title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1265 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Vector distribution and transmission risk of the Zika virus in South and Central America link: https://peerj.com/articles/7920 last-modified: 2019-11-07 description: BackgroundZika is of great medical relevance due to its rapid geographical spread in 2015 and 2016 in South America and its serious implications, for example, certain birth defects. Recent epidemics urgently require a better understanding of geographic patterns of the Zika virus transmission risk. This study aims to map the Zika virus transmission risk in South and Central America. We applied the maximum entropy approach, which is common for species distribution modelling, but is now also widely in use for estimating the geographical distribution of infectious diseases.MethodsAs predictor variables we used a set of variables considered to be potential drivers of both direct and indirect effects on the emergence of Zika. Specifically, we considered (a) the modelled habitat suitability for the two main vector species Aedes aegypti and Ae. albopictus as a proxy of vector species distributions; (b) temperature, as it has a great influence on virus transmission; (c) commonly called evidence consensus maps (ECM) of human Zika virus infections on a regional scale as a proxy for virus distribution; (d) ECM of human dengue virus infections and, (e) as possibly relevant socio-economic factors, population density and the gross domestic product.ResultsThe highest values for the Zika transmission risk were modelled for the eastern coast of Brazil as well as in Central America, moderate values for the Amazon basin and low values for southern parts of South America. The following countries were modelled to be particularly affected: Brazil, Colombia, Cuba, Dominican Republic, El Salvador, Guatemala, Haiti, Honduras, Jamaica, Mexico, Puerto Rico and Venezuela. While modelled vector habitat suitability as predictor variable showed the highest contribution to the transmission risk model, temperature of the warmest quarter contributed only comparatively little. Areas with optimal temperature conditions for virus transmission overlapped only little with areas of suitable habitat conditions for the two main vector species. Instead, areas with the highest transmission risk were characterised as areas with temperatures below the optimum of the virus, but high habitat suitability modelled for the two main vector species.ConclusionModelling approaches can help estimating the spatial and temporal dynamics of a disease. We focused on the key drivers relevant in the Zika transmission cycle (vector, pathogen, and hosts) and integrated each single component into the model. Despite the uncertainties generally associated with modelling, the approach applied in this study can be used as a tool and assist decision making and managing the spread of Zika. creator: Sarah Cunze creator: Judith Kochmann creator: Lisa K. Koch creator: Elisa Genthner creator: Sven Klimpel uri: https://doi.org/10.7717/peerj.7920 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Cunze et al. title: Combining data from different sampling methods to study the development of an alien crab Chionoecetes opilio invasion in the remote and pristine Arctic Kara Sea link: https://peerj.com/articles/7952 last-modified: 2019-11-07 description: Data obtained using three different types of sampling gear is compared and combined to assess the size composition and density of a non-indigenous snow crab population Chionoecetes opilio in the previously free of alien species Kara Sea benthos. The Sigsbee trawl has small mesh and catches even recently settled crabs. The large bottom trawl is able to catch large crabs, but does not retain younger crabs, due to its large mesh. Video sampling allows the observation of larger crabs, although some smaller crabs can also be spotted. The combined use of such gear could provide full scope data of the existing size groups in a population. The density of the crabs was calculated from the video footage. The highest figures were in Blagopoluchiya Bay at 0.87 crabs/m2, where the settlement seems to be reaching its first peak of population growth after the introduction. High density in the Kara Gates Strait at 0.55 crabs/m2, could be due to the close proximity of the Barents Sea from where the crabs can enter by both larval dispersal and active adult migration. All size groups have been present in most sampled areas, which suggest successful settlement and growth of crabs over a number of years. Again, this was not the case in Blagopoluchiya Bay with high density of small crabs (<30 mm CW), which confirms its recent population growth. Male to female ratio was strikingly different between the bays of the Novaya Zemlya Archipelago and west of the Yamal Peninsula (0.8 and 3.8 respectively). Seventy five ovigerous females were caught in 2016, which confirms the presence of a reproducing population in the Kara Sea. The spatial structure of the snow crab population in the Kara Sea is still in the process of formation. The presented data indicates that this process may lead to a complex system, which is based on local recruitment and transport of larvae from the Barents Sea and across the western Kara shelf; formation of nursery grounds; active migration of adults and their concentration in the areas of the shelf with appropriate feeding conditions. creator: Anna K. Zalota creator: Olga L. Zimina creator: Vassily A. Spiridonov uri: https://doi.org/10.7717/peerj.7952 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zalota et al. title: Zooplankton communities in the Drake Passage through environmental boundaries: a snapshot of 2010, early spring link: https://peerj.com/articles/7994 last-modified: 2019-11-07 description: BackgroundSpatial distribution of zooplankton communities influenced by various environmental factors is always important for understanding pelagic ecosystems. The area of the Drake Passage (Southern Ocean) is of particular interest owing to the high spatial and temporal variability of hydrological parameters affecting marine fauna. This study provides a survey of zooplankton composition and spatial distribution along a transect in the Drake Passage sampled during the 31th Cruise of RV “Akademik Sergey Vavilov” in November, 2010. The main aim was to trace the main regularities in spatial zooplankton structure and its relationships with the environmental parameters.MethodologyA total of 43 vertical hauls from the surface to 1,000 m depth were made at 13 stations using the Juday plankton net. 60 taxa were recorded, abundance and biomass of each were assessed. Environmental parameters including temperature, salinity, depth, horizontal distance between stations and surface chlorophyll concentration were tested as environmental factors possibly explaining plankton distribution.ResultsHigher zooplankton abundance and biomass with lower diversity were observed near the Polar Front. Cluster analysis revealed five different groups of zooplankton samples, four of which were arranged mostly by depth. Along the transect within the 1,000 m depth range, the qualitative taxonomical composition differed significantly with depth and to some extent differed also among horizontal hydrological regimes, while the quantitative structure of the communities (abundance of taxa) was mainly determined by depth. Plankton assemblages within the upper 300-m layer depended on hydrological fronts. Abundance of dominant taxa as well as total zooplankton abundance showed a clear correlation with depth, salinity and surface chlorophyll concentration. Some taxa also showed correlations with temperature and latitude. Between the stations the similarity in zooplankton structure was clearly dependent on the distance among them which indicates an importance of latitudinal gradient. Surface chlorophyll concentration was not correlated with zooplankton biomass, which can be explained by the uncompleted seasonal migrations of zooplankton from deeper waters in early spring. creator: Andrey A. Vedenin creator: Eteri I. Musaeva creator: Daria N. Zasko creator: Alexander L. Vereshchaka uri: https://doi.org/10.7717/peerj.7994 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Vedenin et al. title: Idiosyncratic changes in spring arrival dates of Pacific Northwest migratory birds link: https://peerj.com/articles/7999 last-modified: 2019-11-07 description: Shifts in the timing of bird migration have been associated with climatic change and species traits. However, climatic change does not affect all species or geographic locations equally. Climate in the Pacific Northwest has shifted during the last century with mean temperatures increasing by 1 °C but little change in total annual precipitation. Few long-term data on migration phenology of birds are available in the Pacific Northwest. We analyzed trends in spring arrival dates from a site in the Oregon Coast Range where nearly daily inventories of birds were conducted in 24 of 29 years. Several species showed statistically significant shifts in timing of first spring arrivals. Six of 18 species occur significantly earlier now than during the initial phase of the study. One species arrives significantly later. Eleven show no significant shifts in timing. We associated trends in spring migration phenology with regional climatic variables, weather (precipitation and temperature), traits of species such as migration strategy, foraging behavior, diet, and habitat use, and regional trends in abundance as indexed by Breeding Bird Survey data. We found no set of variables consistently correlated with avian phenological changes. Post hoc analyses of additional climate variables revealed an association of migratory arrival dates across the 18 species with rainfall totals in northern California, presumably indicating that songbird arrival dates in Oregon are slowed by spring storm systems in California. When only the six species with the most strongly advancing arrival dates were analyzed, winter maximum temperatures in the preceding three winters appeared consistently in top models, suggesting a possible role for food availability early in spring to promote the survival and successful reproduction of the earliest-arriving birds. However, additional data on food availability and avian survival and reproductive success are required to test that hypothesis. Despite the appearance of some climate variables in top models, there remains a mismatch between strongly advancing arrival dates in some songbirds and a lack of clear directional change in those climate variables. We conclude that either some previously unrecognized variable or combination of variables has affected the timing of migration in some species but not others, or the appearance of statistically significant directional changes over time can occur without being driven by consistent environmental or species-specific factors. creator: W. Douglas Robinson creator: Christina Partipilo creator: Tyler A. Hallman creator: Karan Fairchild creator: James P. Fairchild uri: https://doi.org/10.7717/peerj.7999 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Robinson et al. title: The urban-rural disparity in the prevalence and risk factors of hypertension among the elderly in China—a cross-sectional study link: https://peerj.com/articles/8015 last-modified: 2019-11-07 description: IntroductionThis study aimed to assess the prevalence of hypertension and to explore the disparities of its risk factors among urban and rural elderly.MethodData of hypertensive patients were collected from the China Health and Retirement Longitudinal Study (CHARLS) 2015. Stratified sample households were selected from 450 villages or communities of 150 counties from 28 provinces. Multivariable logistic regression was performed to analyze the factors correlated with hypertension.ResultsPrevalence of HBP was 47.6% (95% CI [45.2%–50.1%]) in total and it was close between urban and rural population (48.6% vs 47.2%). Factors associated with HBP were different between urban and rural areas. In urban areas, hypertension was significantly associated with literacy and diabetes in both genders, high BMI level and smoke quitters in males, and physical activity and dyslipidemia in females. In rural areas, hypertension was significantly associated with older age, higher BMI level in both males and females, and dyslipidemia in males.ConclusionsThe prevalence are about the same among urban and rural residents, but their risk factors vary from each other. Disparity in the risk factors between urban and rural population should be taken into consideration for further intervention. creator: Hongxun Song creator: Da Feng creator: Ruoxi Wang creator: Jian Yang creator: Yuanqing Li creator: Junliang Gao creator: Zi Wang creator: Ziqi Yan creator: Chengxu Long creator: Jiawei Zhou creator: Zhanchun Feng uri: https://doi.org/10.7717/peerj.8015 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Song et al. title: Genome-wide identification and characterization of the MADS-box gene family in Salix suchowensis link: https://peerj.com/articles/8019 last-modified: 2019-11-07 description: MADS-box genes encode transcription factors that participate in various plant growth and development processes, particularly floral organogenesis. To date, MADS-box genes have been reported in many species, the completion of the sequence of the willow genome provides us with the opportunity to conduct a comprehensive analysis of the willow MADS-box gene family. Here, we identified 60 willow MADS-box genes using bioinformatics-based methods and classified them into 22 M-type (11 Mα, seven Mβ and four Mγ) and 38 MIKC-type (32 MIKCc and six MIKC*) genes based on a phylogenetic analysis. Fifty-six of the 60 SsMADS genes were randomly distributed on 19 putative willow chromosomes. By combining gene structure analysis with evolutionary analysis, we found that the MIKC-type genes were more conserved and played a more important role in willow growth. Further study showed that the MIKC* type was a transition between the M-type and MIKC-type. Additionally, the number of MADS-box genes in gymnosperms was notably lower than that in angiosperms. Finally, the expression profiles of these willow MADS-box genes were analysed in five different tissues (root, stem, leave, bud and bark) and validated by RT-qPCR experiments. This study is the first genome-wide analysis of the willow MADS-box gene family, and the results establish a basis for further functional studies of willow MADS-box genes and serve as a reference for related studies of other woody plants. creator: Yanshu Qu creator: Changwei Bi creator: Bing He creator: Ning Ye creator: Tongming Yin creator: Li-an Xu uri: https://doi.org/10.7717/peerj.8019 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Qu et al. title: Competing endogenous RNA (ceRNA) hypothetic model based on comprehensive analysis of long non-coding RNA expression in lung adenocarcinoma link: https://peerj.com/articles/8024 last-modified: 2019-11-07 description: BackgroundNon-small cell lung cancer (NSCLC) is a major subtype of lung cancer with high malignancy and bad prognosis, consisted of lung adenocarcinomas (LUAD) and lung squamous cell carcinomas (LUSC) chiefly. Multiple studies have indicated that competing endogenous RNA (ceRNA) network centered long noncoding RNAs (lncRNAs) can regulate gene expression and the progression of various cancers. However, the research about lncRNAs-mediated ceRNA network in LUAD is still lacking.MethodsIn this study, we analyzed the RNA-seq database from The Cancer Genome Atlas (TCGA) and obtained dysregulated lncRNAs in NSCLC, then further identified survival associated lncRNAs through Kaplan–Meier analysis. Quantitative real time PCR (qRT-PCR) was performed to confirm their expression in LUAD tissues and cell lines. The ceRNA networks were constructed based on DIANA-TarBase and TargetScan databases and visualized with OmicShare tools. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to investigate the potential function of ceRNA networks.ResultsIn total, 1,437 and 1,699 lncRNAs were found to be up-regulated in LUAD and LUSC respectively with 895 lncRNAs overlapping (|log2FC| > 3, adjusted P value <0.01). Among which, 222 lncRNAs and 46 lncRNAs were associated with the overall survival (OS) of LUAD and LUSC, and 18 out of 222 up-regulated lncRNAs were found to have inverse correlation with LUAD patients’ OS (|log2FC| > 3, adjusted P value < 0.02). We selected 3 lncRNAs (CASC8, LINC01842 and VPS9D1-AS1) out of these 18 lncRNAs and confirmed their overexpression in lung cancer tissues and cells. CeRNA networks were further constructed centered CASC8, LINC01842 and VPS9D1-AS1 with 3 miRNAs and 100 mRNAs included respectively.ConclusionThrough comprehensively analyses of TCGA, our study identified specific lncRNAs as candidate diagnostic and prognostic biomarkers for LUAD. The novel ceRNA network we created provided more insights into the regulatory mechanisms underlying LUAD. creator: Xiwen Wang creator: Rui Su creator: Qiqiang Guo creator: Jia Liu creator: Banlai Ruan creator: Guiling Wang uri: https://doi.org/10.7717/peerj.8024 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wang et al. title: Effect of different ergonomic supports on muscle activity of dentists during posterior composite restoration link: https://peerj.com/articles/8028 last-modified: 2019-11-07 description: BackgroundThe aim of this study was to evaluate the effect of different ergonomic supports on the muscle activity of two trunk muscles while a group of dentists performed a common dental procedure on a phantom head, divided into three tasks.MethodsA one-way repeated measures study (ANOVA) was conducted on a group of 36 dentists. The middle trapezius and lumbar erector spinae muscles were measured with and without the use of different ergonomic supports (ergonomic stool, magnification lenses and both) using a portable surface electromyography (sEMG) device. Intraclass correlation coefficients (ICCs) and the absolute standard error of measurement (SEM) were used to establish the reliability of the baseline measures without ergonomic supports.ResultsThe sEMG showed excellent ICCs (ranging from 0.92 to 0.99) and SEM. Bonferroni post hoc tests showed differences between the three ergonomic supports (p < 0.001) in both muscles studied. The lowest muscle activity measurement occurred with the isolated used of magnification lenses. The use of the ergonomic stool increased the muscle activity of the middle trapezius and lumbar erector spinae muscles to a greater extent than the magnification lenses. The combination of the ergonomic stool and the magnification lenses produced a different effect on each muscle. creator: Manuel López-Nicolás creator: José A. García-Vidal creator: Francesc Medina-Mirapeix creator: Joaquín P. Sánchez-Onteniente creator: Juan D. Berná Mestre creator: Rodrigo Martín-San Agustín creator: María P. Escolar-Reina uri: https://doi.org/10.7717/peerj.8028 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 López-Nicolás et al. title: Genome-wide analysis of transcription factors related to anthocyanin biosynthesis in carmine radish (Raphanus sativus L.) fleshy roots link: https://peerj.com/articles/8041 last-modified: 2019-11-07 description: Carmine radish produced in Chongqing is famous for containing a natural red pigment (red radish pigment). However, the anthocyanin biosynthesis transcriptome and the expression of anthocyanin biosynthesis-related genes in carmine radish have not been fully investigated. Uncovering the mechanism of anthocyanin biosynthesis in the ‘Hongxin 1’ carmine radish cultivar has become a dominant research topic in this field. In this study, a local carmine radish cultivar named ‘Hongxin 1’ containing a highly natural red pigment was used to analyze transcription factors (TFs) related to anthocyanin biosynthesis during the dynamic development of fleshy roots. Based on RNA sequencing data, a total of 1,747 TFs in 64 TF families were identified according to their DNA-binding domains. Of those, approximately 71 differentially expressed transcription factors (DETFs) were commonly detected in any one stage compared with roots in the seedling stage (SS_root). Moreover, 26 transcripts of DETFs targeted by 74 miRNAs belonging to 25 miRNA families were identified, including MYB, WRKY, bHLH, ERF, GRAS, NF-YA, C2H2-Dof, and HD-ZIP. Finally, eight DETF transcripts belonging to the C2C2-Dof, bHLH and ERF families and their eight corresponding miRNAs were selected for qRT-PCR to verify their functions related to anthocyanin biosynthesis during the development of carmine radish fleshy roots. Finally, we propose a putative miRNA-target regulatory model associated with anthocyanin biosynthesis in carmine radish. Our findings suggest that sucrose synthase might act as an important regulator to modulate anthocyanin biosynthesis in carmine radish by inducing several miRNAs (miR165a-5p, miR172b, miR827a, miR166g and miR1432-5p) targeting different ERFs than candidate miRNAs in the traditional WMBW complex in biological processes. creator: Jian Gao creator: Hua Peng creator: Fabo Chen creator: Mao Luo creator: Wenbo Li uri: https://doi.org/10.7717/peerj.8041 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Gao et al. title: Chronic trace metals effects of mine tailings on estuarine assemblages revealed by environmental DNA link: https://peerj.com/articles/8042 last-modified: 2019-11-07 description: Mine tailing disasters have occurred worldwide and contemporary release of tailings of large proportions raise concerns of the chronic impacts that trace metals may have on the aquatic biodiversity. Environmental metabarcoding (eDNA) offers an as yet poorly explored opportunity for biological monitoring of impacted aquatic ecosystems from mine tailings and contaminated sediments. eDNA has been increasingly recognized to be an effective method to detect previously unrecognized small-sized Metazoan taxa, but their ecological responses to environmental pollution has not been assessed by metabarcoding. Here, we evaluated chronic effects of trace metal contamination from sediment eDNA of the Rio Doce estuary, 1.7 years after the Samarco mine tailing disaster, which released over 40 million m3 of iron tailings in the Rio Doce river basin. We identified 123 new sequence variants environmental taxonomic units (eOTUs) of benthic taxa and an assemblage composition dominated by Nematoda, Crustacea and Platyhelminthes; typical of other estuarine ecosystems. We detected environmental filtering on the meiofaunal assemblages and multivariate analysis revealed strong influence of Fe contamination, supporting chronic impacts from mine tailing deposition in the estuary. This was in contrast to environmental filtering of meiofaunal assemblages of non-polluted estuaries. Here, we suggest that the eDNA metabarcoding technique provides an opportunity to fill up biodiversity gaps in coastal marine ecology and may become a valid method for long term monitoring studies in mine tailing disasters and estuarine ecosystems with high trace metals content. creator: Angelo F. Bernardino creator: Fabiano S. Pais creator: Louisi S. Oliveira creator: Fabricio A. Gabriel creator: Tiago O. Ferreira creator: Hermano M. Queiroz creator: Ana Carolina A. Mazzuco uri: https://doi.org/10.7717/peerj.8042 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Bernardino et al.