-modified: 2019-02-12 description: BackgroundThere is limited evidence about the effects of United States (US) nation-level policy changes on the incidence of alcohol drinking and tobacco smoking. To investigate the potential primary prevention effects on precocious drug use and to clarify lag-time issues, we estimated incidence rates for specified intervals anticipating and lagging after drug policy enactment. Our hypotheses are (a) reductions in underage drinking or smoking onset and (b) increases of incidence at the legal age (i.e., 21 for drinking and 18 for smoking).MethodsThe study population is 12–23-year-old non-institutionalized US civilian residents. Estimates are from 30 community samples drawn to be nationally representative for the US National Surveys on Drug Use and Health 1979–2015. Estimates were year-by-year annual incidence rates for alcohol drinking and tobacco smoking by 12–23-year-olds, age by age. Meta-regressions estimate age-specific incidence over time.ResultsIncidence of underage alcohol drinking declined and followed a trend line that started before 1984 enactment of the National Minimum Drinking Age Act, but increased drinking incidence for 21 year olds was observed approximately 10 years after policy enactment. Eight years after the Synar amendment enactment, evidence of reduced smoking incidence started to emerge. Among 18 year olds, a slight increase in tobacco smoking incidence occurred about 10 years after the Synar amendment.ConclusionOnce nation-level policies affecting drug sales to minors are enacted, one might have to wait almost a decade before seeing tangible policy effects on drug use incidence rates. creator: Hui G. Cheng creator: Dukernse Augustin creator: Eric H. Glass creator: James C. Anthony uri: https://doi.org/10.7717/peerj.6356 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Cheng et al. title: Modeling the spatial structure of the endemic mara (Dolichotis patagonum) across modified landscapes link: https://peerj.com/articles/6367 last-modified: 2019-02-12 description: Across modified landscapes, anthropic factors can affect habitat selection by animals and consequently their abundance and distribution patterns. The study of the spatial structure of wild populations is crucial to gain knowledge on species’ response to habitat quality, and a key for the design and implementation of conservation actions. This is particularly important for a low-density and widely distributed species such as the mara (Dolichotis patagonum), a large rodent endemic to Argentina across the Monte and Patagonian drylands where extensive sheep ranching predominates. We aimed to assess the spatial variation in the abundance of maras and to identify the natural and anthropic factors influencing the observed patterns in Península Valdés, a representative landscape of Patagonia. We conducted ground surveys during the austral autumn from 2015 to 2017. We built density surface models to account for the variation in mara abundance, and obtained a map of mara density at a resolution of four km2. We estimated an overall density of 0.93 maras.km−2 for the prediction area of 3,476 km2. The location of ranch buildings, indicators of human presence, had a strong positive effect on the abundance of maras, while the significant contribution of the geographic longitude suggested that mara density increases with higher rainfall. Although human presence favored mara abundance, presumably by providing protection against predators, it is likely that the association could bring negative consequences for maras and other species. The use of spatial models allowed us to provide the first estimate of mara abundance at a landscape scale and its spatial variation at a high resolution. Our approach can contribute to the assessment of mara population abundance and the factors shaping its spatial structure elsewhere across the species range, all crucial attributes to identify and prioritize conservation actions. creator: Milagros Antún creator: Ricardo Baldi uri: https://doi.org/10.7717/peerj.6367 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Antún and Baldi title: Overexpression of OsFTL10 induces early flowering and improves drought tolerance in Oryza sativa L. link: https://peerj.com/articles/6422 last-modified: 2019-02-12 description: Flowering time control is critically important for the reproductive accomplishment of higher plants as floral transition can be affected by both environmental and endogenous signals. Flowering Locus T-like (FTL) genes are major genetic determinants of flowering in plants. In rice, 13 OsFTL genes have been annotated in the genome and amongst them, Hd3a (OsFTL2) and RFT1 (OsFTL3) have been studied extensively and their functions are confirmed as central florigens that control rice flowering under short day and long day environment, respectively. In this report, a rice OsFTL gene, OsFTL10, was characterized, and its function on flowering and abiotic stress was investigated. The expression level of OsFTL10 was high in young seedlings and shown to be induced by GA3 and drought stress. Overexpression of OsFTL10 resulted in earlier flowering in rice plants by up to 2 weeks, through up-regulation of the downstream gene OsMADS15. OsFTL10 also regulated Ehd1 and OsMADS51 through a feedback mechanism. The OsFTL10 protein was also detected in both nucleus and cytoplasm. Furthermore, yeast two hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) results show that OsFTL10 could interact with multiple 14-3-3s, suggesting that OsFTL10 might function in a similar way to Hd3a in promoting rice flowering by forming a FAC complex with 14-3-3, and OsFD1. Further experiments revealed that constitutive expression of OsFTL10 improved the drought tolerance of transgenic plants by stimulating the expression of drought responsive genes. These results suggest that rice FTL genes might function in flowering promotion and responses to environmental signals. creator: Maichun Fang creator: Zejiao Zhou creator: Xusheng Zhou creator: Huiyong Yang creator: Meiru Li creator: Hongqing Li uri: https://doi.org/10.7717/peerj.6422 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Fang et al. title: Production of eugenol from fungal endophytes Neopestalotiopsis sp. and Diaporthe sp. isolated from Cinnamomum loureiroi leaves link: https://peerj.com/articles/6427 last-modified: 2019-02-12 description: Endophytic fungi, which colonize within a host plant without causing any apparent diseases, have been considered as an important source of bioactive secondary metabolites containing antimicrobial and antioxidant activities. The aim of this research was to isolate the endophytic fungi of Cinnamomum loureiroi and then to screen their antimicrobial and antioxidant activities. A total of 11 fungal endophytes were isolated from healthy leaves of Cinnamomum loureiroi belonging to six genera: Botryosphaeria, Colletotrichum, Diaporthe, Fusarium, Neopestalotiopsis, and Pestalotiopsis. All isolated strains were cultured and further extracted with ethyl acetate solvent. Antimicrobial activity of all crude endophytic fungal extracts was analyzed using disc diffusion assay against six bacterial and two fungal pathogens. Crude extracts of strains MFLUCC15-1130 and MFLUCC15-1131 showed broad-spectrum antimicrobial activity against all tested pathogens. Activity against Bacillus cereus and Staphylococcus epidermidis was notable, showing the lowest minimum inhibitory concentration at 3.91 μg/mL. Antioxidant activity of all crude endophytic fungal extracts was also evaluated based on 2,2-diphenyl-1-picrylhydrazyl assay. Significant antioxidant activity was detected in the crude extracts of fungus MFLUCC15-1130 and MFLUCC15-1131 with IC50 of 22.92 ± 0.67 and 37.61 ± 0.49 μg/mL, respectively. Using molecular identification, MFLUCC15-1130 and MFLUCC15-1131 were identified as Neopestalotiopsis sp. and Diaporthe sp., respectively. The major chemical constituents produced by both crude extracts were identified by gas chromatography-mass spectrometry. Eugenol, myristaldehyde, lauric acid, and caprylic acid were the primary antimicrobial and antioxidant compounds in both crude extracts. This is the first report of eugenol being a biologically active compound of Neopestalotiopsis sp. and Diaporthe sp. fungal endophytes. Eugenol has been reported as antimicrobial and antioxidant agents with agronomic applications. Thus the two newly-isolated endophytes may be used for eugenol production, which in turn can be used in a variety of applications. creator: Chutima Tanapichatsakul creator: Sarunpron Khruengsai creator: Sakon Monggoot creator: Patcharee Pripdeevech uri: https://doi.org/10.7717/peerj.6427 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Tanapichatsakul et al. title: The association between meteorological variables and road traffic injuries: a study from Macao link: https://peerj.com/articles/6438 last-modified: 2019-02-12 description: ObjectiveCorrelation analysis and multiple linear regression analysis were conducted to estimate the influence of meteorological factors on road traffic injuries stratified by severity. Crash rate was defined as mean monthly road traffic accidents per 1,000 vectors.DesignEcological time-series study.SettingMacao traffic accident registry database between January 1st, 2001 and November 31st, 2016.ParticipantsIn total, 393,176 traffic accidents and 72,501 cases of road traffic injuries (RTIs) were enrolled; patients’ severity was divided into mild injury, required hospitalisation, and death.ExposureVariation of monthly meteorological factors.Main outcome measureWeather-condition-related road traffic accidents, injuries, and deaths.ResultsWindy weather significantly correlated with increased number of traffic accidents among all transport vectors (r = .375 to .637; p < 0.001). Multiple linear regression showed temperature (B = 0.704; p < 0.05) and humidity (B =  − 0.537; p < 0.001) were independent factors for mild injury. The role of windy weather was relatively more obvious among patients with severe injuries (B = 0.304; p < 0.001) or those who died (B = 0.015; p < 0.001). A longer duration of sunshine was also associated to RTI-related deaths (B = 0.015; p < 0.001). In total, 13.4% of RTIs were attributable to meteorological factors and may be preventable.ConclusionThe World Health Organization stated that RTIs are a major but neglected public health challenge. This study demonstrates meteorological factors have significant effects on any degree of RTIs. The results may not be generalized to other climates or populations while the findings may have implications in both preventing injuries and to announce safety precautions regarding trauma and motor vehicle collisions to the general public by public agencies. creator: Chon-Fu Lio creator: Hou-Hon Cheong creator: Chon-Hou Un creator: Iek-Long Lo creator: Shin-Yi Tsai uri: https://doi.org/10.7717/peerj.6438 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Lio et al. title: Engineering of CHO cells for the production of vertebrate recombinant sialyltransferases link: https://peerj.com/articles/5788 last-modified: 2019-02-11 description: BackgroundSialyltransferases (SIATs) are a family of enzymes that transfer sialic acid (Sia) to glycan chains on glycoproteins, glycolipids, and oligosaccharides. They play key roles in determining cell–cell and cell-matrix interactions and are important in neuronal development, immune regulation, protein stability and clearance. Most fully characterized SIATs are of mammalian origin and these have been used for in vitro and in vivo modification of glycans. Additional versatility could be achieved by the use of animal SIATs from other species that live in much more variable environments. Our aim was to generate a panel of stable CHO cell lines expressing a range of vertebrate SIATs with different physicochemical and functional properties.MethodsThe soluble forms of various animal ST6Gal and ST3Gal enzymes were stably expressed from a Gateway-modified secretion vector in CHO cells. The secreted proteins were IMAC-purified from serum-free media. Functionality of the protein was initially assessed by lectin binding to the host CHO cells. Activity of purified proteins was determined by a number of approaches that included a phosphate-linked sialyltransferase assay, HILIC-HPLC identification of sialyllactose products and enzyme-linked lectin assay (ELLA).ResultsA range of sialyltransferase from mammals, birds and fish were stably expressed in CHO Flp-In cells. The stable cell lines expressing ST6Gal1 modify the glycans on the surface of the CHO cells as detected by fluorescently labelled lectin microscopy. The catalytic domains, as isolated by Ni Sepharose from culture media, have enzymatic activities comparable to commercial enzymes. Sialyllactoses were identified by HILIC-HPLC on incubation of the enzymes from lactose or whey permeate. The enzymes also increased SNA-I labelling of asialofetuin when incubated in a plate format.ConclusionStable cell lines are available that may provide options for the in vivo sialylation of glycoproteins. Proteins are active and should display a variety of biological and physicochemical properties based on the animal source of the enzyme. creator: Benoit Houeix creator: Michael T. Cairns uri: https://doi.org/10.7717/peerj.5788 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Houeix and Cairns title: Potential ecotoxicological effects of antimicrobial surface coatings: a literature survey backed up by analysis of market reports link: https://peerj.com/articles/6315 last-modified: 2019-02-11 description: This review was initiated by the COST action CA15114 AMICI “Anti-Microbial Coating Innovations to prevent infectious diseases,” where one important aspect is to analyze ecotoxicological impacts of antimicrobial coatings (AMCs) to ensure their sustainable use. Scopus database was used to collect scientific literature on the types and uses of AMCs, while market reports were used to collect data on production volumes. Special attention was paid on data obtained for the release of the most prevalent ingredients of AMCs into the aqueous phase that was used as the proxy for their possible ecotoxicological effects. Based on the critical analysis of 2,720 papers, it can be concluded that silver-based AMCs are by far the most studied and used coatings followed by those based on titanium, copper, zinc, chitosan and quaternary ammonium compounds. The literature analysis pointed to biomedicine, followed by marine industry, construction industry (paints), food industry and textiles as the main fields of application of AMCs. The published data on ecotoxicological effects of AMCs was scarce, and also only a small number of the papers provided information on release of antimicrobial ingredients from AMCs. The available release data allowed to conclude that silver, copper and zinc are often released in substantial amounts (up to 100%) from the coatings to the aqueous environment. Chitosan and titanium were mostly not used as active released ingredients in AMCs, but rather as carriers for other release-based antimicrobial ingredients (e.g., conventional antibiotics). While minimizing the prevalence of healthcare-associated infections appeared to be the most prosperous field of AMCs application, the release of environmentally hazardous ingredients of AMCs into hospital wastewaters and thus, also the environmental risks associated with AMCs, comprise currently only a fraction of the release and risks of traditional disinfectants. However, being proactive, while the use of antimicrobial/antifouling coatings could currently pose ecotoxicological effects mainly in marine applications, the broad use of AMCs in other applications like medicine, food packaging and textiles should be postponed until reaching evidences on the (i) profound efficiency of these materials in controlling the spread of pathogenic microbes and (ii) safety of AMCs for the human and ecosystems. creator: Merilin Rosenberg creator: Krunoslav Ilić creator: Katre Juganson creator: Angela Ivask creator: Merja Ahonen creator: Ivana Vinković Vrček creator: Anne Kahru uri: https://doi.org/10.7717/peerj.6315 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Rosenberg et al. title: Integrating gross morphology and bone histology to assess skeletal maturity in early dinosauromorphs: new insights from Dromomeron (Archosauria: Dinosauromorpha) link: https://peerj.com/articles/6331 last-modified: 2019-02-11 description: Understanding growth patterns is central to properly interpreting paleobiological signals in tetrapods, but assessing skeletal maturity in some extinct clades may be difficult when growth patterns are poorly constrained by a lack of ontogenetic series. To overcome this difficulty in assessing the maturity of extinct archosaurian reptiles—crocodylians, birds and their extinct relatives—many studies employ bone histology to observe indicators of the developmental stage reached by a given individual. However, the relationship between gross morphological and histological indicators of maturity has not been examined in most archosaurian groups. In this study, we examined the gross morphology of a hypothesized growth series of Dromomeron romeri femora (96.6–144.4 mm long), the first series of a non-dinosauriform dinosauromorph available for such a study. We also histologically sampled several individuals in this growth series. Previous studies reported that D. romeri lacks well-developed rugose muscle scars that appear during ontogeny in closely related dinosauromorph taxa, so integrating gross morphology and histological signal is needed to determine reliable maturity indicators for early bird-line archosaurs. We found that, although there are small, linear scars indicating muscle attachment sites across the femur, the only rugose muscle scar that appears during ontogeny is the attachment of the M. caudofemoralis longus, and only in the largest-sampled individual. This individual is also the only femur with histological indicators that asymptotic size had been reached, although smaller individuals possess some signal of decreasing growth rates (e.g., decreasing vascular density). The overall femoral bone histology of D. romeri is similar to that of other early bird-line archosaurs (e.g., woven-bone tissue, moderately to well-vascularized, longitudinal vascular canals). All these data indicate that the lack of well-developed femoral scars is autapomorphic for this species, not simply an indication of skeletal immaturity. We found no evidence of the high intraspecific variation present in early dinosaurs and other dinosauriforms, but a limited sample size of other early bird-line archosaur growth series make this tentative. The evolutionary history and phylogenetic signal of gross morphological features must be considered when assessing maturity in extinct archosaurs and their close relatives, and in some groups corroboration with bone histology or with better-known morphological characters is necessary. creator: Christopher T. Griffin creator: Lauren S. Bano creator: Alan H. Turner creator: Nathan D. Smith creator: Randall B. Irmis creator: Sterling J. Nesbitt uri: https://doi.org/10.7717/peerj.6331 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Griffin et al.