title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1788 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Spotted hyaena space use in relation to human infrastructure inside a protected area link: https://peerj.com/articles/2596 last-modified: 2016-10-19 description: Increasing human population growth has led to elevated levels of human-carnivore conflict. However, some carnivore populations have adapted to urban environments and the resources they supply. Such associations may influence carnivore ecology, behaviour and life-history. Pockets of urbanisation sometimes occur within protected areas, so that anthropogenic influences on carnivore biology are not necessarily confined to unprotected areas. In this study we evaluated associations between human infrastructure and related activity and space use of spotted hyaenas within one of the largest protected areas in South Africa, the Kruger National Park. Home range size was smaller for the dominant female of a clan living in close proximity to humans than that of the dominant female of a clan without direct access to human infrastructure. The home range including human infrastructure was also used less evenly during the night, presumably when the animals were active. Within this home range, a village area was preferred during the night, when the least modified areas within the village were preferred and administration and highly modified areas were avoided. During the day, however, there were no preference or avoidance of the village area, but all habitats except unmodified habitats within the village area were avoided. We suggest that human infrastructure and associated activity influenced hyaena space use, primarily through alterations in the spatial distribution of food. However, these effects may have been indirectly caused by habitat modification that generated favourable hunting habitat rather than a direct effect caused by access to human food such as garbage. Because of the often pivotal effects of apex predators in terrestrial ecosystems, we encourage further work aimed to quantify how human presence influences large carnivores and associated ecosystem processes within protected areas. creator: Lydia E. Belton creator: Elissa Z. Cameron creator: Fredrik Dalerum uri: https://doi.org/10.7717/peerj.2596 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Belton et al. title: A reappraisal of Theroteinus (Haramiyida, Mammaliaformes) from the Upper Triassic of Saint-Nicolas-de-Port (France) link: https://peerj.com/articles/2592 last-modified: 2016-10-19 description: The earliest mammaliaforms are difficult to assess because the fossil record is poor and because their distinctive morphologies cannot be directly compared with more recent mammaliaforms. This is especially true for the haramiyid genus Theroteinus, only known in the Saint-Nicolas-de-Port locality (Rhaetian, France). This study presents a new definition of the type-species Theroteinus nikolai. A new species Theroteinus rosieriensis, sp. nov., is named and distinguished by the lingual shift of distal cusps, a larger size, and a stockier occlusal outline. Comparisons with Eleutherodon, Megaconus and Millsodon suggest that Theroteinus has potential close relatives among the Jurassic haramiyids. creator: Maxime Debuysschere uri: https://doi.org/10.7717/peerj.2592 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Debuysschere title: Green synthesis of silver nanoparticles in aloe vera plant extract prepared by a hydrothermal method and their synergistic antibacterial activity link: https://peerj.com/articles/2589 last-modified: 2016-10-19 description: BackgroundThere is worldwide interest in silver nanoparticles (AgNPs) synthesized by various chemical reactions for use in applications exploiting their antibacterial activity, even though these processes exhibit a broad range of toxicity in vertebrates and invertebrates alike. To avoid the chemical toxicity, biosynthesis (green synthesis) of metal nanoparticles is proposed as a cost-effective and environmental friendly alternative. Aloe vera leaf extract is a medicinal agent with multiple properties including an antibacterial effect. Moreover the constituents of aloe vera leaves include lignin, hemicellulose, and pectins which can be used in the reduction of silver ions to produce as AgNPs@aloe vera (AgNPs@AV) with antibacterial activity.MethodsAgNPs were prepared by an eco-friendly hydrothermal method using an aloe vera plant extract solution as both a reducing and stabilizing agent. AgNPs@AV were characterized using XRD and SEM. Additionally, an agar well diffusion method was used to screen for antimicrobial activity. MIC and MBC were used to correlate the concentration of AgNPs@AV its bactericidal effect. SEM was used to investigate bacterial inactivation. Then the toxicity with human cells was investigated using an MTT assay.ResultsThe synthesized AgNPs were crystalline with sizes of 70.70 ± 22-192.02 ± 53 nm as revealed using XRD and SEM. The sizes of AgNPs can be varied through alteration of times and temperatures used in their synthesis. These AgNPs were investigated for potential use as an antibacterial agent to inhibit pathogenic bacteria. Their antibacterial activity was tested on S. epidermidis and P. aeruginosa. The results showed that AgNPs had a high antibacterial which depended on their synthesis conditions, particularly when processed at 100 oC for 6 h and 200 oC for 12 h. The cytotoxicity of AgNPs was determined using human PBMCs revealing no obvious cytotoxicity. These results indicated that AgNPs@AV can be effectively utilized in pharmaceutical, biotechnological and biomedical applications.DiscussionAloe vera extract was processed using a green and facile method. This was a hydrothermal method to reduce silver nitrate to AgNPs@AV. Varying the hydrothermal temperature provided the fine spherical shaped nanoparticles. The size of the nanomaterial was affected by its thermal preparation. The particle size of AgNPs could be tuned by varying both time and temperature. A process using a pure AG phase could go to completion in 6 h at 200 oC, whereas reactions at lower temperatures required longer times. Moreover, the antibacterial effect of this hybrid nanomaterial was sufficient that it could be used to inhibit pathogenic bacteria since silver release was dependent upon its particle size. The high activity of the largest AgNPs might have resulted from a high concentration of aloe vera compounds incorporated into the AgNPs during hydrothermal synthesis. creator: Patcharaporn Tippayawat creator: Nutthakritta Phromviyo creator: Parichart Boueroy creator: Apiwat Chompoosor uri: https://doi.org/10.7717/peerj.2589 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Tippayawat et al. title: Residency in white-eared hummingbirds (Hylocharis leucotis) and its effect in territorial contest resolution link: https://peerj.com/articles/2588 last-modified: 2016-10-19 description: BackgroundTerritory owners usually defeat intruders. One explanation for this observation is the uncorrelated asymmetry hypothesis which argues that contests might be settled by an arbitrary convention such as “owners win.” We studied the effect of territorial residency on contest asymmetries in the white-eared hummingbird (Hylocharis leucotis) in a fir forest from central Mexico.MethodsTwenty white-eared male adult hummingbird territories were monitored during a winter season, recording the territorial behavior of the resident against intruding hummingbirds. The size and quality of the territory were related to the probability that the resident would allow the use of flowers by the intruder. Various generalized models (logistical models) were generated to describe the probabilities of victory for each individual resident depending on the different combinations of three predictor variables (territory size, territory quality, and intruder identity).ResultsIn general, small and low quality territory owners tend to prevent conspecific intruders from foraging at a higher rate, while they frequently fail to exclude heterospecific intruders such as the magnificent hummingbird (Eugenes fulgens) or the green violetear hummingbird (Colibri thalassinus) on any territory size. Our results showed that the identity of the intruder and the size and quality of the territory determined the result of the contests, but not the intensity of defense.DiscussionInitially, the rule that “the resident always wins” was supported, since no resident was expelled from its territory during the study. Nevertheless, the resident-intruder asymmetries during the course of a day depended on different factors, such as the size and quality of the territory and, mainly, the identity of the intruders. Our results showed that flexibility observed in contest tactics suggests that these tactics are not fixed but are socially plastic instead and they can be adjusted to specific circumstances. creator: Verónica Mendiola-Islas creator: Carlos Lara creator: Pablo Corcuera creator: Pedro Luis Valverde uri: https://doi.org/10.7717/peerj.2588 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Mendiola-Islas et al. title: Performance of joint modelling of time-to-event data with time-dependent predictors: an assessment based on transition to psychosis data link: https://peerj.com/articles/2582 last-modified: 2016-10-19 description: Joint modelling has emerged to be a potential tool to analyse data with a time-to-event outcome and longitudinal measurements collected over a series of time points. Joint modelling involves the simultaneous modelling of the two components, namely the time-to-event component and the longitudinal component. The main challenges of joint modelling are the mathematical and computational complexity. Recent advances in joint modelling have seen the emergence of several software packages which have implemented some of the computational requirements to run joint models. These packages have opened the door for more routine use of joint modelling. Through simulations and real data based on transition to psychosis research, we compared joint model analysis of time-to-event outcome with the conventional Cox regression analysis. We also compared a number of packages for fitting joint models. Our results suggest that joint modelling do have advantages over conventional analysis despite its potential complexity. Our results also suggest that the results of analyses may depend on how the methodology is implemented. creator: Hok Pan Yuen creator: Andrew Mackinnon uri: https://doi.org/10.7717/peerj.2582 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Yuen and Mackinnon title: Systematic review on the conservation genetics of African savannah elephants link: https://peerj.com/articles/2567 last-modified: 2016-10-19 description: BackgroundIn this paper we review the conservation genetics of African savannah elephants, aiming to understand the spatio-temporal research trends and their underlying factors. As such, we explore three questions associated to the conservation genetics and molecular ecology of these elephants: (1) what are the research trends concerning the conservation genetics of Loxodonta africana? (2) Do richer countries conduct more research on the genetics of African elephants? (3) Which attributes influence where scholars conduct their research?Materials and MethodsWe examined available peer-reviewed publications from 1993 to 2014 in complementary online databases, including the ISI/Web of Science (WoS), Scopus and Google Scholar (GS), and searched for publications in scientific journals as well as in the reference section of these publications. We analyzed the annual trend of publications in this field of research, including the number of authors, levels of collaboration among authors, year of publication, publishing journal and the countries from where genetic samples were collected. Additionally, we identified main research clusters, authors, and institutional collaborations, based on co-citation and co-occurrence networks.ResultsWe found that during the study period there was a positive trend in the number of publications and a reduction in the number of authors per paper. Twenty-five countries contributed, with the majority of publications authored by researchers in the USA, Kenya and South Africa. The majority of samples were collected in Kenya, Tanzania and South Africa. Research outputs are associated with the existence of long-term conservation/research projects and research potential as measured by the literacy rate and the number of higher education institutions in a country. Five research clusters were identified, focusing on the origin and evolution of the species, methodological issues and the relatedness among elephant species.ConclusionsResearch in this field should be expanded to additional countries harboring elephant populations to enable a more comprehensive understanding of the population structure and genetic differentiation of the species, and to cope with challenges associated with the conservation of the species such as illegal hunting, habitat fragmentation, species reintroduction and climate change. creator: Daniel Zacarias creator: Luis Mauricio Bini creator: Rafael Loyola uri: https://doi.org/10.7717/peerj.2567 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Zacarias et al. title: A small molecule targeting protein translation does not rescue spatial learning and memory deficits in the hAPP-J20 mouse model of Alzheimer’s disease link: https://peerj.com/articles/2565 last-modified: 2016-10-19 description: A small molecule named ISRIB has recently been described to enhance memory in rodents. In this study we aimed to test whether ISRIB would reverse learning and memory deficits in the J20 mouse model of human amyloid precursor protein (hAPP) overexpression, a model that simulates many aspects of Alzheimer’s disease in which memory deficits are a hallmark feature. We did not observe a significant rescue effect with ISRIB treatment on spatial learning and memory as assessed in the Morris water maze in J20 mice. We also did not observe a significant enhancement of spatial learning or memory in nontransgenic mice with ISRIB treatment, although a trend emerged for memory enhancement in one cohort of mice. Future preclinical studies with ISRIB would benefit from additional robust markers of target engagement in the brain. creator: Erik C.B. Johnson creator: Jing Kang uri: https://doi.org/10.7717/peerj.2565 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Johnson and Kang title: Beech cupules as keystone structures for soil fauna link: https://peerj.com/articles/2562 last-modified: 2016-10-19 description: Facilitative or positive interactions are ubiquitous in nature and play a fundamental role in the configuration of ecological communities. In particular, habitat modification and niche construction, in which one organism locally modifies abiotic conditions and favours other organisms by buffering the effects of adverse environmental factors, are among the most relevant facilitative interactions. In line with this, ‘keystone structures’, which provide resources, refuge, or advantageous services decisive for other species, may allow the coexistence of various species and thus considerably contribute to diversity maintenance. Beech cupules are woody husks harbouring beech fruits that remain in the forest soil for relatively long periods of time. In this study, we explored the potential role of these cupules in the distribution and maintenance of the soil fauna inhabiting the leaf litter layer. We experimentally manipulated cupule availability and soil moisture in the field to determine if such structures are limiting and can provide moist shelter to soil animals during drought periods, contributing to minimize desiccation risks. We measured invertebrate abundances inside relative to outside the cupules, total abundances in the leaf litter and animal body sizes, in both dry and wet experimental plots. We found that these structures are preferentially used by the most abundant groups of smaller soil animals—springtails, mites and enchytraeids—during droughts. Moreover, beech cupules can be limiting, as an increase in use was found with higher cupule densities, and are important resources for many small soil invertebrates, driving the spatial structure of the soil community and promoting higher densities in the leaf litter, probably through an increase in habitat heterogeneity. We propose that fruit woody structures should be considered ‘keystone structures’ that contribute to soil community maintenance. Therefore, beech trees may indirectly facilitate soil fauna activities through their decaying fruit husks, hence acting as ecosystem engineers. creator: Nereida Melguizo-Ruiz creator: Gerardo Jiménez-Navarro creator: Jordi Moya-Laraño uri: https://doi.org/10.7717/peerj.2562 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Melguizo-Ruiz et al. title: Determining the distribution loss of brown eared-pheasant (Crossoptilon mantchuricum) using historical data and potential distribution estimates link: https://peerj.com/articles/2556 last-modified: 2016-10-19 description: We analyzed the synchronous relationship between forest cover and species distribution to explain the contraction in the distribution range of the brown eared-pheasant (Crossoptilon mantchuricum) in China. Historical resources can provide effective records for reconstructing long-term distribution dynamics. The brown eared-pheasant’s historical distribution from 25 to 1947 CE, which included the three provinces of Shaanxi, Shanxi, and Hebei based on this species’ habitat selection criteria, the history of the forests, ancient climate change records, and fossil data. The current species distribution covers Shaanxi, Shanxi, and Hebei provinces, as well as Beijing city, while Shanxi remains the center of the distribution area. MaxEnt model indicated that the suitable conditions of the brown eared-pheasant had retreated to the western regions of Shanxi and that the historical distribution area had reduced synchronously with the disappearance of local forest cover in Shanxi. We built a correlative relationship between the presence/absence of brown eared-pheasants and forest coverage and found that forest coverage in the north, northeast, central, and southeast areas of the Shanxi province were all less than 10% in 1911. Wild brown eared-pheasants are stable in the Luliang Mountains, where forest coverage reached 13.2% in 2000. Consequently, we concluded that the distribution of this species is primarily determined by vegetation conditions and that forest cover was the most significant determining factor. creator: Yilin Li creator: Xinhai Li creator: Zitan Song creator: Changqing Ding uri: https://doi.org/10.7717/peerj.2556 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Li et al. title: Viral recombination blurs taxonomic lines: examination of single-stranded DNA viruses in a wastewater treatment plant link: https://peerj.com/articles/2585 last-modified: 2016-10-18 description: Understanding the structure and dynamics of microbial communities, especially those of economic concern, is of paramount importance to maintaining healthy and efficient microbial communities at agricultural sites and large industrial cultures, including bioprocessors. Wastewater treatment plants are large bioprocessors which receive water from multiple sources, becoming reservoirs for the collection of many viral families that infect a broad range of hosts. To examine this complex collection of viruses, full-length genomes of circular ssDNA viruses were isolated from a wastewater treatment facility using a combination of sucrose-gradient size selection and rolling-circle amplification and sequenced on an Illumina MiSeq. Single-stranded DNA viruses are among the least understood groups of microbial pathogens due to genomic biases and culturing difficulties, particularly compared to the larger, more often studied dsDNA viruses. However, the group contains several notable well-studied examples, including agricultural pathogens which infect both livestock and crops (Circoviridae and Geminiviridae), and model organisms for genetics and evolution studies (Microviridae). Examination of the collected viral DNA provided evidence for 83 unique genotypic groupings, which were genetically dissimilar to known viral types and exhibited broad diversity within the community. Furthermore, although these genomes express similarities to known viral families, such as Circoviridae, Geminiviridae, and Microviridae, many are so divergent that they may represent new taxonomic groups. This study demonstrated the efficacy of the protocol for separating bacteria and large viruses from the sought after ssDNA viruses and the ability to use this protocol to obtain an in-depth analysis of the diversity within this group. creator: Victoria M. Pearson creator: S. Brian Caudle creator: Darin R. Rokyta uri: https://doi.org/10.7717/peerj.2585 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Pearson et al.