title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1049 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Flavoured water consumption alters pharmacokinetic parameters and increases exposure of erlotinib and gefitinib in a preclinical study using Wistar rats link: https://peerj.com/articles/9881 last-modified: 2020-09-22 description: BackgroundErlotinib (ERL) and Gefitinib (GEF) are considered first line therapy for the management of non-small cell lung carcinoma (NSCLC). Like other tyrosine kinase inhibitors (TKIs), ERL and GEF are mainly metabolized by the cytochrome P450 (CYP450) CYP3A4 isoform and are substrates for transporter proteins with marked inter-/intra-individual pharmacokinetic (PK) variability. Therefore, ERL and GEF are candidates for drug-drug and food-drug interactions with a consequent effect on drug exposure and/or drug-related toxicities. In recent years, the consumption of flavoured water (FW) has gained in popularity. Among multiple ingredients, fruit extracts, which might constitute bioactive flavonoids, can possess an inhibitory effect on the CYP450 enzymes or transporter proteins. Therefore, in this study we investigated the effects of different types of FW on the PK parameters of ERL and GEF in Wistar rats.MethodsERL and GEF PK parameters in different groups of rats after four weeks consumption of different flavours of FW, namely berry, peach, lime, and pineapple, were determined from plasma drug concentrations using ultra-performance liquid chromatography–tandem mass spectrometry (UPLC-MS/MS).ResultsData indicated that tested FWs altered the PK parameters of both ERL and GEF differently. Lime water had the highest impact on most of ERL and GEF PK parameters, with a significant increase in Cmax (95% for ERL, 58% for GEF), AUC0–48 (111% for ERL, 203% for GEF), and AUC0–∞ (200% for ERL, 203% for GEF), along with a significant decrease in the apparent oral clearance of both drugs (65% for ERL, 67% for GEF). The order by which FW affected the PK parameters for ERL and GEF was as follows: lime > pineapple > berry > peach.ConclusionThe present study indicates that drinking FW could be of significance in rats receiving ERL or GEF. Our results indicate that the alteration in PKs was mostly recorded with lime, resulting in an enhanced bioavailability, and reduced apparent oral clearance of the drugs. Peach FW had a minimum effect on the PK parameters of ERL and no significant effect on GEF PKs. Accordingly, it might be of clinical importance to evaluate the PK parameters of ERL and GEF in human subjects who consume FW while receiving therapy. creator: Aliyah Almomen creator: Hadir M. Maher creator: Nourah Z. Alzoman creator: Shereen M. Shehata creator: Amal Alsubaie uri: https://doi.org/10.7717/peerj.9881 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Almomen et al. title: The reuse of public datasets in the life sciences: potential risks and rewards link: https://peerj.com/articles/9954 last-modified: 2020-09-22 description: The ‘big data’ revolution has enabled novel types of analyses in the life sciences, facilitated by public sharing and reuse of datasets. Here, we review the prodigious potential of reusing publicly available datasets and the associated challenges, limitations and risks. Possible solutions to issues and research integrity considerations are also discussed. Due to the prominence, abundance and wide distribution of sequencing data, we focus on the reuse of publicly available sequence datasets. We define ‘successful reuse’ as the use of previously published data to enable novel scientific findings. By using selected examples of successful reuse from different disciplines, we illustrate the enormous potential of the practice, while acknowledging the respective limitations and risks. A checklist to determine the reuse value and potential of a particular dataset is also provided. The open discussion of data reuse and the establishment of this practice as a norm has the potential to benefit all stakeholders in the life sciences. creator: Katharina Sielemann creator: Alenka Hafner creator: Boas Pucker uri: https://doi.org/10.7717/peerj.9954 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Sielemann et al. title: Analysis of dynamic and widespread lncRNA and miRNA expression in fetal sheep skeletal muscle link: https://peerj.com/articles/9957 last-modified: 2020-09-22 description: The sheep is an economically important animal, and there is currently a major focus on improving its meat quality through breeding. There are variations in the growth regulation mechanisms of different sheep breeds, making fundamental research on skeletal muscle growth essential in understanding the regulation of (thus far) unknown genes. Skeletal muscle development is a complex biological process regulated by numerous genes and non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). In this study, we used deep sequencing data from sheep longissimus dorsi (LD) muscles sampled at day 60, 90, and 120 of gestation, as well as at day 0 and 360 following birth, to identify and examine the lncRNA and miRNA temporal expression profiles that regulate sheep skeletal myogenesis. We stained LD muscles using histological sections to analyse the area and circumference of muscle fibers from the embryonic to postnatal development stages. Our results showed that embryonic skeletal muscle growth can be characterized by time. We obtained a total of 694 different lncRNAs and compared the differential expression between the E60 vs. E90, E90 vs. E120, E120 vs. D0, and D0 vs. D360 lncRNA and gene samples. Of the total 701 known sheep miRNAs we detected, the following showed a wide range of expression during the embryonic stage: miR-2387, miR-105, miR-767, miR-432, and miR-433. We propose that the detected lncRNA expression was time-specific during the gestational and postnatal stages. GO and KEGG analyses of the genes targeted by different miRNAs and lncRNAs revealed that these significantly enriched processes and pathways were consistent with skeletal muscle development over time across all sampled stages. We found four visual lncRNA–gene regulatory networks that can be used to explore the function of lncRNAs in sheep and may be valuable in helping improve muscle growth. This study also describes the function of several lncRNAs that interact with miRNAs to regulate myogenic differentiation. creator: Chao Yuan creator: Ke Zhang creator: Yaojing Yue creator: Tingting Guo creator: Jianbin Liu creator: Chune Niu creator: Xiaoping Sun creator: Ruilin Feng creator: Xiaolong Wang creator: Bohui Yang uri: https://doi.org/10.7717/peerj.9957 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Yuan et al. title: Species distribution modelling of Bryde’s whales, humpback whales, southern right whales, and sperm whales in the southern African region to inform their conservation in expanding economies link: https://peerj.com/articles/9997 last-modified: 2020-09-22 description: In southern African waters, information about species distribution and habitat preferences of many cetacean species is limited, despite the recent economic growth that may affect them. We determined the relative importance of eight environmental variables (bathymetry, distance to shore, slope, chlorophyll-a, salinity, eastwards sea water velocity, northwards sea water velocity and sea surface temperature) as drivers of seasonal habitat preferences of Bryde’s whales (Balaenoptera brydei), humpback whales (Megaptera novaeangliae), southern right whales (Eubalaena australis) and sperm whales (Physeter macrocephalus). Using presence only data from multiple sources, we constructed predictive species distribution models (SDMs) consisting of ensembles of seven algorithms for these species during both summer and winter. Predicted distribution for all cetaceans was high in southern Africa and, in particular, within the South African Exclusive Economic Zone (EEZ). Predictive models indicated a more pronounced seasonal variation for humpback, sperm and southern right whales than for Bryde’s whales. Southern right whales occurred closer to shore during winter, humpback whales were more likely to occur along the east coast in winter and the west coast in summer, and sperm whales were more concentrated off the shelf in winter. Our study shows that ensemble models using historical, incidental and scientific data, in conjunction with modern environmental variables, can provide baseline knowledge on important environmental drivers of cetacean distribution for conservation purposes. Results of this study can further be used to help develop marine spatial plans and identify important marine mammal areas. creator: Jean Purdon creator: Fannie W. Shabangu creator: Dawit Yemane creator: Marc Pienaar creator: Michael J. Somers creator: Ken Findlay uri: https://doi.org/10.7717/peerj.9997 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Purdon et al. title: Quinquelaophonte enormis sp. nov., a new interstitial copepod (Harpacticoida: Laophontidae) from Korea link: https://peerj.com/articles/10007 last-modified: 2020-09-22 description: We collected an undescribed laophontid copepod from a coarse sand habitat on the east coast of Korea and named it Quinquelaophonte enormissp. nov. We compared the detailed morphological characteristics of the new species with those of congeneric species. Among them, the new species shows a superficial resemblance to the Californian species Quinquelaophonte longifurcataLang, 1965. However, the two species are easily distinguishable by the setation of the syncoxa on the maxilliped and the fourth swimming leg. The new species has the variable setation on the second to fourth swimming legs. The variations appear among individuals or between the left and right rami of a pair of legs in a single specimen. Although complex chaetotaxical polymorphism occur in this new species, we used myCOI and Cytb to confirm that the new species is not a species complex. Also, partial sequences of 18S and 28S ribosomal RNA genes were used to analyze the position of the new species within the family Laophontidae. The new speciesis the fourteenth Quinquelaophonte species in the world and the second species in Korea. creator: Jaehyun Kim creator: Eunjung Nam creator: Wonchoel Lee uri: https://doi.org/10.7717/peerj.10007 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kim et al. title: Genome-wide identification and expression analysis of the ERF transcription factor family in pineapple (Ananas comosus (L.) Merr.) link: https://peerj.com/articles/10014 last-modified: 2020-09-22 description: Pineapple (Ananas comosus (L.) Merr.) is an important tropical fruit with high economic value. The quality and yield of pineapple will be affected by various environmental conditions. Under adverse conditions, plants can produce a complex reaction mechanism to enhance their resistance. It has been reported that the member of ethylene responsive transcription factors (ERFs) plays a crucial role in plant developmental process and stress response. However, the function of these proteins in pineapple remains limited. In this study, a total of 74 ERF genes (AcoERFs) were identified in pineapple genome, named from AcoERF1 to AcoERF74, and divided into 13 groups based on phylogenetic analysis. We also analyzed gene structure, conserved motif and chromosomal location of AcoERFs, and the AcoERFs within the same group possess similar gene structures and motif compositions. Three genes (AcoERF71, AcoERF73 and AcoERF74) were present on unanchored scaffolds, so they could not be conclusively mapped on chromosome. Synteny and cis-elements analysis of ERF genes provided deep insight into the evolution and function of pineapple ERF genes. Furthermore, we analyzed the expression profiling of AcoERF in different tissues and developmental stages, and 22 AcoERF genes were expressed in all examined tissues, in which five genes (AcoERF13, AcoERF16, AcoERF31, AcoERF42, and AcoERF65) had high expression levels. Additionally, nine AcoERF genes were selected for functional verification by qRT-PCR. These results provide useful information for further investigating the evolution and functions of ERF family in pineapple. creator: Youmei Huang creator: Yanhui Liu creator: Man Zhang creator: Mengnan Chai creator: Qing He creator: Bello Hassan Jakada creator: Fangqian Chen creator: Huihuang Chen creator: Xingyue Jin creator: Hanyang Cai creator: Yuan Qin uri: https://doi.org/10.7717/peerj.10014 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Huang et al. title: No Mow May lawns have higher pollinator richness and abundances: An engaged community provides floral resources for pollinators link: https://peerj.com/articles/10021 last-modified: 2020-09-22 description: No Mow May is a community science initiative popularized in recent years that encourages property owners to limit their lawn mowing practices during the month of May. The goal of No Mow May is to provide early season foraging resources for pollinators that emerge in the spring, especially in urban landscapes when few floral resources are available. We worked with the city council of Appleton, Wisconsin, USA. to allow No Mow May to take place in May 2020. Four hundred and thirty-five property owners registered for No Mow May in Appleton. We measured floral and bee richness and abundance in the yards of a subset of homes (N = 20) located near regularly mowed urban parks (N = 15) at the end of the month. We found that homes that participated in No Mow May had more diverse and abundant flora than regularly mowed green spaces throughout the city. No Mow May homes had three times higher bee richness and five times higher bee abundances than frequently mowed greenspaces. Using generalized linear models, we found that the best predictor of bee richness was the size of the designated unmowed area, and the best predictors of bee abundances were the size of the unmowed area as well as floral richness. While our findings cannot conclusively attribute increases in bee abundances and richness to the No Mow May efforts, our data does show that bee pollinators make use of no mow spaces as key floral resources during early spring in the upper midwestern United States. A post-No Mow May survey revealed that the participants were keen to increase native floral resources in their yards, increase native bee nesting habitat, reduce mowing intensities, and limit herbicide, pesticide, and fertilizer applications to their lawns. The No Mow May initiative educated an engaged community on best practices to improve the conservation of urban pollinators in future years. creator: Israel Del Toro creator: Relena R. Ribbons uri: https://doi.org/10.7717/peerj.10021 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Del Toro and Ribbons title: A comparison of sex, morphology, physiology and behavior of black-capped chickadees trapped using two common capture methods link: https://peerj.com/articles/10037 last-modified: 2020-09-22 description: Many biological studies require the capture of individuals for sampling, for example for measurement of morphological or physiological traits, or for marking individuals for later observations. Capture methods employed often vary both within and between studies, and these differing methods could be more or less effective in capture of different individuals based on their morphology or behavior. If individuals that are prone to capture by the selected method differ with respect to traits of interest, such sampling bias could generate misleading or simply inaccurate results. The selection of capture methods could introduce two different forms of sampling bias, with the individuals that are sampled differing from the population at large or with individuals sampled via one method differing from individuals that could be sampled using a different method. We investigated this latter form of sampling bias by comparing individual birds sampled using two common capture techniques. We caught free-ranging black-capped chickadees (Poecile atricapillus) using walk-in traps baited with seed and mist nets paired with playback of an audio stimulus (conspecific mobbing calls). We measured 18 traits that we expect might vary among birds that are trappable by these differing methods—one that targets birds that are food motivated and potentially less neophobic and another that targets birds that respond readily to a perceived predation risk. We found no differences in the sex, morphology, initial and stress-induced corticosterone concentrations, behavioral response to a novel object, or behavioral response to a predator between individuals captured by these two methods. Individual variation in the behavioral response to a novel object was greater among birds caught by mist nets, suggesting this method might provide a sample that better reflects population-level individual variation. We do not know if the birds caught by these two methods provide a representative sample of the population at large, but can conclude that selection of either of these two common capture methods can similarly sample mean trait values of a population of interest. To accurately assess individual variation, particularly in behavior, mist nets might be preferable. creator: Sara M. Burns creator: Frances Bonier uri: https://doi.org/10.7717/peerj.10037 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Burns and Bonier title: A laboratory comparison of the interactions between three plastic mulch types and 38 active substances found in pesticides link: https://peerj.com/articles/9876 last-modified: 2020-09-21 description: BackgroundIn semi-arid regions, the use of plastic mulch and pesticides in conventional agriculture is nearly ubiquitous. Although the sorption of pesticides on Low Density Polyethylene (LDPE) has been previously studied, no data are available for other plastics such as Pro-oxidant Additive Containing (PAC) plastics or “biodegradable” (Bio) plastics. The aim of this research was to measure the sorption pattern of active substances from pesticides on LDPE, PAC and Bio plastic mulches and to compare the decay of the active substances in the presence and absence of plastic debris.MethodsFor this purpose, 38 active substances from 17 insecticides, 15 fungicides and six herbicides commonly applied with plastic mulching in South-east Spain were incubated with a 3 × 3 cm2 piece of plastic mulch (LDPE, PAC and Bio). The incubation was done in a solution of 10% acetonitrile and 90% distilled water at 35 °C for 15 days in the dark. The Quick Easy Cheap Effective Rugged Safe approach was adapted to extract the pesticides.ResultsThe sorption behavior depended on both the pesticide and the plastic mulch type. On average, the sorption percentage was ~23% on LDPE and PAC and ~50% on Bio. The decay of active substances in the presence of plastic was ~30% lesser than the decay of active substances in solution alone. This study is the first attempt at assessing the behavior of a diversity of plastic mulches and pesticides to further define research needs. creator: Nicolas Beriot creator: Paul Zomer creator: Raul Zornoza creator: Violette Geissen uri: https://doi.org/10.7717/peerj.9876 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Beriot et al. title: Nest-site selection and breeding success of passerines in the world’s southernmost forests link: https://peerj.com/articles/9892 last-modified: 2020-09-21 description: BackgroundBirds can maximize their reproductive success through careful selection of nest-sites. The ‘total-foliage’ hypothesis predicts that nests concealed in vegetation should have higher survival. We propose an additional hypothesis, the ‘predator proximity’ hypothesis, which states that nests placed farther from predators would have higher survival. We examined these hypotheses in the world’s southernmost forests of Navarino Island, in the Cape Horn Biosphere reserve, Chile (55°S). This island has been free of mammalian ground predators until recently, and forest passerines have been subject to depredation only by diurnal and nocturnal raptors.MethodsDuring three breeding seasons (2014–2017), we monitored 104 nests for the five most abundant open-cup forest-dwelling passerines (Elaenia albiceps, Zonotrichia capensis, Phrygilus patagonicus, Turdus falcklandii, and Anairetes parulus). We identified nest predators using camera traps and assessed whether habitat characteristics affected nest-site selection and survival.ResultsNest predation was the main cause of nest failure (71% of failed nests). Milvago chimango was the most common predator, depredating 13 (87%) of the 15 nests where we could identify a predator. By contrast, the recently introduced mammal Neovison vison, the only ground predator, depredated one nest (7%). Species selected nest-sites with more understory cover and taller understory, which according to the total-foliage hypothesis would provide more concealment against both avian and mammal predators. However, these variables negatively influenced nest survival. The apparent disconnect between selecting nest-sites to avoid predation and the actual risk of predation could be due to recent changes in the predator assemblage driven by an increased abundance of native M. chimango associated with urban development, and/or the introduction of exotic mammalian ground predators to this island. These predator assemblage changes could have resulted in an ecological trap. Further research will be needed to assess hypotheses that could explain this mismatch between nest-site selection and nest survival. creator: Rocío Fernanda Jara creator: Ramiro Daniel Crego creator: Michael David Samuel creator: Ricardo Rozzi creator: Jaime Enrique Jiménez uri: https://doi.org/10.7717/peerj.9892 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Jara et al.