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: Field evaluation of the potential for avian exposure to clothianidin following the planting of clothianidin-treated corn seed link: https://peerj.com/articles/5880 last-modified: 2018-11-07 description: The objective of this study was to quantify consumption of clothianidin-treated corn seed by birds following standard planting practices. Based on post-planting seed counts on 21 fields in southwestern Ontario, Canada, between 29 and 813 seeds/ha (mean of 224 ± 167 (SD)) were estimated to remain on the soil surface immediately post planting (i.e., less than one seed per 10 m2). This represents between 0.03 and 1.2% of the total sown seeds. The number of seeds missing on each field on the third day after planting as a result of any process (e.g., removal by foraging birds or mammals or burial as a result of heavy rains) ranged from 0 to 136 seeds/ha (0 to 0.0136 seeds/m2). Behavior monitoring of individual birds and 24 h remote video surveillance were deployed to investigate how much of the treated seed remaining on the soil surface was consumed by birds. Spotting scopes were used to monitor the full duration of the field visits of 596 individual birds during morning hours for three consecutive days after planting on the 21 fields. Two birds were observed consuming treated seeds (one seed each) and three birds consumed seeds for which the treatment status could not be visually confirmed. Additionally, constant (24 h) video surveillance for 2–4 days immediately after planting was deployed at 24 areas where multiple treated seeds were found on the soil surface. Across 1,380 h of collected video footage (including both day and night periods), no birds were observed to consume any treated seeds. This study provides field evidence of two factors that determine exposure of birds to clothianidin-treated corn seeds: (1) standard sowing practices in Ontario are effective at burying treated seeds such that the proportion of sown seeds that remain on the soil surface after planting is low, and (2) birds monitored on these fields consumed very few of the clothianidin-treated corn seeds remaining on the soil surface after planting. As these results are dependent on planting techniques and seed characteristics, they are not necessarily applicable to other types of clothianidin treated seed. creator: Sean McGee creator: Melissa Whitfield-Aslund creator: Daiana Duca creator: Nicole Kopysh creator: Tereza Dan creator: Loren Knopper creator: Larry Brewer uri: https://doi.org/10.7717/peerj.5880 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 McGee et al. title: PromoterPredict: sequence-based modelling of Escherichia coli σ70 promoter strength yields logarithmic dependence between promoter strength and sequence link: https://peerj.com/articles/5862 last-modified: 2018-11-07 description: We present PromoterPredict, a dynamic multiple regression approach to predict the strength of Escherichia coli promoters binding the σ70 factor of RNA polymerase. σ70 promoters are ubiquitously used in recombinant DNA technology, but characterizing their strength is demanding in terms of both time and money. We parsed a comprehensive database of bacterial promoters for the −35 and −10 hexamer regions of σ70-binding promoters and used these sequences to construct the respective position weight matrices (PWM). Next we used a well-characterized set of promoters to train a multivariate linear regression model and learn the mapping between PWM scores of the −35 and −10 hexamers and the promoter strength. We found that the log of the promoter strength is significantly linearly associated with a weighted sum of the −10 and −35 sequence profile scores. We applied our model to 100 sets of 100 randomly generated promoter sequences to generate a sampling distribution of mean strengths of random promoter sequences and obtained a mean of 6E-4 ± 1E-7. Our model was further validated by cross-validation and on independent datasets of characterized promoters. PromoterPredict accepts −10 and −35 hexamer sequences and returns the predicted promoter strength. It is capable of dynamic learning from user-supplied data to refine the model construction and yield more robust estimates of promoter strength. PromoterPredict is available as both a web service (https://promoterpredict.com) and standalone tool (https://github.com/PromoterPredict). Our work presents an intuitive generalization applicable to modelling the strength of other promoter classes. creator: Ramit Bharanikumar creator: Keshav Aditya R. Premkumar creator: Ashok Palaniappan uri: https://doi.org/10.7717/peerj.5862 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Bharanikumar et al. title: Application of a MALDI-TOF analysis platform (ClinProTools) for rapid and preliminary report of MRSA sequence types in Taiwan link: https://peerj.com/articles/5784 last-modified: 2018-11-07 description: BackgroundThe accurate and rapid preliminarily identification of the types of methicillin-resistant Staphylococcus aureus (MRSA) is crucial for infection control. Currently, however, expensive, time-consuming, and labor-intensive methods are used for MRSA typing. By contrast, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a potential tool for preliminary lineage typing. The approach has not been standardized, and its performance has not been analyzed in some regions with geographic barriers (e.g., Taiwan Island).MethodsThe mass spectra of 306 MRSA isolates were obtained from multiple reference hospitals in Taiwan. The multilocus sequence types (MLST) of the isolates were determined. The spectra were analyzed for the selection of characteristic peaks by using the ClinProTools software. Furthermore, various machine learning (ML) algorithms were used to generate binary and multiclass models for classifying the major MLST types (ST5, ST59, and ST239) of MRSA.ResultsA total of 10 peaks with the highest discriminatory power (m/z range: 2,082–6,594) were identified and evaluated. All the single peaks revealed significant discriminatory power during MLST typing. Moreover, the binary and multiclass ML models achieved sufficient accuracy (82.80–94.40% for binary models and >81.00% for multiclass models) in classifying the major MLST types.ConclusionsA combination of MALDI-TOF MS analysis and ML models is a potentially accurate, objective, and efficient tool for infection control and outbreak investigation. creator: Hsin-Yao Wang creator: Frank Lien creator: Tsui-Ping Liu creator: Chun-Hsien Chen creator: Chao-Jung Chen creator: Jang-Jih Lu uri: https://doi.org/10.7717/peerj.5784 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Wang et al. title: Diurnal and seasonal variation of particle and dissolved organic matter release by the coral Acropora tenuis link: https://peerj.com/articles/5728 last-modified: 2018-11-07 description: Release rates of particulate organic carbon and nitrogen (POC and PON) and dissolved organic carbon (DOC) from the scleractinian coral Acropora tenuis were measured during the day and night in summer and winter seasons. Physiological parameters including calcification, photosynthesis and respiration rates were also measured simultaneously. The release rate of both POC and DOC was significantly higher in summer compared to winter and higher during the day compared to the night. The daily release rate of total organic carbon (POC + DOC) was 1,094 and 219 μmol C cm−2 d−1 for summer and winter, respectively, being 4.9 times higher in summer. The POC:PON ratios of the particulate organic matter released during daytime in both seasons (summer: 12.8 ± 5.7, winter: 12.0 ± 4.1) were significantly higher than those during nighttime (summer: 6.1 ± 2.5, winter: 2.2 ± 1.8). The DOC:POC ratio was 0.5 ± 0.03 during summer and 0.32 ± 0.98 during winter, suggesting higher mucus release in particulate form. Daily net production was estimated to be 199 and 158 μg C cm−2d−1 for summer and winter, respectively, with the amount of carbon released as mucus accounting for 6.5% and 1.6% of the net carbon fixation, respectively. The study reveals diurnal and seasonal changes in the quantity and quality of mucus released from this coral species. Since coral mucus is used as a food source by reef macro-organisms, and can also serve as an energy source for micro-organisms, the observed changes in mucus release rates are expected to influence the seasonal dynamics of organic carbon and nitrogen cycling over coral reefs. creator: Haruko Kurihara creator: Nao Ikeda creator: Yu Umezawa uri: https://doi.org/10.7717/peerj.5728 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Kurihara et al. title: Hemiparasitic plants increase alpine plant richness and evenness but reduce arbuscular mycorrhizal fungal colonization in dominant plant species link: https://peerj.com/articles/5682 last-modified: 2018-11-07 description: Hemiparasitic plants increase plant biodiversity by reducing the abundance of dominant plant species, allowing for the establishment of subordinate species. Hemiparasites reduce host resources by directly removing nutrients from hosts, competing for light and space, and may indirectly reduce host resources by disrupting plant associations with symbiotic root fungi, like arbuscular mycorrhizal fungi and dark-septate endophytes. Here, we explored how a generalist hemiparasite, Castilleja, influences plant richness, evenness, community composition, and mycorrhizal colonization patterns across a ∼1,000 m elevational gradient in the North American Rocky Mountains. We hypothesized that the presence of Castilleja would be associated with increased plant richness and evenness, shaping plant community composition, and would reduce mycorrhizal colonization within dominant plant taxa. However, the magnitude of the effects would be contingent upon climate contexts, that is, elevation. Overall, we found that the presence of Castilleja was associated with an 11% increase in plant richness and a 5% increase in plant evenness, regardless of elevation. However, we found that the presence of Castilleja influenced plant composition at only two of the five sites and at the remaining three of five sites, plot pairing was the only predictor that influenced composition. Additionally, we found that the presence of Castilleja reduced mycorrhizal fungal colonization within dominant plant species by ∼20%, regardless of elevation. Taken together, our results suggest that hemiparasites regulate plant diversity, evenness, and interactions with mycorrhizal fungi independent of abiotic and biotic contexts occurring at the site, although overall effect on community composition is likely driven by site-level factors. creator: Michael McKibben creator: Jeremiah A. Henning uri: https://doi.org/10.7717/peerj.5682 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 McKibben and Henning title: Mapping the distribution of scale-rayed wrasse Acantholabrus palloni in Swedish Skagerrak using angling records link: https://peerj.com/articles/5900 last-modified: 2018-11-06 description: In this paper, we map the distribution of scale-rayed wrasse Acantholabrus palloni in eastern Skagerrak based on a combination of verified and personally communicated angling records. Long thought to be occasional vagrants outside its known range in the eastern Atlantic Ocean and Mediterranean Sea, we ask if this rare and understudied labrid has expanded its range and become established in Swedish waters. A recent surge in verified angling records in the Swedish Anglers Association’s specimen database Storfiskregistret provides information to suggest that this species should no longer be considered an occasional guest, but rather a species established in the Swedish parts of Skagerrak. These records are supported by additional personal communications with anglers. The species is currently well spread geographically along the Swedish Skagerrak coast, with many locations providing repeated captures of adult fish over multiple years. The typical Swedish catch sites are rocky reefs located between the general 40- and 80-m depth curves, likely influenced by currents bringing higher-salinity water from the North Sea. The present study show that angling records can provide an important, but underutilized, resource for mapping the distribution of data-deficient fish species. creator: Joacim Näslund creator: Markus Lundgren uri: https://doi.org/10.7717/peerj.5900 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Näslund and Lundgren title: Trait-based predation suitability offers insight into effects of changing prey communities link: https://peerj.com/articles/5899 last-modified: 2018-11-06 description: Increasing environmental pressures and human impacts are reshaping community structures and species interactions throughout all trophic levels. The morphological and behavioural characteristics of species communities contain key ecological information on why prey species appear attractive to predators but are rarely applied when exploring predator-prey (PP) relationships. Expanding our knowledge on how changing prey communities can alter the food resource suitability (RS) for predators is vital for understanding PP dynamics in changing ecosystems. Detailed predator diet data are commonly restricted to commercially important species and often not available over long temporal scales. To find out whether structural changes of prey communities impact the food RS for predator communities over space and time, we apply a novel framework to describe and interpret changes in predator diet-suitability based on predation-relevant traits of prey. We use information on described feeding links from the literature to compile the prey spectrum for each predator and subsequently translate the prey-species into a prey-trait spectrum. For each predator, we then calculate a frequency-based prey-trait affinity score and relate it to the available food resource pool, the community weighted means of prey traits, resulting in a prey-suitability measure. We aim to reveal whether a described multi-decadal change in the community structure of zoobenthos had an impact on the food suitability for the benthic-feeding fish in a coastal system of the Baltic Sea. We assess the direction of change in resource quality from the perspective of benthic-feeding fish and describe predator-specific responses to examine which species are likely to profit or be disadvantaged by changes in their prey spectrum. Furthermore, we test the relationship between functional diversity of prey communities and food suitability for predators, and whether predation linkage-structures are affected through prey community-changes. Our results show that changes in zoobenthic communities had a positive effect on the food suitability for most benthic-feeding fish, implying more suitable food resources. Species-specific responses of predators suggest varying plasticity to cope with prey assemblages of different trait compositions. Additionally, the functional diversity of zoobenthos had a positive effect on the food suitability for predator fish. The changing trait compositions of prey influenced the PP linkage-structure, indicating varying specialisation of benthic feeding fish towards available food resources. Our findings suggest that changing morphological characteristics of prey can impact food RS features for its predators. This approach enables long-term evaluation of prey quality characteristics where no detailed diet data is available and allows for cross-system comparison as it is not relying on taxonomic identities per se. creator: Benjamin Weigel creator: Erik Bonsdorff uri: https://doi.org/10.7717/peerj.5899 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Weigel and Bonsdorff title: Experimental food supplementation increases reproductive effort in the Variable Antshrike in subtropical Brazil link: https://peerj.com/articles/5898 last-modified: 2018-11-06 description: Food limitation may interact with nest predation and influence nesting patterns, such as breeding season length and renesting intervals. If so, reproductive effort should change with food availability. Thus, when food is limited, birds should have fewer attempts and shorter seasons than when food is not limiting. Here we experimentally test that increased food availability results in increased reproductive effort in a fragmented landscape in the Variable Antshrike (Thamnophilus caerulescens) in southern Brazil. We followed nesting pairs in a naturally fragmented habitat and experimentally supplemented food for half of those pairs. Birds were seen, but evidence of nesting was never found in two small fragments, even though these fragments were larger than individual territories. Pairs with supplemented food were more likely to increase clutch size from two to three eggs and tended to renest sooner (20 d on average) than control pairs. Also, fragment size was associated with breeding patterns, although fragment replicates were unavailable. Nest duration, nest success and breeding season length were all greater, while renesting intervals were shorter, in the largest fragments. Simulations showed that only the largest fragments were able to have a net production of young. Food availability clearly influenced reproductive effort and as a consequence, because of the interaction with predation risk, forest fragments of varying sizes will have complex reproductive dynamics. creator: James J. Roper creator: André M.X. Lima creator: Angélica M.K. Uejima uri: https://doi.org/10.7717/peerj.5898 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Roper et al. title: Sociality genes are associated with human-directed social behaviour in golden and Labrador retriever dogs link: https://peerj.com/articles/5889 last-modified: 2018-11-06 description: BackgroundDogs have human-directed social skills that allow them to communicate and cooperate with humans. We have previously identified two loci on chromosome 26 associated with human contact-seeking behaviors during an unsolvable problem task in laboratory beagles (Persson et al., 2016). The aim of the present study was to verify the single nucleotide polymorphisms (SNPs) in additional dog breeds. We also studied how the allele frequencies have changed during domestication and recent selection.MethodsDogs of two breeds, 61 golden retrievers and 100 Labrador retrievers, were phenotyped and genotyped, and 19 wolves were genotyped. The Labrador retrievers were divided into common and field type by pedigree data to make it possible to study the effects of recent selection. All dogs were tested in an unsolvable problem task where human-directed social behaviors were scored. DNA from dogs (buccal swabs) and wolves (blood or brain tissue) was analyzed for genotype on two of the previously identified SNP markers, BICF2G630798942 (SNP1) and BICF2S23712114 (SNP2), by pyrosequencing.ResultsThere was genetic variation for SNP1 in both dog breeds whereas the wolves were fixed for this polymorphism, and for SNP2 there was variation in both dogs and wolves. For both SNPs, Labrador retriever types differed significantly in allele frequencies. We found associations between SNPs and human-directed social behavior in both dog breeds. In golden retrievers, SNP1 was associated with physical contact variables, for example, with the duration of physical contact with the owner (F2,56 = 4.389, p = 0.017). SNP2 was associated with several behavioral variables in both breeds, among others owner gazing frequency in both golden retrievers (F2,55 = 6.330, p = 0.003) and Labradors (F1,93 = 5.209, p = 0.025).DiscussionOur results verify the association between the previously identified SNPs and human-directed social behavior scored in an unsolvable problem task. Differences in allele frequencies suggest that these loci have been affected by selection. The results indicate that these genomic regions are involved in human-directed social behavior in not only beagles but in other dog breeds as well. We hypothesize that they may have been important during dog domestication. creator: Mia E. Persson creator: Ann-Sofie Sundman creator: Lise-Lotte Halldén creator: Agaia J. Trottier creator: Per Jensen uri: https://doi.org/10.7717/peerj.5889 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Persson et al. title: Canadian packaged gluten-free foods are less nutritious than their regular gluten-containing counterparts link: https://peerj.com/articles/5875 last-modified: 2018-11-06 description: BackgroundA strict gluten-free (GF) diet is required for the management of celiac disease (CD). The nutritional adequacy of this diet has been questioned due to the elimination of wheat, an important vehicle for micronutrient fortification and source of fibre. While novel and/or reformulated packaged GF products have rapidly entered the marketplace, providing alternatives to wheat-based staples, it is unknown whether these new products are nutritionally comparable.MethodsFrom a database of 3,851 foods collected across 21 grocery stores in Eastern Canada, we compared the nutrient content of 398 unique GF items with 445 gluten-containing (GC) equivalents. Wilcoxon rank tests were conducted on listed nutrient content (g, mg, µg) per 100 g of product and the nutrient contribution of iron, folate and fibre were evaluated using Health Canada’s nutrient claim regulations.ResultsGF staples (cereals, breads, flours, pastas) contained 1.3 times more fat and less iron (by 55%), folate (by 44%) and protein (by 36%), than GC counterparts (P < 0.0001). On average, GF pastas had only 37% of the fibre in GC pastas (P < 0.0001). Notably, GF and GC flours were equivalent in nutrient content. Despite GF and GC flours having similar nutritional content, the vast majority of the processed GF foods fell short in key nutrients.DiscussionPackaged GF foods in Canada are generally less nutritious than their GC counterparts, suggesting that GF diets should not be promoted to those who do not require it. The use of nutrient-dense GF flours in homemade foods may improve nutrient intakes on the GF diet. creator: Jennifer A. Jamieson creator: Mary Weir creator: Laura Gougeon uri: https://doi.org/10.7717/peerj.5875 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Jamieson et al.