title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1777 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Salivary microbiomes of indigenous Tsimane mothers and infants are distinct despite frequent premastication link: https://peerj.com/articles/2660 last-modified: 2016-11-03 description: BackgroundPremastication, the transfer of pre-chewed food, is a common infant and young child feeding practice among the Tsimane, forager-horticulturalists living in the Bolivian Amazon. Research conducted primarily with Western populations has shown that infants harbor distinct oral microbiota from their mothers. Premastication, which is less common in these populations, may influence the colonization and maturation of infant oral microbiota, including via transmission of oral pathogens. We collected premasticated food and saliva samples from Tsimane mothers and infants (9–24 months of age) to test for evidence of bacterial transmission in premasticated foods and overlap in maternal and infant salivary microbiota. We extracted bacterial DNA from two premasticated food samples and 12 matched salivary samples from maternal-infant pairs. DNA sequencing was performed with MiSeq (Illumina). We evaluated maternal and infant microbial composition in terms of relative abundance of specific taxa, alpha and beta diversity, and dissimilarity distances.ResultsThe bacteria in saliva and premasticated food were mapped to 19 phyla and 400 genera and were dominated by Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. The oral microbial communities of Tsimane mothers and infants who frequently share premasticated food were well-separated in a non-metric multi-dimensional scaling ordination (NMDS) plot. Infant microbiotas clustered together, with weighted Unifrac distances significantly differing between mothers and infants. Infant saliva contained more Firmicutes (p < 0.01) and fewer Proteobacteria (p < 0.05) than did maternal saliva. Many genera previously associated with dental and periodontal infections, e.g. Neisseria, Gemella, Rothia, Actinomyces, Fusobacterium, and Leptotrichia, were more abundant in mothers than in infants.ConclusionsSalivary microbiota of Tsimane infants and young children up to two years of age do not appear closely related to those of their mothers, despite frequent premastication and preliminary evidence that maternal bacteria is transmitted to premasticated foods. Infant physiology and diet may constrain colonization by maternal bacteria, including several oral pathogens. creator: Cliff S. Han creator: Melanie Ann Martin creator: Armand E.K. Dichosa creator: Ashlynn R. Daughton creator: Seth Frietze creator: Hillard Kaplan creator: Michael D. Gurven creator: Joe Alcock uri: https://doi.org/10.7717/peerj.2660 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Han et al. title: Sevoflurane postconditioning attenuates cardiomyocyte hypoxia/reoxygenation injury via restoring mitochondrial morphology link: https://peerj.com/articles/2659 last-modified: 2016-11-03 description: BackgroundAnesthetic postconditioning is a cellular protective approach whereby exposure to a volatile anesthetic renders a tissue more resistant to subsequent ischemic/reperfusion event. Sevoflurane postconditioning (SPostC) has been shown to exert cardioprotection against ischemia/reperfusion injury, but the underlying mechanism is unclear. We hypothesized that SPostC protects cardiomyocytes against hypoxia/reoxygenation (H/R) injury by maintaining/restoring mitochondrial morphological integrity, a critical determinant of cell fate.MethodsPrimary cultures of neonatal rat cardiomyocytes (NCMs) were subjected to H/R injury (3 h of hypoxia followed by 3 h reoxygenation). Intervention with SPostC (2.4% sevoflurane) was administered for 15 min upon the onset of reoxygenation. Cell viability, Lactate dehydrogenase (LDH) level, cell death, mitochondrial morphology, mitochondrial membrane potential and mitochondrial permeability transition pore (mPTP) opening were assessed after intervention. Mitochondrial fusion and fission regulating proteins (Drp1, Fis1, Mfn1, Mfn2 and Opa1) were assessed by immunofluorescence staining and western blotting was performed to determine the level of protein expression.ResultsCardiomyocyte H/R injury resulted in significant increases in LDH release and cell death that were concomitant with reduced cell viability and reduced mitochondrial interconnectivity (mean area/perimeter ratio) and mitochondrial elongation, and with reduced mitochondrial membrane potential and increased mPTP opening. All the above changes were significantly attenuated by SPostC. Furthermore, H/R resulted in significant reductions in mitochondrial fusion proteins Mfn1, Mfn2 and Opa1 and significant enhancement of fission proteins Drp1 and Fis1. SPostC significantly enhanced Mfn2 and Opa1 and reduced Drp1, without significant impact on Mfn1 and Fis1.ConclusionsSevoflurane postconditioning attenuates cardiomyocytes hypoxia/reoxygenation injury (HRI) by restoring mitochondrial fusion/fission balance and morphology. creator: Jin Yu creator: Jianjiang Wu creator: Peng Xie creator: Yiliyaer Maimaitili creator: Jiang Wang creator: Zhengyuan Xia creator: Feng Gao creator: Xing Zhang creator: Hong Zheng uri: https://doi.org/10.7717/peerj.2659 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Yu et al. title: Foliar fungal communities strongly differ between habitat patches in a landscape mosaic link: https://peerj.com/articles/2656 last-modified: 2016-11-03 description: BackgroundDispersal events between habitat patches in a landscape mosaic can structure ecological communities and influence the functioning of agrosystems. Here we investigated whether short-distance dispersal events between vineyard and forest patches shape foliar fungal communities. We hypothesized that these communities homogenize between habitats over the course of the growing season, particularly along habitat edges, because of aerial dispersal of spores.MethodsWe monitored the richness and composition of foliar and airborne fungal communities over the season, along transects perpendicular to edges between vineyard and forest patches, using Illumina sequencing of the Internal Transcribed Spacer 2 (ITS2) region.ResultsIn contrast to our expectation, foliar fungal communities in vineyards and forest patches increasingly differentiate over the growing season, even along habitat edges. Moreover, the richness of foliar fungal communities in grapevine drastically decreased over the growing season, in contrast to that of forest trees. The composition of airborne communities did not differ between habitats. The composition of oak foliar fungal communities change between forest edge and centre.DiscussionThese results suggest that dispersal events between habitat patches are not major drivers of foliar fungal communities at the landscape scale. Selective pressures exerted in each habitat by the host plant, the microclimate and the agricultural practices play a greater role, and might account for the differentiation of foliar fugal communities between habitats. creator: Thomas Fort creator: Cécile Robin creator: Xavier Capdevielle creator: Laurent Delière creator: Corinne Vacher uri: https://doi.org/10.7717/peerj.2656 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Fort et al. title: Phytogeographic and genetic variation in Sorbus, a traditional antidiabetic medicine—adaptation in action in both a plant and a discipline link: https://peerj.com/articles/2645 last-modified: 2016-11-03 description: Mountain ash (Sorbus decora and S. americana) is used by the Cree Nation of the James Bay region of Quebec (Eeyou Istchee) as traditional medicine. Its potential as an antidiabetic medicine is thought to vary across its geographical range, yet little is known about the factors that affect its antioxidant capacity. Here, we examined metabolite gene expression in relation to antioxidant activity, linking phytochemistry and medicinal potential. Samples of leaf and bark from S. decora and S. americana were collected from 20 populations at four different latitudes. Two genes known to produce antidiabetic substances, flavonol synthase and squalene synthase, were analyzed using quantitative real time PCR. Gene expression was significantly higher for flavonol synthase compared to squalene synthase and increased in the most Northern latitude. Corresponding differences observed in the antioxidant capacity of ethanolic extracts from the bark of Sorbus spp. confirm that plants at higher latitudes increase production of stress-induced secondary metabolites and support Aboriginal perceptions of their higher medicinal potential. Modern genetic techniques such as quantitative real time PCR offer unprecedented resolution to substantiate and scrutinise Aboriginal medicinal plant perception. Furthermore, it offers valuable insights into how environmental stress can trigger an adaptive response resulting in the accumulation of secondary metabolites with human medicinal properties. creator: Anna Bailie creator: Sebastien Renaut creator: Eliane Ubalijoro creator: José A. Guerrero-Analco creator: Ammar Saleem creator: Pierre Haddad creator: John T. Arnason creator: Timothy Johns creator: Alain Cuerrier uri: https://doi.org/10.7717/peerj.2645 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Bailie et al. title: Mathematical models are a powerful method to understand and control the spread of Huanglongbing link: https://peerj.com/articles/2642 last-modified: 2016-11-03 description: Huanglongbing (HLB), or citrus greening, is a global citrus disease occurring in almost all citrus growing regions. It causes substantial economic burdens to individual growers, citrus industries and governments. Successful management strategies to reduce disease burden are desperately needed but with so many possible interventions and combinations thereof it is difficult to know which are worthwhile or cost-effective. We review how mathematical models have yielded useful insights into controlling disease spread for other vector-borne plant diseases, and the small number of mathematical models of HLB. We adapt a malaria model to HLB, by including temperature-dependent psyllid traits, “flushing” of trees, and economic costs, to show how models can be used to highlight the parameters that require more data collection or that should be targeted for intervention. We analyze the most common intervention strategy, insecticide spraying, to determine the most cost-effective spraying strategy. We find that fecundity and feeding rate of the vector require more experimental data collection, for wider temperatures ranges. Also, the best strategy for insecticide intervention is to spray for more days rather than pay extra for a more efficient spray. We conclude that mathematical models are able to provide useful recommendations for managing HLB spread. creator: Rachel A. Taylor creator: Erin A. Mordecai creator: Christopher A. Gilligan creator: Jason R. Rohr creator: Leah R. Johnson uri: https://doi.org/10.7717/peerj.2642 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Taylor et al. title: Germination pretreatments to break hard-seed dormancy in Astragalus cicer L. (Fabaceae) link: https://peerj.com/articles/2621 last-modified: 2016-11-03 description: Conservationists often propagate rare species to improve their long-term population viability. However, seed dormancy can make propagation efforts challenging by substantially lowering seed germination. Here I statistically compare several pretreatment options for seeds of Astragalus cicer L.: unscarified controls and scarification via physical damage, hot water, acid, and hydrogen peroxide. Although only 30% of unscarified seeds germinated, just physical scarification significantly improved germination, whereas one treatment, hot water, resulted in no germination at all. I recommend that rare species of Astragalus, as well as other hard-seeded legumes, be pretreated using physical scarification. Other methods may require considerable optimization, wasting precious time and seeds. creator: Joseph M. Statwick uri: https://doi.org/10.7717/peerj.2621 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Statwick title: Phylogeography of Arenaria balearica L. (Caryophyllaceae): evolutionary history of a disjunct endemic from the Western Mediterranean continental islands link: https://peerj.com/articles/2618 last-modified: 2016-11-03 description: Although it has been traditionally accepted that Arenaria balearica (Caryophyllaceae) could be a relict Tertiary plant species, this has never been experimentally tested. Nor have the palaeohistorical reasons underlying the highly fragmented distribution of the species in the Western Mediterranean region been investigated. We have analysed AFLP data (213) and plastid DNA sequences (226) from a total of 250 plants from 29 populations sampled throughout the entire distribution range of the species in Majorca, Corsica, Sardinia, and the Tuscan Archipelago. The AFLP data analyses indicate very low geographic structure and population differentiation. Based on plastid DNA data, six alternative phylogeographic hypotheses were tested using Approximate Bayesian Computation (ABC). These analyses revealed ancient area fragmentation as the most probable scenario, which is in accordance with the star-like topology of the parsimony network that suggests a pattern of long term survival and subsequent in situ differentiation. Overall low levels of genetic diversity and plastid DNA variation were found, reflecting evolutionary stasis of a species preserved in locally long-term stable habitats. creator: Javier Bobo-Pinilla creator: Sara B. Barrios de León creator: Jaume Seguí Colomar creator: Giuseppe Fenu creator: Gianluigi Bacchetta creator: Julio Peñas de Giles creator: María Montserrat Martínez-Ortega uri: https://doi.org/10.7717/peerj.2618 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Bobo-Pinilla et al. title: Analyzing pathogen suppressiveness in bioassays with natural soils using integrative maximum likelihood methods in R link: https://peerj.com/articles/2615 last-modified: 2016-11-03 description: The potential of soils to naturally suppress inherent plant pathogens is an important ecosystem function. Usually, pathogen infection assays are used for estimating the suppressive potential of soils. In natural soils, however, co-occurring pathogens might simultaneously infect plants complicating the estimation of a focal pathogen’s infection rate (initial slope of the infection-curve) as a measure of soil suppressiveness. Here, we present a method in R correcting for these unwanted effects by developing a two pathogen mono-molecular infection model. We fit the two pathogen mono-molecular infection model to data by using an integrative approach combining a numerical simulation of the model with an iterative maximum likelihood fit. We show that in presence of co-occurring pathogens using uncorrected data leads to a critical under- or overestimation of soil suppressiveness measures. In contrast, our new approach enables to precisely estimate soil suppressiveness measures such as plant infection rate and plant resistance time. Our method allows a correction of measured infection parameters that is necessary in case different pathogens are present. Moreover, our model can be (1) adapted to use other models such as the logistic or the Gompertz model; and (2) it could be extended by a facilitation parameter if infections in plants increase the susceptibility to new infections. We propose our method to be particularly useful for exploring soil suppressiveness of natural soils from different sites (e.g., in biodiversity experiments). creator: Björn C. Rall creator: Ellen Latz uri: https://doi.org/10.7717/peerj.2615 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Rall and Latz title: Alterations to the middle cerebral artery of the hypertensive-arthritic rat model potentiates intracerebral hemorrhage link: https://peerj.com/articles/2608 last-modified: 2016-11-03 description: AimsWe have recently created an age-dependent hypertensive-mono-arthritic animal model from the stroke-resistant spontaneously hypertensive rat to model populations with autoimmune disease who are hypertensive and are prone to stroke. The model exhibits signs of hemorrhagic stroke (HS) subsequent to chronic inflammation and hypertension. HS is also associated with the inability of middle cerebral arteries to undergo pressure dependent constriction (PDC). We investigated alterations in the cerebrovasculature of our hypertensive mono-arthritic animals that develop stroke.Main MethodsAnimals were fed either a high salt diet (HSD) (4% NaCl) or Purina chow (0.58% NaCl) from weaning. Complete Freund’s Adjuvant (CFA) was injected into the left hind paw at 21–28 weeks; controls received saline and histological and functional studies were performed.ResultsBrain damage was more prominent with the high salt, with inflammation exacerbating the damage. High salt alone significantly decreased middle cerebral artery’s (MCA’s) ability to undergo PDC. Inflammation significantly decreased the ability of cerebrovasculature to respond to pressure step in the regular salt diet. The responses to vasoactive peptides were also significantly attenuated in both inflamed groups regardless of diet.ConclusionInduction of chronic systemic inflammation increases brain damage, and affect the MCA’s vasogenic function, decreasing its ability to respond to intraluminal pressure. HSD further exacerbates organ damage associated with chronic inflammation, further compromising cerebrovascular function, and likely increasing the incidence of intracerebral hemorrhage and injury. creator: Amy Randell creator: Killol Chokshi creator: Brittany Kane creator: Hilary Chang creator: Safaa Naiel creator: Jeffrey G. Dickhout creator: Noriko Daneshtalab uri: https://doi.org/10.7717/peerj.2608 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Randell et al. title: Environmental, land cover and land use constraints on the distributional patterns of anurans: Leptodacylus species (Anura, Leptodactylidae) from Dry Chaco link: https://peerj.com/articles/2605 last-modified: 2016-11-03 description: Subtropical dry forests are among the most vulnerable biomes to land transformation at a global scale. Among them, the Dry Chaco suffers an accelerated change due to agriculture expansion and intensification. The Dry Chaco ecoregion is characterized by high levels of endemisms and species diversity, which are the result of a variety of climates and reliefs, allowing a wide variety of environments. The amphibian group exhibits a high richness in the Dry Chaco, which has been barely studied in relation to land cover changes. We used ecological niche models (ENMs) to assess the potential geographic distribution of 10 Leptodactylus species (Anura, Leptodactylidae), which are mainly distributed within the Dry Chaco. We characterized these distributions environmentally, analyzed their overlap with land cover classes, and assessed their diversity of ecoregions. Also, we evaluated how these species potential distribution is affected by the transformation of land, and quantified the proportional area of the potential distribution in protected areas. We found that temperature seasonality is the main constraint to the occurrence of the species studied, whose main habitats are savannas, grasslands and croplands. The main threats to these species are the effects of climate change over spatial patterns of seasonality, which could affect their breeding and reproduction mode; the loss of their natural habitat; the exposure to contaminants used by intensive agriculture and their underrepresentation in protected areas. creator: Regina Gabriela Medina creator: Maria Laura Ponssa creator: Ezequiel Aráoz uri: https://doi.org/10.7717/peerj.2605 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Medina et al.