title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1357 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: The microbiome profiling of fungivorous black tinder fungus beetle Bolitophagus reticulatus reveals the insight into bacterial communities associated with larvae and adults link: https://peerj.com/articles/6852 last-modified: 2019-05-07 description: Saproxylic beetles play a crucial role in key processes occurring in forest ecosystems, and together with fungi contribute to the decomposition and mineralization of wood. Among this group are mycetophilic beetles which associate with wood-decaying fungi and use the fruiting body for nourishment and development. Therefore, their feeding strategy (especially in the case of fungivorous species) requires special digestive capabilities to take advantage of the nutritional value of fungal tissue. Although polypore-beetle associations have been investigated in numerous studies, detailed studies focusing on the microbiome associated with species feeding on fruiting bodies of polypores remain limited. Here we investigated the bacterial communities associated with larvae and adults of Bolitophagus reticulatus collected from Fomes fomentarius growing on two different host tree: beech (Fagus sp.) and birch (Betula sp.), respectively. Among 24 identified bacterial phyla, three were the most relatively abundant (Proteobacteria, Actinobacteria and Bacteroidetes). Moreover, we tried to find unique patterns of bacteria abundances which could be correlated with the long-term field observation showing that the fruiting bodies of F. fomentarius, growing on birch are more inhabited by beetles than fruiting bodies of the same fungus species growing on beech. Biochemical analyses showed that the level of protease inhibitors and secondary metabolites in F. fomentarius is higher in healthy fruiting bodies than in the inhabited ones. However, tested microbiome samples primarily clustered by developmental stage of B. reticulatus and host tree did not appear to impact the taxonomic distribution of the communities. This observation was supported by statistical analyses. creator: Agnieszka Kaczmarczyk-Ziemba creator: Grzegorz K. Wagner creator: Krzysztof Grzywnowicz creator: Marek Kucharczyk creator: Sylwia Zielińska uri: https://doi.org/10.7717/peerj.6852 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Kaczmarczyk-Ziemba et al. title: Promotion of growth and metal accumulation of alfalfa by coinoculation with Sinorhizobium and Agrobacterium under copper and zinc stress link: https://peerj.com/articles/6875 last-modified: 2019-05-07 description: The Legume-Rhizobium symbiosis has been proposed as a promising technique for the phytoremediation of contaminated soils due to its beneficial activity in symbiotic nitrogen fixation. However, numerous studies have shown that excessive heavy metals reduce the efficiency of symbiotic nodulation with Rhizobium and inhibit plant growth. In this study, we aimed to evaluate the synergistic effects of IAA-producing bacteria and Rhizobium on Medicago lupulina growth under Cu and Zn stress. Pot experiments showed that 400 mg kg−1 Cu2 + and Zn2 + greatly inhibited plant growth, but dual inoculation of Medicago lupulina with Sinorhizobium meliloti CCNWSX0020 and Agrobacterium tumefaciens CCNWGS0286 significantly increased the number of nodules and plant biomass by enhancing antioxidant activities. Under double stress of 400 mg kg−1 Cu2 + and Zn2 +, the nodule number and nitrogenase activities of dual-inoculated plants were 48.5% and 154.4% higher, respectively, than those of plants inoculated with Sinorhizobium meliloti. The root and above-ground portion lengths of the dual-inoculated plants were 32.6% and 14.1% greater, respectively, than those of the control, while the root and above-ground portion dry weights were 34.3% and 32.2% greater, respectively, than those of the control. Compared with S. meliloti and A. tumefaciens single inoculation, coinoculation increased total Cu uptake by 39.1% and 47.5% and increased total Zn uptake by 35.4% and 44.2%, respectively, under double metal stress conditions. Therefore, coinoculation with Sinorhizobium meliloti and Agrobacterium tumefaciens enhances metal phytoextraction by increasing plant growth and antioxidant activities under Cu/Zn stress, which provides a new approach for bioremediation in heavy metal-contaminated soil. creator: Liru Jian creator: Xiaoli Bai creator: Hui Zhang creator: Xiuyong Song creator: Zhefei Li uri: https://doi.org/10.7717/peerj.6875 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Jian et al. title: Cortical modulation of pupillary function: systematic review link: https://peerj.com/articles/6882 last-modified: 2019-05-07 description: BackgroundThe pupillary light reflex is the main mechanism that regulates the pupillary diameter; it is controlled by the autonomic system and mediated by subcortical pathways. In addition, cognitive and emotional processes influence pupillary function due to input from cortical innervation, but the exact circuits remain poorly understood. We performed a systematic review to evaluate the mechanisms behind pupillary changes associated with cognitive efforts and processing of emotions and to investigate the cerebral areas involved in cortical modulation of the pupillary light reflex.MethodologyWe searched multiple databases until November 2018 for studies on cortical modulation of pupillary function in humans and non-human primates. Of 8,809 papers screened, 258 studies were included.ResultsMost investigators focused on pupillary dilatation and/or constriction as an index of cognitive and emotional processing, evaluating how changes in pupillary diameter reflect levels of attention and arousal. Only few tried to correlate specific cerebral areas to pupillary changes, using either cortical activation models (employing micro-stimulation of cortical structures in non-human primates) or cortical lesion models (e.g., investigating patients with stroke and damage to salient cortical and/or subcortical areas). Results suggest the involvement of several cortical regions, including the insular cortex (Brodmann areas 13 and 16), the frontal eye field (Brodmann area 8) and the prefrontal cortex (Brodmann areas 11 and 25), and of subcortical structures such as the locus coeruleus and the superior colliculus.ConclusionsPupillary dilatation occurs with many kinds of mental or emotional processes, following sympathetic activation or parasympathetic inhibition. Conversely, pupillary constriction may occur with anticipation of a bright stimulus (even in its absence) and relies on a parasympathetic activation. All these reactions are controlled by subcortical and cortical structures that are directly or indirectly connected to the brainstem pupillary innervation system. creator: Costanza Peinkhofer creator: Gitte M. Knudsen creator: Rita Moretti creator: Daniel Kondziella uri: https://doi.org/10.7717/peerj.6882 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Peinkhofer et al. title: Chemovariation and antibacterial activity of extracts and isolated compounds from species of Ixora and Greenea (Ixoroideae, Rubiaceae) link: https://peerj.com/articles/6893 last-modified: 2019-05-07 description: BackgroundA large number of secondary metabolites can be obtained from plants used for traditional medicine in two related genera (Ixora and Greenea) in the subfamily Ixoroideae (Rubiaceae), but there are only a few detailed studies on their bioactivities. Therefore, the main goals of this study were to determine the antibacterial activities of lipophilic extracts from plants of some Ixora and Greenea species native to Thailand, and to isolate some pure compounds from those extracts. Moreover, we compared the occurrence of compounds in different plant parts of samples from different habitats to better understand their variation.MethodsA total of 56 lipophilic extracts were obtained from the leaves, stem bark, and root bark of eight Ixora and two Greenea species collected at various locations in Thailand. Isolated compounds were identified using nuclear magnetic resonance. Antimicrobial activities were evaluated against four Gram-positive and nine Gram-negative human pathogenic bacterial strains.ResultsExtracts from I. javanica, I. nigricans, I. brunonis, and G. montana, along with isolated scopoletin, exhibited antibacterial activities against Gram-positive methicillin-resistant Staphylococcus aureus ATCC 43300, with minimum inhibitory concentration values ranging from 64 to 256 µg/mL. The occurrence of scopoletin, isofraxidin, and geniposidic acid in lipophilic extracts showed some variation among different plant parts and species.ConclusionsLipophilic extracts of Ixora and Greenea species have the potential to be developed as anti-Gram-positive agents, in particular to counter infections of methicillin-resistant S. aureus strains. The chemical profiles showed differences between floristic regions but similarity within the same plant parts. creator: Raveevatoo Buathong creator: Voradol Chamchumroon creator: Johann Schinnerl creator: Markus Bacher creator: Wichai Santimaleeworagun creator: Ekaphan Kraichak creator: Srunya Vajrodaya uri: https://doi.org/10.7717/peerj.6893 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Buathong et al. title: Accuracy of a deep convolutional neural network in detection of retinitis pigmentosa on ultrawide-field images link: https://peerj.com/articles/6900 last-modified: 2019-05-07 description: Evaluating the discrimination ability of a deep convolution neural network for ultrawide-field pseudocolor imaging and ultrawide-field autofluorescence of retinitis pigmentosa. In total, the 373 ultrawide-field pseudocolor and ultrawide-field autofluorescence images (150, retinitis pigmentosa; 223, normal) obtained from the patients who visited the Department of Ophthalmology, Tsukazaki Hospital were used. Training with a convolutional neural network on these learning data objects was conducted. We examined the K-fold cross validation (K = 5). The mean area under the curve of the ultrawide-field pseudocolor group was 0.998 (95% confidence interval (CI) [0.9953–1.0]) and that of the ultrawide-field autofluorescence group was 1.0 (95% CI [0.9994–1.0]). The sensitivity and specificity of the ultrawide-field pseudocolor group were 99.3% (95% CI [96.3%–100.0%]) and 99.1% (95% CI [96.1%–99.7%]), and those of the ultrawide-field autofluorescence group were 100% (95% CI [97.6%–100%]) and 99.5% (95% CI [96.8%–99.9%]), respectively. Heatmaps were in accordance with the clinician’s observations. Using the proposed deep neural network model, retinitis pigmentosa can be distinguished from healthy eyes with high sensitivity and specificity on ultrawide-field pseudocolor and ultrawide-field autofluorescence images. creator: Hiroki Masumoto creator: Hitoshi Tabuchi creator: Shunsuke Nakakura creator: Hideharu Ohsugi creator: Hiroki Enno creator: Naofumi Ishitobi creator: Eiko Ohsugi creator: Yoshinori Mitamura uri: https://doi.org/10.7717/peerj.6900 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Masumoto et al. title: Metacommunity patterns of Amazonian Odonata: the role of environmental gradients and major rivers link: https://peerj.com/articles/6472 last-modified: 2019-05-06 description: BackgroundWe identified and classified damselfly (Zygoptera) and dragonfly (Anisoptera) metacommunities in Brazilian Amazonia, relating species distribution patterns to known biological gradients and biogeographical history. We expected a random distribution of both Zygoptera and Anisoptera within interfluves. At the Amazonian scale, we expected Anisoptera metacommunities to be randomly distributed due to their higher dispersal ability and large environmental tolerance. In contrast, we expected Zygoptera communities to exhibit a Clementsian pattern, limited by the large Amazonia rivers due to their low dispersal ability.MethodsWe used a dataset of 58 first-to-third order well-sampled streamlets in four Amazonian interfluves and applied an extension of the Elements of Metacommunity Structure (EMS) framework, in which we order Zygoptera and Anisoptera metacommunities by known spatial and biogeographic predictors.ResultsAt the Amazonian scale, both Zygoptera and Anisoptera presented a Clementsian pattern, driven by the same environmental and biogeographical predictors, namely biogeographic region (interfluve), annual mean temperature, habitat integrity and annual precipitation. At the interfluve scale, results were less consistent and only partially support our hypothesis. Zygoptera metacommunities at Guiana and Anisoptera metacommunities at Tapajós were classified as random, suggesting that neutral processes gain importance at smaller spatial scales.DiscussionOur findings were consistent with previous studies showing that environmental gradients and major rivers limit the distribution of Odonata communities, supporting that larger Amazonian rivers act as barriers for the dispersal of this group. In addition, the importance of habitat integrity indicates that intactness of riparian vegetation is an important filter shaping metacommunity structure of Amazonian stream Odonata. creator: Fernanda Alves-Martins creator: Leandro Schlemmer Brasil creator: Leandro Juen creator: Paulo De Marco Jr creator: Juliana Stropp creator: Joaquín Hortal uri: https://doi.org/10.7717/peerj.6472 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Alves-Martins et al. title: Molecular evolution of the VacA p55 binding domain of Helicobacter pylori in mestizos from a high gastric cancer region of Colombia link: https://peerj.com/articles/6634 last-modified: 2019-05-06 description: The stomach bacterium Helicobacter pylori is one of the most prevalent pathogens in humans, closely linked with serious diseases such as gastric cancer. The microbe has been associated with its host for more than 100,000 years and escorted modern humans out of Africa. H. pylori is predominantly transmitted within families and dispersed globally, resulting in distinct phylogeographic patterns, which can be utilized to investigate migrations and bioturbation events in human history. Latin America was affected by several human migratory waves due to the Spanish colonisation that drastically changed the genetic load and composition of the bacteria and its host. Genetic evidence indicates that independent evolutionary lines of H. pylori have evolved in mestizos from Colombia and other countries in the region during more than 500 years since colonisation. The vacuolating cytotoxin VacA represents a major virulence factor of the pathogen comprising two domains, p33 and p55, the latter of which is essential for binding to the host epithelial cell. The evolution of the VacA toxin in Colombia has been strongly biased due to the effects of Spanish colonization. However, the variation patterns and microevolution of the p55 domain have not yet been described for this population. In the present study, we determined the genetic polymorphisms and deviations in the neutral model of molecular evolution in the p55 domain of 101 clinical H. pylori isolates collected in Bogotá, a city located in Andean mountains characterized by its high gastric cancer risk and its dominant mestizo population. The microevolutionary patterns of the p55 domain were shaped by recombination, purifying and episodic diversifying positive selection. Furthermore, amino acid positions 261 and 321 in the p55 domain of VacA show a high variability among mestizos clinical subsets, suggesting that natural selection in H. pylori may operate differentially in patients with different gastric diseases. creator: Andrés J. Gutiérrez-Escobar creator: María M. Bravo creator: Orlando Acevedo creator: Steffen Backert uri: https://doi.org/10.7717/peerj.6634 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Gutiérrez-Escobar et al. title: Optimization of extraction conditions and determination of purine content in marine fish during boiling link: https://peerj.com/articles/6690 last-modified: 2019-05-06 description: BackgroundGout is the second most common metabolic disease affecting human health. The disease of gout is closely related to the level of uric acid, which is the end-product of human purine metabolism. Moreover, food is the main way of external ingestion of purine.MethodA simple and time-saving method was developed to extract purines like adenine, hypoxanthine, guanine, and xanthine from marine fish by single factor design combined with Box–Behnken. The contents of these purines in the edible parts and internal organs of marine fish, as well as Scophthalmus maximus, were determined by high-performance liquid chromatography to investigate the relationship between the boiling process and purine content.ResultThe mixed-acid method was chosen for the extraction of purine bases and the extraction conditions were as follows: mixture acid 90.00% TFA/80.00% FA (v/v, 1:1); hydrolysis temperature 90.00 °C; time 10.00 min; liquid-to-solid ratio 30:1. The total purine content of the edible parts (eyes, dorsal muscles, abdominal muscles, and skin) was the highest in Scophthalmus maximus, followed by sphyraena, Sardinella, Trichiurus lepturus, Scomberomorus niphonius, Pleuronectiformes, Sea catfish, Anguillidae, and Rajiformes. Moreover, boiling significantly reduced the purine content in the marine fish because of the transfer of the purines to the cooking liquid during boiling. Scophthalmus maximus, Sphyraena, and Sardinella were regard as high-purine marine fish, which we should eat less. We also confirmed that boiling significantly transferred purine bases from fish to cooking liquid. Thus, boiling could reduce the purine content of fish, thereby reducing the risk of hyperuricemia and gout. creator: Tingting Li creator: Likun Ren creator: Dangfeng Wang creator: Minjie Song creator: Qiuying Li creator: Jianrong Li uri: https://doi.org/10.7717/peerj.6690 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Li et al. title: Molecular epidemiology of coagulase-negative Staphylococcus species isolated at different lactation stages from dairy cattle in the United States link: https://peerj.com/articles/6749 last-modified: 2019-05-06 description: BackgroundCoagulase negative Staphylococcus (CNS) species are currently the most prevalent intra-mammary pathogens causing subclinical mastitis and occasional clinical mastitis or persistent infection in lactating dairy cattle. More than 10 CNS species have been identified, but they are generally managed as one group on most dairies in the United States. However, improved management decisions and treatment outcomes may be achieved with better understanding of the prevalent species, pathogenicity and strain diversity within and across dairies.MethodologyA total of 604 CNS isolates were cultured from milk samples collected during a dry-cow treatment clinical trial conducted on 6 dairy herds in 4 states in the US. All the study cows were randomized to receive 1 of the 3 different intra-mammary antimicrobial infusions (Quatermaster, Spectramast DC or ToMorrow Dry Cow) at dry-off. Milk samples were collected at dry-off, calving (0–6 days in milk, DIM), post-calving (7–13 DIM) and at mastitis events within the first 100 DIM. The CNS isolates were identified to species level by partial sequencing of the rpoβ gene, and genetic relatedness within species was investigated by phylogenetic analysis of the pulse-field gel electrophoresis profiles of the isolates.ResultsThe major CNS species identified were S. chromogenes (48.3%), S. haemolyticus (17.9%), S. simulans and S. epidermidis (each at 6.5%). Other CNS species identified at lower frequencies included S. hominis, S. auricularis, S. sciuri, S. spp KS-SP, S. capitis, S. cohnii, S. warneri, S. pasteuri, S. xylosus, S. hyicus, S. equorum, S. microti, S. rostri, S. gallinarum, S. saprophyticus and S. succinus. Phylogenetic analyses of the major species types demonstrated an association between genetic relatedness and epidemiological distributions of S. chromogenes, S. simulans, S. haemolyticus and S. auricularis. Additionally, identical strains of S. chromogenes and S. simulans were isolated from the same udder quarter of several cows at consecutive sample stages. The rest of the minor species had no deducible genetic-epidemiological link.DiscussionThe observed association between genetic and epidemiological distributions indicated animal-adapted nature of four CNS species, suggesting possible host-adapted and environmental transmission of these species. Multi-stage isolation of the same udder quarter strain was evidence for chronic intra-mammary infection.ConclusionThe different CNS species and strains circulating on US dairy herds were genetically diverse. Four species identified were likely udder-adapted pathogens, 2 of which caused persistent infection. Our findings are important in guiding the design of effective mastitis control strategies. creator: Stephen N. Jenkins creator: Emmanuel Okello creator: Paul V. Rossitto creator: Terry W. Lehenbauer creator: John Champagne creator: Maria C.T. Penedo creator: Andréia G. Arruda creator: Sandra Godden creator: Paul Rapnicki creator: Patrick J. Gorden creator: Leo L. Timms creator: Sharif S. Aly uri: https://doi.org/10.7717/peerj.6749 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Jenkins et al. title: Hatchery-reared enhancement program for silver carp (Hypophthalmichthys molitrix) in the middle Yangtze River: monitoring the effectiveness based on parentage analysis link: https://peerj.com/articles/6836 last-modified: 2019-05-06 description: IntroductionA hatchery-reared silver carp (Hypophthalmichthys molitrix) program has been intensively carried out since 2010 to enhance the rapidly declining fisheries production in the middle Yangtze River. However, only a little information regarding the effectiveness of the enhancement program has been reported. In this context, this study investigates on an enhancement program through monitoring the efficacy based on parentage analysis.MethodsA total of 1,529 hatchery-reared fish and 869 larvae were sampled from the middle Yangtze River in 2016 and 2017 and were genotyped by thirteen microsatellite loci. Based on the results of parentage analysis the larvae were divided into three populations: (1) larvae population with both parents being hatchery-reared fish (=R), (2) larvae population with only a male or a female parent being hatchery-reared fish (=H), and (3) larvae population with no hatchery-reared fish parent (=W). The following analyses were also carried out: (1) assessing the contribution of hatchery-reared offspring to larval resources, and (2) evaluating the genetic effect of stock enhancement on the wild population.ResultsIn total, 10.37% and 11.56% of larvae were identified as the offspring produced by hatchery-reared fish released in 2016 and 2017, respectively. In 2017, some of the larvae were assigned unambiguously to hatchery-reared fish released in 2016. In terms of the number of offspring produced, the hatchery-reared fish have shown significant variations. No significant differences were found among all the larvae populations concerning genetic parameters for diversity. High levels of genetic diversity of all larvae populations were obtained. Low FSTvalues obtained from pairwise FST analysis, as well as the analysis of molecular variance (AMOVA), revealed high genetic structural similarity among all the larvae populations. The genetic composition of the W larvae population in 2017 was different from that of all other larvae populations (all larvae populations in 2016, and R and H larvae populations in 2017), as demonstrated from the results of STRUCTURE and PCA analyses.ConclusionIt was demonstrated that hatchery-reared fish are successful in producing the offspring in the natural environment during multiple years, which might assist in increasing the abundance of larvae. The hatchery-reared fish had variations in terms of the success rates on reproduction. Also, the hatchery-reared enhancement program had no significant effect on the genetic diversity or the genetic structure of wild populations. However, the genetic component of the W larvae population in 2017 was changed as compared to 2016, which was not due to the hatchery-reared enhancement program for silver carp. This could be due to flooding, but the specific causes need further studies. Our results clearly show the necessity to continuously inspect the genetic impact of the enhancement program so that historical information can be utilized for further research. creator: Huijuan Chen creator: Dengqiang Wang creator: Xinbin Duan creator: Shaoping Liu creator: Daqing Chen creator: Yun Li uri: https://doi.org/10.7717/peerj.6836 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Chen et al.