title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1244 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Prey-tracking behavior and prey preferences in a tree-climbing firefly link: https://peerj.com/articles/8080 last-modified: 2019-12-16 description: Prey-tracking behavior is common in snail-killing predators, but in the family Lampyridae, this behavior has been validated in only a single species even though this Coleopteran family includes many specialist snail predators. The endemic firefly Pyrocoelia atripennis is a major snail-killing predator in the Yaeyama Islands of Japan, and the larvae often climb on the trees and grasses at night. This tree-climbing behavior is relevant to larval food choices and anti-predatory defenses of land snails. This study examined whether lampyrid larvae can track snail mucus trails and examined larval prey preferences using alternative choice experiments. In addition, predation trials were conducted to evaluate which snail species are potential prey. P. atripennis larvae significantly selected mucous trails over distilled water or control (no-trail) treatments. In addition, a semi-arboreal species was preferred over a ground-dwelling species. In predation trials, the larvae preyed on five out of 10 endemic snail species, all of which were semi-arboreal or arboreal species. Ground-dwelling Cyclophoridae and Aegista species have effective anti-predatory defenses consisting of an operculum or “foamy-lid” that fills the shell aperture. Whether the prey has a lid affects the predation success of lampyrid larvae, and larval tree-climbing behavior may be an adaptation used to search for semi-arboreal and arboreal land snails that lack defensive lids. Furthermore, snail mucus left on the plant stem may help the lampyrid larvae to locate their prey. creator: Nozomu Sato uri: https://doi.org/10.7717/peerj.8080 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Sato title: Managing migraine with over-the-counter provision of triptans: the perspectives and readiness of Western Australian community pharmacists link: https://peerj.com/articles/8134 last-modified: 2019-12-16 description: BackgroundDown-scheduling one or more triptans to Schedule 3 (Pharmacist Only Medicine) from Schedule 4 (Prescription Only Medicine) has been debated in Australia for a decade. This study aimed to evaluate the perspectives and readiness of Western Australian (WA) community pharmacists to manage migraine including over-the-counter (OTC) provision of triptans.MethodsData were collected using a self-administered paper-based questionnaire, posted to a random sample of 178 metropolitan and 97 regional pharmacies in WA. Respondent pharmacists were surveyed regarding: knowledge of optimal migraine treatment as per current guidelines, resources required to appropriately recommend triptans and attitudes and perspective toward down-scheduling. Data were analysed using descriptive statistics and multivariate regression analysis. Pharmacist/pharmacy characteristics influencing readiness were evaluated by assigning respondents a score based on responses to Likert scale questions. These questions were assigned to five domains based on an implementation model and these scores were used in a general linear model to identify demographic characteristics associated with readiness across each domain.ResultsA total of 114 of the 275 pharmacies returned useable questionnaires (response rate: 41.5%). The two most commonly recommended first line OTC agents were a combined paracetamol/non-steroidal anti-inflammatory drugs and aspirin (44/104; 42.3% and 22/104; 21.2%, respectively) which provided context to the respondents’ knowledge of optimal migraine treatment. Responses to questions in relation to triptans and the warning signs requiring referral were in line with current guidelines, demonstrating respondents’ knowledge in these areas. Nevertheless, most respondents demonstrated uncertainty in relation to the pathogenesis of migraine. If triptans were available OTC, 66/107 (61.7%) would recommend them first-line. The majority (107/113; 94.7%) agreed that down-scheduling would improve timely access to effective migraine medication and 105/113 (92.9%) agreed that if triptans were down-scheduled, pharmacists may be better able to assist people in the treatment of migraine. Most respondents agreed that additional training and resources, including a guideline for OTC supply of triptans and the management of first-time and repeat migraine would be necessary if triptans were down-scheduled. No single demographic characteristic influenced readiness across all five domains.DiscussionPharmacists were knowledgeable regarding triptans and recognised symptoms requiring referral; migraine knowledge could be improved. Pharmacists supported down-scheduling of one or more triptans in Australia, however they highlighted a need for further training and resources to support migraine diagnosis and provision of OTC triptans. Professional pharmacy bodies should consider these findings when recommending drugs suitable for down-scheduling for pharmacist recommendation. creator: Shaid Booth creator: Richard Parsons creator: Bruce Sunderland creator: Tin Fei Sim uri: https://doi.org/10.7717/peerj.8134 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Booth et al. title: A novel approach to immunoapheresis of C3a/C3 and proteomic identification of associates link: https://peerj.com/articles/8218 last-modified: 2019-12-16 description: BackgroundComplement factor C3 represents the central component of the complement cascade and its activation split product C3a plays an important role in inflammation and disease. Many human disorders are linked to dysregulation of the complement system and alteration in interaction molecules. Therefore, various therapeutic approaches to act on the complement system have been initiated.Methods and ResultsAiming to develop a tool to eliminate C3a/C3 from the circulation, in a first step a high affine murine monoclonal antibody (mAb) (3F7E2-mAb) was generated against complement factor C3 and selected for binding to the C3a region to serve as immunoaffinity reagent. Functional testing of the 3F7E2-mAb revealed an inhibition of Zymosan-induced cleavage of C3a from C3. Subsequently, a C3a/C3 specific 3F7E2-immunoaffinity column was developed and apheresis of C3a/C3 and associates was performed. Finally, a proteomic analysis was carried out for identification of apheresis products. C3a/C3 was liberated from the 3F7E2-column together with 278 proteins. C3a/C3 interaction specificity was validated by using a haptoglobin immunoaffinity column as control and biostatistic analysis revealed 39 true C3a/C3 interactants.ConclusionA novel and functionally active mAb was developed against complement factor C3a/C3 and used in a specific immunoaffinity column that allows apheresis of C3a/C3 and associates and their identification by proteomic analysis. This methodological approach of developing specific antibodies that can be used as immunoaffinity reagents to design immunoaffinity columns for elimination and further identification of associated proteins could open new avenues for the development of tailored immunotherapy in various complement-mediated or autoimmune diseases. creator: Wolfgang Winnicki creator: Peter Pichler creator: Karl Mechtler creator: Richard Imre creator: Ines Steinmacher creator: Gürkan Sengölge creator: Daniela Knafl creator: Georg Beilhack creator: Ludwig Wagner uri: https://doi.org/10.7717/peerj.8218 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Winnicki et al. title: The fast–slow continuum of longevity among yellow-bellied toad populations (Bombina variegata): intrinsic and extrinsic drivers of variation link: https://peerj.com/articles/8233 last-modified: 2019-12-16 description: Yellow-bellied toad populations (Bombina variegata) show a wide fast–slow continuum of the life-history trait longevity ranging from 5 to 23 years. We investigated populations in Germany (n = 8) and Austria (n = 1) to determine their position within the continuum of longevity and the potential drivers of adult survival at the local and the continental scale. Intrinsic and extrinsic factors considered were local weather, nutritional state, allocation of ingested energy to somatic growth, pathogen prevalence, and geographical clines (latitude, altitude, and longitude). Capture-mark-recapture (CMR) monitoring and direct age assessment by skeletochronology allowed for reliable estimates of longevity and adult survival. Raw and corrected recapture rates as well as a probabilistic estimate of the lifespan of the eldest 1% adults of a cohort (CMR data) were used as surrogates for adult survival and thus longevity in a population. Additionally, survival rates were calculated from static life tables based on the age structure (skeletochronological data) of eight populations. Populations in Germany were short-lived with a maximum lifespan of annual cohorts varying from 5 to 8 years, whereas the population in Austria was long-lived with a cohort longevity of 13 to 23 years. We provide evidence that annual survival rates and longevity differ among years and between short- and long-lived populations, but there was no decrease of survival in older toads (i.e. absence of senescence). Variation of weather among years accounted for 90.7% of variance in annual survival rates of short-lived populations, whereas the sources of variation in the long-lived population remained unidentified. At the continental scale, longevity variation among B. variegata populations studied so far did not correspond to geographical clines or climate variation. Therefore, we propose that a population’s position within the fast–slow continuum integrates the response to local environmental stochasticity (extrinsic source of variation) and the efficiency of chemical antipredator protection determining the magnitude of longevity (intrinsic source of variation). creator: Alena Marcella Hantzschmann creator: Birgit Gollmann creator: Günter Gollmann creator: Ulrich Sinsch uri: https://doi.org/10.7717/peerj.8233 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Hantzschmann et al. title: Significance of TP53 mutation in bladder cancer disease progression and drug selection link: https://peerj.com/articles/8261 last-modified: 2019-12-16 description: BackgroundThe tumor protein p53 (TP53) mutant is one of the most frequent mutant genes in bladder cancer. In this study, we assessed the importance of the TP53 mutation in bladder cancer progression and drug selection, and identified potential pathways and core genes associated with the underlying mechanisms.MethodsGene expression data used in this study were downloaded from The Cancer Genome Atlas and cBioportal databases. Drug sensitivity data were obtained from the Genomics of Drug Sensitivity in Cancer. We did functional enrichment analysis by gene set enrichment analysis (GSEA) and the Database for Annotation, Visualization and Integrated Discovery (DAVID).ResultsWe found the TP53 mutation in 50% of bladder cancer patients. Patients with the TP53 mutation were associated with a lower TP53 mRNA expression level, more advanced tumor stage and higher histologic grade. Three drugs, mitomycin-C, doxorubicin and gemcitabine, were especially more sensitive to bladder cancer with the TP53 mutation. As for the mechanisms, we identified 863 differentially expressed genes (DEGs). Functional enrichment analysis suggested that DEGs were primarily enriched in multiple metabolic progressions, chemical carcinogenesis and cancer related pathways. The protein–protein interaction network identified the top 10 hub genes. Our results have suggested the significance of TP53 mutation in disease progression and drug selection in bladder cancer, and identified multiple genes and pathways related in such program, offering novel basis for bladder cancer individualized treatment. creator: Guang Wu creator: Fei Wang creator: Kai Li creator: Shugen Li creator: Chunchun Zhao creator: Caibin Fan creator: Jianqing Wang uri: https://doi.org/10.7717/peerj.8261 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wu et al. title: Algorithms for efficiently collapsing reads with Unique Molecular Identifiers link: https://peerj.com/articles/8275 last-modified: 2019-12-16 description: BackgroundUnique Molecular Identifiers (UMI) are used in many experiments to find and remove PCR duplicates. There are many tools for solving the problem of deduplicating reads based on their finding reads with the same alignment coordinates and UMIs. However, many tools either cannot handle substitution errors, or require expensive pairwise UMI comparisons that do not efficiently scale to larger datasets.ResultsWe reformulate the problem of deduplicating UMIs in a manner that enables optimizations to be made, and more efficient data structures to be used. We implement our data structures and optimizations in a tool called UMICollapse, which is able to deduplicate over one million unique UMIs of length 9 at a single alignment position in around 26 s, using only a single thread and much less than 10 GB of memory.ConclusionsWe present a new formulation of the UMI deduplication problem, and show that it can be solved faster, with more sophisticated data structures. creator: Daniel Liu uri: https://doi.org/10.7717/peerj.8275 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Liu title: Limited initial impacts of biomass harvesting on composition of wood-inhabiting fungi within residual stumps link: https://peerj.com/articles/8027 last-modified: 2019-12-13 description: Growing pressures linked to global warming are prompting governments to put policies in place to find alternatives to fossil fuels. In this study, we compared the impact of tree-length harvesting to more intensive full-tree harvesting on the composition of fungi residing in residual stumps 5 years after harvest. In the tree-length treatment, a larger amount of residual material was left around the residual stumps in contrast to the full-tree treatment where a large amount of woody debris was removed. We collected sawdust from five randomly selected residual stumps in five blocks in each of the tree-length and full-tree treatments, yielding a total of 50 samples (25 in each treatment). We characterized the fungal operational taxonomic units (OTUs) present in each stump using high-throughput DNA sequencing of the fungal ITS region. We observed no differences in Shannon diversity between tree-length and full-tree harvesting. Likewise, we observed few differences in the composition of fungal OTUs among tree-length and full-tree samples using non-metric multidimensional scaling. Using the differential abundance analysis implemented with DESeq2, we did, however, detect several associations between specific fungal taxa and the intensity of residual biomass harvest. For example, Peniophorella pallida (Bres.) KH Larss. and Tephromela sp. were found mainly in the full-tree treatment, while Phlebia livida (Pers.) Bres. and Cladophialophora chaetospira (Grove) Crous & Arzanlou were found mainly in the tree-length treatment. While none of the 20 most abundant species in our study were identified as pathogens we did identify one conifer pathogen species Serpula himantioides (Fr.) P. Karst found mainly in the full-tree treatment. creator: Cédric Boué creator: Tonia DeBellis creator: Lisa A. Venier creator: Timothy T. Work creator: Steven W. Kembel uri: https://doi.org/10.7717/peerj.8027 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Boué et al. title: Invasive alien plants in Polish national parks—threats to species diversity link: https://peerj.com/articles/8034 last-modified: 2019-12-13 description: Due to the relevance of protected areas to the conservation of native biota, the magnitude of invasions and threats posed by alien plants are currently important issues for the preservation of these areas. The paper summarises data on invasive alien plant species presence in the most valuable protected areas in Poland, i.e. national parks (NPs). We investigated the distribution of invasive alien plant species and management attempts concerning those species. We analysed data obtained from 23 national parks originating from published and unpublished sources. Invasive plants were present in all protected areas analysed, from two to 42 species in a particular national park, and 68 in total. The most widely distributed species were: Impatiens parviflora (present in 19 NPs), I. glandulifera (17), Solidago gigantea (17), Reynoutria japonica (17), and Robinia pseudoacacia (16). The conducted analyses showed that the number of invasive species decreased with the higher altitude (asl) of the national park. The most often managed species were Impatiens glandulifera (being removed in seven NPs), I. parviflora (six), Padus serotina (four) and Quercus rubra (four). In the majority of NPs, control activities are limited to small areas and singular species, thus having an incidental character. Only in five objects (Białowieża NP, Biebrza NP, Kampinos NP, Tuchola NP, Wigry NP), management has been focused on several species. We conclude that a lack of comprehensive management of invasive plant species in the majority of national parks currently limits the effectiveness of IAS (invasive alien species) eradication. Exchange of expertise among protected areas, documenting best practice examples, synthesising lessons learnt in IAS management, as well as the development of minimum standards for invasive plants surveillance and management are pivotal. creator: Anna Bomanowska creator: Wojciech Adamowski creator: Izabella Kirpluk creator: Anna Otręba creator: Agnieszka Rewicz uri: https://doi.org/10.7717/peerj.8034 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Bomanowska et al. title: Embryo aggregation regulates in vitro stress conditions to promote developmental competence in pigs link: https://peerj.com/articles/8143 last-modified: 2019-12-13 description: Embryo aggregation is a useful method to produce blastocysts with high developmental competence to generate more offspring in various mammals, but the underlying mechanism(s) regarding the beneficial effects are largely unknown. In this study, we investigated the effects of embryo aggregation using 4-cell stage embryos in in vitro developmental competence and the relationship of stress conditions in porcine early embryogenesis. We conducted aggregation using the well of the well system and confirmed that aggregation using two or three embryos was useful for obtaining blastocysts. Aggregated embryos significantly improved developmental competence, including blastocyst formation rate, blastomere number, ICM/TE ratio, and cellular survival rate, compared to non-aggregated embryos. Investigation into the relationship between embryo aggregation and stress conditions revealed that mitochondrial function increased, and oxidative and endoplasmic reticulum (ER)-stress decreased compared to 1X (non-aggregated embryos) blastocysts. In addition, 3X (three-embryo aggregated) blastocysts increased the expression of pluripotency, anti-apoptosis, and implantation related genes, and decreased expression of pro-apoptosis related genes. Therefore, these findings indicate that embryo aggregation regulates in vitro stress conditions to increase developmental competence and contributes to the in vitro production of high-quality embryos and the large-scale production of transgenic and chimeric pigs. creator: Pil-Soo Jeong creator: Seung-Bin Yoon creator: Mun-Hyeong Lee creator: Hee-Chang Son creator: Hwal-Yong Lee creator: Sanghoon Lee creator: Bon-Sang Koo creator: Kang-Jin Jeong creator: Jong-Hee Lee creator: Yeung Bae Jin creator: Bong-Seok Song creator: Ji-Su Kim creator: Sun-Uk Kim creator: Deog-Bon Koo creator: Bo-Woong Sim uri: https://doi.org/10.7717/peerj.8143 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Jeong et al. title: Resident microbes of lactation rooms and daycares link: https://peerj.com/articles/8168 last-modified: 2019-12-13 description: Dedicated lactation rooms are a modern development as mothers return to work while still providing breastmilk to their absent infants. This study describes the built environment microbiome of lactation rooms and daycares, and explores the influence of temperature and humidity on the microbiome of lactation rooms. Sterile swabs were used to collect samples from five different sites in lactation rooms at University of California, Davis and from five different sites in daycares located in Davis, California. DNA from the swabs was extracted and the V4 region of the 16S rRNA gene was sequenced using Illumina MiSeq. Temperature and relative humidity data were collected on a subset of the lactation rooms. Sampled lactation rooms could be either dedicated lactation rooms or could also serve other functions (e.g., combined lactation room and restroom lounge). The majority of sequence reads were identified as belonging to family Moraxellaceae, with 73% of all reads included in analysis identified as an unknown species of Acinetobacter. Alpha diversity was analyzed using the Shannon index, while beta diversity was analyzed using unweighted and weighted UniFrac distance. The Jaccard distance was used to measure amount of change at sampling locations between time points for analysis of the impact of temperature and humidity on the microbiome. There were significant differences in the beta diversity of the microbiome of lactation rooms by room type. There were also significant differences in the beta diversity of the microbiome by sample collection location. There were no significant differences in either alpha or beta diversity associated with room temperature or humidity. Additional studies are needed to understand if the differences in lactation room type may result in differences in the breastmilk microbiome of milk collected in those rooms, and to what extent any such differences may influence the infant microbiome. creator: Diana H. Taft creator: Samir Akre creator: Nicolas Madrid creator: Andre Knoesen creator: David A. Mills creator: Zachery T. Lewis uri: https://doi.org/10.7717/peerj.8168 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Taft et al.