title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1462 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Evaluation of soil intervention values in mine tailings in northern Chile link: https://peerj.com/articles/5879 last-modified: 2018-11-02 description: The aim of this work is to show a methodological proposal for the analysis of soil intervention values in mine tailings in order to determine the intervention requirements in the commune of Andacollo in northern Chile. The purpose of this analysis is to guide the intervention policies of both private and public organizations. The evaluation method is based on the Dutch legislation. The usability of the proposed methods depends on the available geochemical data from soil samples; in particular, we tackle the case when information regarding clay percentage in the soil is not available. We use the concepts of a threshold factor and an adjusted threshold factor to calculate a weighted intervention ranking. In order to illustrate the utility of this methodological proposal, a case study is carried out with the prescribed approach. In particular, this work presents an analysis of the elements of environmental significance related to the mining activity (Hg, Cd, Pb, As, Cu, Ni, Zn, Cr) in the commune of Andacollo, Coquimbo Region, Chile. The analyzed samples are used to determine where the intervention of tailing deposits is necessary and where a solution to these environmental liabilities is required as soon as possible. Out of the 81 samples evaluated, it was found that 18 require a potential intervention, and of these samples, seven of them are associated with abandoned tailings that, in some cases, are located close to the town center itself, one sample is associated with active tailings and the other 10 with inactive tailings. creator: Elizabeth Lam Esquenazi creator: Brian Keith Norambuena creator: Ítalo Montofré Bacigalupo creator: María Gálvez Estay uri: https://doi.org/10.7717/peerj.5879 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Lam Esquenazi et al. title: Dynamic proteomic changes in soft wheat seeds during accelerated ageing link: https://peerj.com/articles/5874 last-modified: 2018-11-02 description: Previous research demonstrated that soft wheat cultivars have better post-harvest storage tolerance than harder cultivars during accelerated ageing. To better understand this phenomenon, a tandem mass tag-based quantitative proteomic analysis of soft wheat seeds was performed at different storage times during accelerated ageing (germination ratios of 97%, 45%, 28%, and 6%). A total of 1,010 proteins were differentially regulated, of which 519 and 491 were up- and downregulated, respectively. Most of the differentially expressed proteins were predicted to be involved in nutrient reservoir, enzyme activity and regulation, energy and metabolism, and response to stimulus functions, consistent with processes occurring in hard wheat during artificial ageing. Notably, defense-associated proteins including wheatwin-2, pathogenesis-related proteins protecting against fungal invasion, and glutathione S-transferase and glutathione synthetase participating in reactive oxygen species (ROS) detoxification, were upregulated compared to levels in hard wheat during accelerated ageing. These upregulated proteins might be responsible for the superior post-harvest storage-tolerance of soft wheat cultivars during accelerated ageing compared with hard wheat. Although accelerated ageing could not fully mimic natural ageing, our findings provided novel dynamic proteomic insight into soft wheat seeds during seed deterioration. creator: Yangyong Lv creator: Pingping Tian creator: Shuaibing Zhang creator: Jinshui Wang creator: Yuansen Hu uri: https://doi.org/10.7717/peerj.5874 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Lv et al. title: Ontogenetic changes in swimming speed of silver carp, bighead carp, and grass carp larvae: implications for larval dispersal link: https://peerj.com/articles/5869 last-modified: 2018-11-02 description: Bighead, silver, and grass carps are invasive in the waterways of central North America, and grass carp reproduction in tributaries of the Great Lakes has now been documented. Questions about recruitment potential motivate a need for accurate models of egg and larval dispersal. Quantitative data on swimming behaviors and capabilities during early ontogeny are needed to improve these dispersal models. We measured ontogenetic changes in routine and maximum swimming speeds of bighead, grass, and silver carp larvae. Daily measurements of routine swimming speed were taken for two weeks post-hatch using a still camera and the LARVEL program, a custom image-analysis software. Larval swimming speed was calculated using larval locations in subsequent image frames and time between images. Using an endurance chamber, we determined the maximum swimming speed of larvae (post-gas bladder inflation) for four to eight weeks post-hatch. For all species, larval swimming speeds showed similar trends with respect to ontogeny: increases in maximum speed, and decreases in routine speed. Maximum speeds of bighead and grass carp larvae were similar and generally faster than silver carp larvae. Routine swimming speeds of all larvae were highest before gas bladder inflation, most likely because gas bladder inflation allowed the fish to maintain position without swimming. Downward vertical velocities of pre-gas bladder inflation fish were faster than upward velocities. Among the three species, grass carp larvae had the highest swimming speeds in the pre-gas bladder inflation period, and the lowest speeds in the post-gas bladder inflation period. Knowledge of swimming capability of these species, along with hydraulic characteristics of a river, enables further refinement of models of embryonic and larval drift. creator: Amy E. George creator: Tatiana Garcia creator: Benjamin H. Stahlschmidt creator: Duane C. Chapman uri: https://doi.org/10.7717/peerj.5869 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: Elaborate plumage patterning in a Cretaceous bird link: https://peerj.com/articles/5831 last-modified: 2018-11-02 description: Integumentary patterns and colors can differentiate species, sexes, and life changes and can inform on habitat and ecology. However, they are rarely preserved in the fossil record. Here, we report on an extremely well-preserved specimen of the Cretaceous bird Confuciusornis with unprecedented complexity, including small spots on the wings, crest, and throat. Morphological and chemical evidence suggest that these patterns are produced by melanin, but unusual preservation prevents assignment of specific colors. Based on comparisons with extant birds, these patterns were likely used for camouflage, although other functions including sexual signaling cannot be ruled out. Our data show that even more elaborate plumage patterns than the spangles in Anchiornis and stripes in Sinosauropteryx were present at a relatively early stage of avian evolution, showing the significance of coloration and patterning to feather evolution. creator: Quanguo Li creator: Julia A. Clarke creator: Ke-Qin Gao creator: Jennifer A. Peteya creator: Matthew D. Shawkey uri: https://doi.org/10.7717/peerj.5831 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Li et al. title: Structure, dynamics and predicted functional role of the gut microbiota of the blue (Haliotis fulgens) and yellow (H. corrugata) abalone from Baja California Sur, Mexico link: https://peerj.com/articles/5830 last-modified: 2018-11-02 description: The GI microbiota of abalone contains a highly complex bacterial assemblage playing an essential role in the overall health of these gastropods. The gut bacterial communities of abalone species characterized so far reveal considerable interspecific variability, likely resulting from bacterial interactions and constrained by the ecology of their abalone host species; however, they remain poorly investigated. Additionally, the extent to which structural changes in the microbiota entail functional shifts in metabolic pathways of bacterial communities remains unexplored. In order to address these questions, we characterized the gut microbiota of the northeast Pacific blue (Haliotis fulgens or HF) and yellow (Haliotis corrugata or HC) abalone by 16S rRNA gene pyrosequencing to shed light on: (i) their gut microbiota structure; (ii) how bacteria may interact among them; and (iii) predicted shifts in bacterial metabolic functions associated with the observed structural changes. Our findings revealed that Mycoplasma dominated the GI microbiome in both species. However, the structure of the bacterial communities differed significantly in spite of considerable intraspecific variation. This resulted from changes in predominant species composition in each GI microbiota, suggesting host-specific adaptation of bacterial lineages to these sympatric abalone. We hypothesize that the presence of exclusive OTUs in each microbiota may relate to host-specific differences in competitive pressure. Significant differences in bacterial diversity were found between species for the explored metabolic pathways despite their functional overlap. A more diverse array of bacteria contributed to each function in HC, whereas a single or much fewer OTUs were generally observed in HF. The structural and functional analyses allowed us to describe a significant taxonomic split and functional overlap between the microbiota of HF and HC abalone. creator: Francesco Cicala creator: José Alejandro Cisterna-Céliz creator: James D. Moore creator: Axayácatl Rocha-Olivares uri: https://doi.org/10.7717/peerj.5830 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Cicala et al. title: Home sick: impacts of migratory beekeeping on honey bee (Apis mellifera) pests, pathogens, and colony size link: https://peerj.com/articles/5812 last-modified: 2018-11-02 description: Honey bees are important pollinators of agricultural crops and the dramatic losses of honey bee colonies have risen to a level of international concern. Potential contributors to such losses include pesticide exposure, lack of floral resources and parasites and pathogens. The damaging effects of all of these may be exacerbated by apicultural practices. To meet the pollination demand of US crops, bees are transported to areas of high pollination demand throughout the year. Compared to stationary colonies, risk of parasitism and infectious disease may be greater for migratory bees than those that remain in a single location, although this has not been experimentally established. Here, we conducted a manipulative experiment to test whether viral pathogen and parasite loads increase as a result of colonies being transported for pollination of a major US crop, California almonds. We also tested if they subsequently transmit those diseases to stationary colonies upon return to their home apiaries. Colonies started with equivalent numbers of bees, however migratory colonies returned with fewer bees compared to stationary colonies and this difference remained one month later. Migratory colonies returned with higher black queen cell virus loads than stationary colonies, but loads were similar between groups one month later. Colonies exposed to migratory bees experienced a greater increase of deformed wing virus prevalence and load compared to the isolated group. The three groups had similar infestations of Varroa mites upon return of the migratory colonies. However, one month later, mite loads in migratory colonies were significantly lower compared to the other groups, possibly because of lower number of host bees. Our study demonstrates that migratory pollination practices has varying health effects for honey bee colonies. Further research is necessary to clarify how migratory pollination practices influence the disease dynamics of honey bee diseases we describe here. creator: Samantha A. Alger creator: P. Alexander Burnham creator: Zachary S. Lamas creator: Alison K. Brody creator: Leif L. Richardson uri: https://doi.org/10.7717/peerj.5812 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Alger et al. title: Assessment of a mouse xenograft model of primary colorectal cancer with special reference to perfluorooctane sulfonate link: https://peerj.com/articles/5602 last-modified: 2018-11-02 description: Colorectal cancer ranks third among the most commonly diagnosed cancers in the United States. Current therapies have a range of side effects, and the development of a reliable animal model to speed the discovery of safe effective preventative therapies would be of great value. A cross-sectional study in a large Appalachian population recently showed an association between low circulating levels of perfluorooctane sulfonate (PFOS) and a reduced prevalence of colorectal cancer. A study using APCmin (C57BL/6J-ApcMin/J) mice prone to familial adenomatous polyposis found PFOS was protective when exposure occurred during tumor development. To test the possible benefit of PFOS on spontaneous colorectal cancer, we developed a mouse model utilizing primary patient colorectal cancer implants into NSG (NOD.Cg-PrkdcscidIl2rgtm1Wjl/Sz) mice. Study goals included: (1) to assess potential factors supporting the successful use of colorectal cancer from heterogeneous tumors for PDX studies; and, (2) evaluate PFOS as a therapy in tumor matched pairs of mice randomized to receive PFOS or vehicle. The time in days for mice to grow primary tumors to 5 mm took almost 2 months (mean = 53.3, se = 5.7, range = 17–136). Age of mice at implantation, patient age, gender and race appeared to have no discernable effect on engraftment rates. Engraftment rates for low and high-grade patient tumors were similar. PFOS appeared to reduce tumor size dramatically in one group of tumors, those from the right ascending colon. That is, by 5 weeks of treatment in two mice, PFOS had eliminated their 52.4 mm3 and 124.6 mm3 masses completely, an effect that was sustained for 10 weeks of treatment; in contrast, their corresponding matched vehicle control mice had tumors that grew to 472.7 mm3 and 340.1 mm3 in size respectively during the same period. In a third xenograft mouse, the tumor growth was dramatically blunted although not eliminated, and compared favorably to their matched vehicle controls over the same period. These preliminary findings suggested that this mouse model may be advantageous for testing compounds of potential value in the treatment of colorectal cancer, and PFOS may have utility in selected cases. creator: Jeffrey H. Wimsatt creator: Caitlin Montgomery creator: Laurel S. Thomas creator: Charity Savard creator: Rachel Tallman creator: Kim Innes creator: Nezar Jrebi uri: https://doi.org/10.7717/peerj.5602 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wimsatt et al. title: Plant defense elicitors: plant fitness versus wheat stem sawfly link: https://peerj.com/articles/5892 last-modified: 2018-11-01 description: The wheat stem sawfly (WSS), Cephus cinctus Norton, is an important wheat pest in the Northern Great Plains of the USA. No single control measure effectively suppresses WSS damage. This study provides information on the effects on the WSS adult settling preference behavior on wheat plants under laboratory conditions from treatment with both synthetic plant defense elicitors (Actigard® and cis-jasmone) and a botanical insecticide (Azadirachtin®). In addition, field experiments were performed to determine whether these chemicals impact the WSS fitness (larval mortality and larval body weight), winter wheat plant fitness (infestation, stem lodging, yield, and quality), adult population of WSS and Bracon spp., and larval parasitism levels. Our lab results showed that there were no significant differences in adult settling behavior on plants exposed separately to each chemical and control. In contrast, when adults were exposed simultaneously to treated and untreated plants, there was a significant reduction in the percentage of adults settling on Actigard® and Azadirachtin® treated plants compared to plants sprayed with water in the same cage. However, in field situations, regardless of application timing and field location, none of the chemicals significantly reduced adult population or stems damage. The exception was two times applications of Actigard® had significantly lower WSS infested stem damage levels at 30 days after initial treatment applications at Knees and 50 days at Choteau locations compared to control, but without effect at the Conrad location. The field study indicated that two times applications of Actigard® significantly increased diapausing larval mortality percentages and lowered stem lodging levels compared to untreated controls at Knees and Choteau locations, while no effects at Conrad location. Larval body weight was significantly lower in plots treated with Actigard® at Knees and Conrad, but no effects at Choteau. No significant differences were found in wheat yield and quality in plots treated with chemicals and controls at any location. Bracon spp. adult population and parasitism levels were not negatively affected by the use of chemicals. In conclusion, this study offers insights on what treatments should be emphasized in more detail despite variable findings. creator: Govinda Shrestha creator: Shabeg S. Briar creator: Gadi V.P. Reddy uri: https://doi.org/10.7717/peerj.5892 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Shrestha et al. title: Prionochelys matutina Zangerl, 1953 (Testudines: Pan-Cheloniidae) from the Late Cretaceous of the United States and the evolution of epithecal ossifications in marine turtles link: https://peerj.com/articles/5876 last-modified: 2018-11-01 description: BackgroundMany neritic to nearshore species of marine adapted turtle from the Late Cretaceous of North America are thought to represent the stem lineage of Cheloniidae but due to fragmentary holotypes, low total specimen counts, and resultantly incomplete morphological character suites, are routinely placed either within or outside of crown group Chelonioidea leaving their precise cladistic affinities uncertain. Despite this systematic ambiguity, the referral of these species to either the stem of Cheloniidae or Chelonioidea belies the critical importance of these taxa in any investigation into the origins of extant marine turtles. The adequate incorporation of these species into phylogenetic studies requires the formal description of relatively complete specimens, particularly those possessing associated cranial and post-cranial material.MethodsRemarkably complete fossil specimens of several adult and juvenile marine turtles from the Mooreville Chalk and Eutaw Formations (Alabama, USA) are formally described and assigned to Prionochelys matutina. This material provides new information into the anatomy, ontogeny, and cladistic affinities of the species. A phylogenetic hypothesis for Late Cretaceous marine turtles is then generated through the consilience of stratigraphic, morphological, and molecular data.ResultsPhylogenetic analysis places Prionochelys matutina on the stem of Cheloniidae as a member of a monophyletic clade with other putative pan-cheloniids, including Ctenochelys stenoporus, Ctenochelys acris, Peritresius martini, and Peritresius ornatus. The members of this clade possess incipient secondary palates, pronounced carapacial and plastral fontanelles at all stages of development, and are characterized by the presence of superficial ossifications at the apices of the neural keel elevations along the dorsal midline of the carapace.DiscussionThe epithecal osteoderms dorsal to the neural series (epineurals) found in Ctenochelyidae are unique among turtles. The presence of epineurals in ctenochelyid turtles shows that epithecal ossifications arose independently in both leatherback (Dermochelyidae) and hard-shelled (Cheloniidae) marine turtles. Whether or not the epineurals of Ctenochelyidae are homologous with the dermal ossicles comprising the carapace of Dermochelys coriacea remains untested however, histological thin sectioning of dermochelyid and ctenochelyd epithecal elements may reveal meaningful information in future studies. creator: Andrew D. Gentry uri: https://doi.org/10.7717/peerj.5876 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Gentry title: Effect of seasonality on chemical profile and antifungal activity of essential oil isolated from leaves Psidium salutare (Kunth) O. Berg link: https://peerj.com/articles/5476 last-modified: 2018-11-01 description: Medicinal plants play a crucial role in the search for components that are capable of neutralizing the multiple mechanisms of fungal resistance. Psidium salutare (Kunth) O. Berg is a plant native to Brazil used as both food and traditional medicine to treat diseases and symptoms such as stomach ache and diarrhea, whose symptoms could be related to fungal infections from the genus Candida. The objective of this study was to investigate the influence of seasonal variability on the chemical composition of the Psidium salutare essential oil, its antifungal potential and its effect on the Candida albicans morphogenesis. The essential oils were collected in three different seasonal collection periods and isolated by the hydrodistillation process in a modified Clevenger apparatus with identification of the chemical composition determined by gas chromatography coupled to mass spectrometry (GC/MS). The antifungal assays were performed against Candida strains through the broth microdilution method to determine the minimum fungicidal concentration (MFC). Fungal growth was assessed by optical density reading and the Candida albicans dimorphic effect was evaluated by optical microscopy in microculture chambers. The chemical profile of the essential oils identified 40 substances in the different collection periods with γ-terpinene being the predominant constituent. The antifungal activity revealed an action against the C. albicans, C. krusei and C. tropicalis strains with an IC50 ranging from 345.5 to 2,754.2 µg/mL and a MFC higher than 1,024 µg/mL. When combined with essential oils at sub-inhibitory concentrations (MIC/16), fluconazole had its potentiated effect, i.e. a synergistic effect was observed in the combination of fluconazole with P.salutare oil against all Candida strains; however, for C. albicans, its effect was reinforced by the natural product in all the collection periods. The results show that the Psidium salutare oil affected the dimorphic transition capacity, significantly reducing the formation of hyphae and pseudohyphae in increasing concentrations. The results show that P. salutare oil exhibits a significant antifungal activity against three Candida species and that it can act in synergy with fluconazole. These results support the notion that this plant may have a potential use in pharmaceutical and preservative products. creator: Delmacia G. de Macêdo creator: Marta Maria A. Souza creator: Maria Flaviana B. Morais-Braga creator: Henrique Douglas M. Coutinho creator: Antonia Thassya L. dos Santos creator: Rafael P. da Cruz creator: José Galberto M. da Costa creator: Fábio Fernandes G. Rodrigues creator: Lucindo J. Quintans-junior creator: Jackson Roberto G. da Silva Almeida creator: Irwin Rose A. de Menezes uri: https://doi.org/10.7717/peerj.5476 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 de Macêdo et al.