title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1073 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Evidence of transfer of miRNAs from the diet to the blood still inconclusive link: https://peerj.com/articles/9567 last-modified: 2020-09-17 description: MicroRNAs (miRNAs) are short, non-coding, single-strand RNA molecules that act as regulators of gene expression in plants and animals. In 2012, the first evidence was found that plant miRNAs could enter the bloodstream through the digestive tract. Since then, there has been an ongoing discussion about whether miRNAs from the diet are transferred to blood, accumulate in tissues, and regulate gene expression. Different research groups have tried to replicate these findings, using both plant and animal sources. Here, we review the evidence for and against the transfer of diet-derived miRNAs from plants, meat, milk and exosome and their assimilation and putative molecular regulation role in the consuming organism. Some groups using both miRNAs from plant and animal sources have claimed success, whereas others have not shown transfer. In spite of the biological barriers that may limit miRNA transference, several diet-derived miRNAs can transfer into the circulating system and targets genes for transcription regulation, which adds arguments that miRNAs can be absorbed from the diet and target specific genes by regulating their expression. However, many other studies show that cross-kingdom transfer of exogenous miRNAs appears to be insignificant and not biologically relevant. The main source of controversy in plant studies is the lack of reproducibility of the findings. For meat-derived miRNAs, studies concluded that the miRNAs can survive the cooking process; nevertheless, our evidence shows that the bovine miRNAs are not transferred to human bloodstream. The most important contributions and promising evidence in this controversial field is the transference of milk miRNAs in exosomes and the finding that plant miRNAs in beebread regulate honeybee caste development, and cause similar changes when fed to Drosophila. MiRNAs encapsulated in exosomes ensure their stability and resistance in the harsh conditions presented in milk, bloodstream, and gastrointestinaltract to reinforce the idea of transference. Regardless of the model organism, the idea of source of miRNAs, or the approach—bioinformatics or in vivo—the issue of transfer of miRNAs from the diet remains in doubt. Our understanding of the cross-kingdom talk of miRNAs needs more research to study the transfer of “xenomiRs” from different food sources to complement and expand what we know so far regarding the interspecies transfer of miRNAs. creator: Fermín Mar-Aguilar creator: Alejandra Arreola-Triana creator: Daniela Mata-Cardona creator: Vianey Gonzalez-Villasana creator: Cristina Rodríguez-Padilla creator: Diana Reséndez-Pérez uri: https://doi.org/10.7717/peerj.9567 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Mar-Aguilar et al. title: Salinity impairs photosynthetic capacity and enhances carotenoid-related gene expression and biosynthesis in tomato (Solanum lycopersicum L. cv. Micro-Tom) link: https://peerj.com/articles/9742 last-modified: 2020-09-17 description: Carotenoids are essential components of the photosynthetic antenna and reaction center complexes, being also responsible for antioxidant defense, coloration, and many other functions in multiple plant tissues. In tomato, salinity negatively affects the development of vegetative organs and productivity, but according to previous studies it might also increase fruit color and taste, improving its quality, which is a current agricultural challenge. The fruit quality parameters that are increased by salinity are cultivar-specific and include carotenoid, sugar, and organic acid contents. However, the relationship between vegetative and reproductive organs and response to salinity is still poorly understood. Considering this, Solanum lycopersicum cv. Micro-Tom plants were grown in the absence of salt supplementation as well as with increasing concentrations of NaCl for 14 weeks, evaluating plant performance from vegetative to reproductive stages. In response to salinity, plants showed a significant reduction in net photosynthesis, stomatal conductance, PSII quantum yield, and electron transport rate, in addition to an increase in non-photochemical quenching. In line with these responses the number of tomato clusters decreased, and smaller fruits with higher soluble solids content were obtained. Mature-green fruits also displayed a salt-dependent higher induction in the expression of PSY1, PDS, ZDS, and LYCB, key genes of the carotenoid biosynthesis pathway, in correlation with increased lycopene, lutein, β-carotene, and violaxanthin levels. These results suggest a key relationship between photosynthetic plant response and yield, involving impaired photosynthetic capacity, increased carotenoid-related gene expression, and carotenoid biosynthesis. creator: Andrés Leiva-Ampuero creator: Mario Agurto creator: José Tomás Matus creator: Gustavo Hoppe creator: Camila Huidobro creator: Claudio Inostroza-Blancheteau creator: Marjorie Reyes-Díaz creator: Claudia Stange creator: Paulo Canessa creator: Andrea Vega uri: https://doi.org/10.7717/peerj.9742 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Leiva-Ampuero et al. title: Jatropha curcas ortholog of tomato MADS-box gene 6 (JcTM6) promoter exhibits floral-specific activity in Arabidopsis thaliana link: https://peerj.com/articles/9827 last-modified: 2020-09-17 description: BackgroundJatropha curcas L., a perennial oilseed plant, is considered as a promising feedstock for biodiesel production. Genetic modification of flowering characteristics is critical for Jatropha breeding. However, analysis of floral-specific promoters in Jatropha is limited.MethodsIn this study, we isolated the Jatropha ortholog of TM6 (JcTM6) gene from Jatropha flower cDNA library and detected the expression pattern of JcTM6 gene by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). We isolated a 1.8-kb fragment from the 5’ region of the JcTM6 gene and evaluated its spatiotemporal expression pattern in Arabidopsis using the β-glucuronidase (GUS) reporter gene and Arabidopsis ATP/ADP isopentenyltransferase 4 (AtIPT4) gene, respectively.ResultsJcTM6 was identified as a flower-specific gene in Jatropha. As expected, JcTM6 promoter was only active in transgenic Arabidopsis flowers with the strongest activity in stamens. Moreover, JcTM6:AtIPT4 transgenic Arabidopsis showed a phenotype of large flowers without any alterations in other organs. Furthermore, deletion of the region from –1,717 to –876 bp resulted in the disappearance of promoter activity in stamens but an increase in promoter activity in young leaves, sepals, and petals. Deletion analysis suggests that the –1,717- to –876-bp promoter fragment contains regulatory elements that confer promoter activity in stamens and inhibit activity in young leaves, sepals, and petals. creator: Jing-Xian Wang creator: Xin Ming creator: Yan-Bin Tao creator: Zeng-Fu Xu uri: https://doi.org/10.7717/peerj.9827 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2020 Wang et al. title: Association between serum and dietary antioxidant micronutrients and advanced liver fibrosis in non-alcoholic fatty liver disease: an observational study link: https://peerj.com/articles/9838 last-modified: 2020-09-17 description: BackgroundDespite clinical trials with antioxidant supplementation, few studies have been conducted to evaluate the nutritional status of antioxidant vitamins and minerals, and none have reported on the status of these serum antioxidants associated with the dietary intake of antioxidants by non-alcoholic fatty liver disease (NAFLD) patients.ObjectiveTo evaluate association between serum and dietetics antioxidants with liver fibrosis in patients with NAFLD.MethodsAcross-section analysis with out with 72 patients diagnosed with NAFLD. Hepatic fibrosis was measured by FibroScan®, and liver stiffness ≥7.9 kPa was considered to indicate advanced fibrosis. Retinol, alpha-tocopherol, ascorbic acid, beta-carotene, serum zinc, and selenium were evaluated, as was the dietary intake of these micronutrients in the previous 24 h (using 24-h dietary recall). The Mann–Whitney test was used to compare the fibrosis groups and, a linear regression analysis was performed to determine associated risk factors between age, sex, BMI, hepatic fibrosis, and serum antioxidants.ResultsA high proportion of inadequate serum retinol (20.8%), vitamin C (27%), and selenium (73.6%) was observed in the patients with NAFLD, in addition to a significant inadequacy of vitamin A (98.3%) and vitamin E (100%) intake. Patients with advanced liver fibrosis had reduced levels of serum retinol (P = 0.002), with liver fibrosis being the independent risk factor associated with serum retinol lower.ConclusionHepatic fibrosis was associated with a reduction in serum retinol and was reduced in advanced fibrosis. NAFLD patients showed an important serum deficiency and insufficient dietary intake of the evaluated micronutrients. creator: Juliana Moraes Coelho creator: Katia Cansanção creator: Renata de Mello Perez creator: Nathalie Carvalho Leite creator: Patrícia Padilha creator: Andrea Ramalho creator: Wilza Peres uri: https://doi.org/10.7717/peerj.9838 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Coelho et al. title: lcc: an R package to estimate the concordance correlation, Pearson correlation and accuracy over time link: https://peerj.com/articles/9850 last-modified: 2020-09-17 description: Background and ObjectiveObservational studies and experiments in medicine, pharmacology and agronomy are often concerned with assessing whether different methods/raters produce similar values over the time when measuring a quantitative variable. This article aims to describe the statistical package lcc, for are, that can be used to estimate the extent of agreement between two (or more) methods over the time, and illustrate the developed methodology using three real examples.MethodsThe longitudinal concordance correlation, longitudinal Pearson correlation, and longitudinal accuracy functions can be estimated based on fixed effects and variance components of the mixed-effects regression model. Inference is made through bootstrap confidence intervals and diagnostic can be done via plots, and statistical tests.ResultsThe main features of the package are estimation and inference about the extent of agreement using numerical and graphical summaries. Moreover, our approach accommodates both balanced and unbalanced experimental designs or observational studies, and allows for different within-group error structures, while allowing for the inclusion of covariates in the linear predictor to control systematic variations in the response. All examples show that our methodology is flexible and can be applied to many different data types.ConclusionsThe lcc package, available on the CRAN repository, proved to be a useful tool to describe the agreement between two or more methods over time, allowing the detection of changes in the extent of agreement. The inclusion of different structures for the variance-covariance matrices of random effects and residuals makes the package flexible for working with different types of databases. creator: Thiago P. Oliveira creator: Rafael A. Moral creator: Silvio S. Zocchi creator: Clarice G.B. Demetrio creator: John Hinde uri: https://doi.org/10.7717/peerj.9850 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Oliveira et al. title: Earthworms accelerate rice straw decomposition and maintenance of soil organic carbon dynamics in rice agroecosystems link: https://peerj.com/articles/9870 last-modified: 2020-09-17 description: BackgroundTo promote straw degradation, we inoculated returned farmland straw with earthworms (Pheretima guillelmi). Increasing the number of earthworms may generally alter soil organic carbon (SOC) dynamics and the biological activity of agricultural soils.MethodsWe performed soil mesocosm experiments with and without earthworms to assess the decomposition and microbial mineralization of returned straw and soil enzyme activity across different time periods.ResultsWhen earthworms were present in soil, the surface residues were completely consumed during the first four weeks, but when earthworms were absent, most of the residues remained on the soil surface after 18 weeks. On day 28, the SOC content was significantly higher in the treatment where both earthworms and residue had been added. The SOC content was lower in the treatment where earthworms but no residue had been added. The organic carbon content in water-stable macroaggregates showed the same trend. During the first 14 weeks, the soil basal respiration was highest in the treatments with both residues and earthworms. From weeks 14 to 18, basal respiration was highest in the treatments with residues but without earthworms. We found a significant positive correlation between soil basal respiration and soil dissolved organic carbon content. Earthworms increased the activity of protease, invertase, urease and alkaline phosphatase enzymes, but decreased β-cellobiohydrolase, β-glucosidase and xylosidase activity, as well as significantly reducing ergosterol content.ConclusionThe primary decomposition of exogenous rice residues was mainly performed by earthworms. Over a short period of time, they converted plant carbon into soil carbon and increased SOC. The earthworms played a key role in carbon conversion and stabilization. In the absence of exogenous residues, earthworm activity accelerated the decomposition of original organic carbon in the soil, reduced SOC, and promoted carbon mineralization. creator: Ke Song creator: Lijuan Sun creator: Weiguang Lv creator: Xianqing Zheng creator: Yafei Sun creator: William Terzaghi creator: Qin Qin creator: Yong Xue uri: https://doi.org/10.7717/peerj.9870 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Song et al. title: Wild meat hunting and use by sedentarised Baka Pygmies in southeastern Cameroon link: https://peerj.com/articles/9906 last-modified: 2020-09-17 description: As a result of sedentarisation many Baka Pygmies have changed their mobility patterns away from nomadic lifestyles to living in roadside villages. These settled groups are increasingly dependent on cultivated foods but still rely on forest resources. The level of dependence on hunting of wild animals for food and cash, as well as the hunting profiles of sedentarised Pygmy groups is little known. In this study we describe the use of wild meat in 10 Baka villages along the Djoum-Mintom road in southeastern Cameroon. From data collected from 1,946 hunting trips by 121 hunters, we show that most trips are of around 13 hours and a median of eight hours. A mean ± SD of 1.15 ± 1.11 animal carcasses are taken in a single trip; there was a positive correlation between duration of trips and carcasses. A total of 2,245 carcasses of 49 species of 24 animal families were taken in the study; species diversity was similar in all villages except one. Most hunted animals were mammals, with ungulates contributing the highest proportion. By species, just over half of the animal biomass extracted by all hunters in the studied villages was provided by four mammal species. Most animals were trapped (65.77% ± 16.63), followed by shot with guns (22.56% ± 17.72), other methods (8.69% ± 6.96) and with dogs (2.96% ± 4.49). A mean of 7,569.7 ± 6,103.4 kg yr−1 (2,080.8–19,351.4) were extracted per village, giving 75,697 kg yr−1 in total, which is equivalent to 123 UK dairy cattle. In all villages, 48.07% ± 17.58 of animals hunted were consumed by the hunter and his family, around 32.73% ± 12.55, were sold, followed by a lower percentage of carcasses partially sold and consumed (19.21% ± 17.02). Between 60% and 80% of carcasses belonged to the “least concern” category, followed by “near threatened”, “vulnerable” and, rarely “endangered”. The only endangered species hunted was the chimpanzee (Pan troglodytes). We suggest that hunting is a critical activity that provides a vital source of food for our study communities. Measured wild meat extraction levels are likely to be sustainable if hunter densities do not increase. creator: Eva Avila Martin creator: Guillermo Ros Brull creator: Stephan M. Funk creator: Luca Luiselli creator: Robert Okale creator: Julia E. Fa uri: https://doi.org/10.7717/peerj.9906 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Avila Martin et al. title: Estimating the impact of lock-down, quarantine and sensitization in a COVID-19 outbreak: lessons from the COVID-19 outbreak in China link: https://peerj.com/articles/9933 last-modified: 2020-09-17 description: In recent history, COVID-19 is one of the worst infectious disease outbreaks currently affecting humanity globally. Using real data on the COVID-19 outbreak from 22 January 2020 to 30 March 2020, we developed a mathematical model to investigate the impact of control measures in reducing the spread of the disease. Analyses of the model were carried out to determine the dynamics. The results of the analyses reveal that, using the data from China, implementing all possible control measures best reduced the rate of secondary infections. However, quarantine (isolation) of infectious individuals is shown to have the most dominant effect. This possibility emphasizes the need for extensive testing due to the possible prevalence of asymptomatic COVID-19 cases. creator: Obiora C. Collins creator: Kevin J. Duffy uri: https://doi.org/10.7717/peerj.9933 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Collins and Duffy title: Cocoa colonic phenolic metabolites are related to HDL-cholesterol raising effects and methylxanthine metabolites and insoluble dietary fibre to anti-inflammatory and hypoglycemic effects in humans link: https://peerj.com/articles/9953 last-modified: 2020-09-17 description: BackgroundIn many cocoa intervention studies, health outcomes are related to cocoa components without taking into account the bioavailability of the main bioactive components: phenolic compounds and methylxanthines.MethodsThe present work associates the results of bioavailability and randomised controlled crossover studies in humans carried out with similar cocoa products, so that the main phenol and methylxanthine metabolites observed in plasma and urine are associated to the health effects observed in the chronic studies. We outstand that doses of cocoa and consumption rate used are realistic. In the bioavailability study, a conventional (CC) and a methylxanthine-polyphenol rich (MPC) cocoa product were used, whereas in the chronic study a dietary fibre-rich (DFC) and a polyphenol-rich (PC) product were studied in healthy and cardiovascular risk subjects.Results and DiscussionThe main phenolic metabolites formed after CC and MPC intake, 5-(4′-hydroxyphenyl)-γ-valerolactone-3′-sulfate, 3′-methyl-epicatechin-5-sulfate, 4-hydroxy-5-(4′-hydroxyphenyl)valeric acid-sulfate, 5-phenyl-γ-valerolactone--sulfate and 5-(4′-hydroxyphenyl)-γ-valerolactone-3′-glucuronide, may contribute to the changes in cholesterol (and indirectly HDL-cholesterol) observed after the regular intake of both DFC and PC, in healthy and cardiovascular risk subjects, whereas 7-methylxanthine (the main cocoa methylxanthine metabolite) and theobromine, together with its content in insoluble dietary fibre, may be responsible for the decrease of IL-1β and hypoglycemic effects observed with DFC. With both phenolic and methylxanthine metabolites a strong dose–response effect was observed.ConclusionAfter the regular consumption of both DFC and PC, positive changes were observed in volunteer’s lipid profile, which may be related to the long-lasting presence of colonic phenolic metabolites in blood. In contrast, the anti-inflammatory and hypoglycemic effects were only observed with DFC, and these may be related to methylxanthine metabolites, and it is likely that insoluble dietary fibre may have also played a role. creator: Beatriz Sarriá creator: Miren Gomez-Juaristi creator: Sara Martínez López creator: Joaquín García Cordero creator: Laura Bravo creator: Mª Raquel Mateos Briz uri: https://doi.org/10.7717/peerj.9953 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Sarriá et al. title: Role of reactive oxygen species and isoflavonoids in soybean resistance to the attack of the southern green stink bug link: https://peerj.com/articles/9956 last-modified: 2020-09-17 description: Southern green stink bugs (Nezara viridula L.) are one of the major pests in many soybean producing areas. They cause a decrease in yield and affect seed quality by reducing viability and vigor. Alterations have been reported in the oxidative response and in the secondary metabolites in different plant species due to insect damage. However, there is little information available on soybean-stink bug interactions. In this study we compare the response of undamaged and damaged seeds by Nezara viridula in two soybean cultivars, IAC-100 (resistant) and Davis (susceptible), grown under greenhouse conditions. Pod hardness, H2O2 generation, enzyme activities in guaiacol peroxidase (GPOX), catalase (CAT) and superoxide dismutase (SOD) as well as lipoxygenase expression and isoflavonoid production were quantified. Our results showed a greater resistance of IAC-100 to pod penetration, a decrease in peroxide content after stink bug attack, and higher GPOX, CAT and SOD activities in seeds due to the genotype and to the genotype-interaction with the herbivory treatment. Induction of LOX expression in both cultivars and higher production of isoflavonoids in IAC-100 were also detected. It was then concluded that the herbivory stink bug induces pathways related to oxidative stress and to the secondary metabolites in developing seeds of soybean and that differences between cultivars hold promise for a plant breeding program. creator: Ivana Sabljic creator: Jesica A. Barneto creator: Karina B. Balestrasse creator: Jorge A. Zavala creator: Eduardo A. Pagano uri: https://doi.org/10.7717/peerj.9956 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Sabljic et al.