title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1520 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Biochemical and genetic analyses of the oomycete Pythium insidiosum provide new insights into clinical identification and urease-based evolution of metabolism-related traits link: https://peerj.com/articles/4821 last-modified: 2018-06-05 description: The oomycete microorganism, Pythium insidiosum, causes the life-threatening infectious condition, pythiosis, in humans and animals worldwide. Affected individuals typically endure surgical removal of the infected organ(s). Detection of P. insidiosum by the established microbiological, immunological, or molecular methods is not feasible in non-reference laboratories, resulting in delayed diagnosis. Biochemical assays have been used to characterize P. insidiosum, some of which could aid in the clinical identification of this organism. Although hydrolysis of maltose and sucrose has been proposed as the key biochemical feature useful in discriminating P. insidiosum from other oomycetes and fungi, this technique requires a more rigorous evaluation involving a wider selection of P. insidiosum strains. Here, we evaluated 10 routinely available biochemical assays for characterization of 26 P. insidiosum strains, isolated from different hosts and geographic origins. Initial assessment revealed diverse biochemical characteristics across the P. insidiosum strains tested. Failure to hydrolyze sugars is observed, especially in slow-growing strains. Because hydrolysis of maltose and sucrose varied among different strains, use of the biochemical assays for identification of P. insidiosum should be cautioned. The ability of P. insidiosum to hydrolyze urea is our focus, because this metabolic process relies on the enzyme urease, an important virulence factor of other pathogens. The ability to hydrolyze urea varied among P. insidiosum strains and was not associated with growth rates. Genome analyses demonstrated that urease- and urease accessory protein-encoding genes are present in both urea-hydrolyzing and non-urea-hydrolyzing strains of P. insidiosum. Urease genes are phylogenetically conserved in P. insidiosum and related oomycetes, while the presence of urease accessory protein-encoding genes is markedly diverse in these organisms. In summary, we dissected biochemical characteristics and drew new insights into clinical identification and urease-related evolution of P. insidiosum. creator: Theerapong Krajaejun creator: Thidarat Rujirawat creator: Teerat Kanpanleuk creator: Pitak Santanirand creator: Tassanee Lohnoo creator: Wanta Yingyong creator: Yothin Kumsang creator: Pattarana Sae-Chew creator: Weerayuth Kittichotirat creator: Preecha Patumcharoenpol uri: https://doi.org/10.7717/peerj.4821 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Krajaejun et al. title: The energetic cost of mounting an immune response for Pallas’s long-tongued bat (Glossophaga soricina) link: https://peerj.com/articles/4627 last-modified: 2018-06-05 description: The acute phase response (APR) is the first line of defense of the vertebrate immune system against pathogens. Mounting an immune response is believed to be energetically costly but direct measures of metabolic rate during immune challenges contradict this assumption. The energetic cost of APR for birds is higher than for rodents, suggesting that this response is less expensive for mammals. However, the particularly large increase in metabolic rate after APR activation for a piscivorous bat (Myotis vivesi) suggests that immune response might be unusually costly for bats. Here we quantified the energetic cost and body mass change associated with APR for the nectarivorous Pallas’s long-tongued bat (Glossophaga soricina). Activation of the APR resulted in a short-term decrease in body mass and an increase in resting metabolic rate (RMR) with a total energy cost of only 2% of the total energy expenditure estimated for G. soricina. This increase in RMR was far from the large increase measured for piscivorous bats; rather, it was similar to the highest values reported for birds. Overall, our results suggest that the costs of APR for bats may vary interspecifically. Measurement of the energy cost of vertebrate immune response is limited to a few species and further work is warranted to evaluate its significance for an animal’s energy budget. creator: Lucia V. Cabrera-Martínez creator: L. Gerardo Herrera M. creator: Ariovaldo P. Cruz-Neto uri: https://doi.org/10.7717/peerj.4627 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Cabrera-Martínez et al. title: Diversity, host-specificity and stability of sponge-associated fungal communities of co-occurring sponges link: https://peerj.com/articles/4965 last-modified: 2018-06-04 description: Fungi play a critical role in a range of ecosystems; however, their interactions and functions in marine hosts, and particular sponges, is poorly understood. Here we assess the fungal community composition of three co-occurring sponges (Cymbastela concentrica, Scopalina sp., Tedania anhelans) and the surrounding seawater over two time points to help elucidate host-specificity, stability and potential core members, which may shed light into the ecological function of fungi in sponges. The results showed that ITS-amplicon-based community profiling likely provides a more realistic assessment of fungal diversity in sponges than cultivation-dependent approaches. The sponges studied here were found to contain phylogenetically diverse fungi (eight fungal classes were observed), including members of the family Togniniaceae and the genus Acrostalagmus, that have so far not been reported to be cultured from sponges. Fungal communities within any given sponge species were found to be highly variable compared to bacterial communities, and influenced in structure by the community of the surrounding seawater, especially considering temporal variation. Nevertheless, the sponge species studied here contained a few “variable/core” fungi that appeared in multiple biological replicates and were enriched in their relative abundance compared to seawater communities. These fungi were the same or highly similar to fungal species detected in sponges around the world, which suggests a prevalence of horizontal transmission where selectivity and enrichment of some fungi occur for those that can survive and/or exploit the sponge environment. Our current sparse knowledge about sponge-associated fungi thus indicate that fungal communities may perhaps not play as an important ecological role in the sponge holobiont compared to bacterial or archaeal symbionts. creator: Mary T.H.D. Nguyen creator: Torsten Thomas uri: https://doi.org/10.7717/peerj.4965 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Nguyen and Thomas title: D-GENIES: dot plot large genomes in an interactive, efficient and simple way link: https://peerj.com/articles/4958 last-modified: 2018-06-04 description: Dot plots are widely used to quickly compare sequence sets. They provide a synthetic similarity overview, highlighting repetitions, breaks and inversions. Different tools have been developed to easily generated genomic alignment dot plots, but they are often limited in the input sequence size. D-GENIES is a standalone and web application performing large genome alignments using minimap2 software package and generating interactive dot plots. It enables users to sort query sequences along the reference, zoom in the plot and download several image, alignment or sequence files. D-GENIES is an easy-to-install, open-source software package (GPL) developed in Python and JavaScript. The source code is available at https://github.com/genotoul-bioinfo/dgenies and it can be tested at http://dgenies.toulouse.inra.fr/. creator: Floréal Cabanettes creator: Christophe Klopp uri: https://doi.org/10.7717/peerj.4958 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Cabanettes and Klopp title: Adaptive genetic variation at three loci in South African vervet monkeys (Chlorocebus pygerythrus) and the role of selection within primates link: https://peerj.com/articles/4953 last-modified: 2018-06-04 description: Vervet monkeys (Chlorocebus pygerythrus) are one of the most widely distributed non-human primate species found in South Africa. They occur across all the South African provinces, inhabiting a large variety of habitats. These habitats vary sufficiently that it can be assumed that various factors such as pathogen diversity could influence populations in different ways. In turn, these factors could lead to varied levels of selection at specific fitness linked loci. The Toll-like receptor (TLR) gene family, which play an integral role in vertebrate innate immunity, is a group of fitness linked loci which has been the focus of much research. In this study, we assessed the level of genetic variation at partial sequences of two TLR loci (TLR4 and 7) and a reproductively linked gene, acrosin (ACR), across the different habitat types within the vervet monkey distribution range. Gene variation and selection estimates were also made among 11–21 primate species. Low levels of genetic variation for all three gene regions were observed within vervet monkeys, with only two polymorphic sites identified for TLR4, three sites for TLR7 and one site for ACR. TLR7 variation was positively correlated with high mean annual rainfall, which was linked to increased pathogen abundance. The observed genetic variation at TLR4 might have been influenced by numerous factors including pathogens and climatic conditions. The ACR exonic regions showed no variation in vervet monkeys, which could point to the occurrence of a selective sweep. The TLR4 and TLR7 results for the among primate analyses was mostly in line with previous studies, indicating a higher rate of evolution for TLR4. Within primates, ACR coding regions also showed signs of positive selection, which was congruent with previous reports on mammals. Important additional information to the already existing vervet monkey knowledge base was gained from this study, which can guide future research projects on this highly researched taxon as well as help conservation agencies with future management planning involving possible translocations of this species. creator: Willem G. Coetzer creator: Trudy R. Turner creator: Christopher A. Schmitt creator: J. Paul Grobler uri: https://doi.org/10.7717/peerj.4953 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Coetzer et al. title: Bioheat transfer model of transcutaneous spinal cord stimulation-induced temperature changes link: https://peerj.com/articles/4921 last-modified: 2018-06-04 description: Transcutaneous spinal cord stimulation (tSCS) has been extensively studied due to its promising application in motor function restoration. Many previous studies have explored both the essential mechanism of action and the methods for determining optimal stimulation parameters. In contrast, the bioheat transfer analysis of tSCS therapy has not been investigated to the same extent, despite widely existing, and being of great significance in assuring a stable and thermally safe treatment. In this paper, we concentrated on the thermal effects of tSCS using a finite element-based method. By coupling the electric field and bioheat field, systematic finite element simulations were performed on a human spinal cord model to survey the influence of anatomical structures, blood perfusion, and stimulation parameters on temperature changes for the first time. The results show that tSCS-induced temperature rise mainly occurs in the skin and fat layers and varies due to individual differences. The current density distribution along with the interactions of multiple biothermal effects synthetically determines the thermal status of the whole spinal cord model. Smaller stimulation electrodes have a higher risk of thermal damage when compared with larger electrodes. Increasing the stimulation intensity will result in more joule heat accumulation, hence an increase in the temperature. Among all configurations in this study that simulated the clinical tSCS protocols, the temperature rise could reach up to 9.4 °C on the skin surface depending on the stimulation parameters and tissue blood perfusion. creator: Luyao Chen creator: Ang Ke creator: Peng Zhang creator: Zhaolong Gao creator: Xuecheng Zou creator: Jiping He uri: https://doi.org/10.7717/peerj.4921 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Chen et al. title: Pro-inflammatory AGE-RAGE signaling is activated during arousal from hibernation in ground squirrel adipose link: https://peerj.com/articles/4911 last-modified: 2018-06-04 description: BackgroundInflammation is generally suppressed during hibernation, but select tissues (e.g. lung) have been shown to activate both antioxidant and pro-inflammatory pathways, particularly during arousal from torpor when breathing rates increase and oxidative metabolism fueling the rewarming process produces more reactive oxygen species. Brown and white adipose tissues are now understood to be major hubs for the regulation of immune and inflammatory responses, yet how these potentially damaging processes are regulated by fat tissues during hibernation has hardly been studied. The advanced glycation end-product receptor (RAGE) can induce pro-inflammatory responses when bound by AGEs (which are glycated and oxidized proteins, lipids, or nucleic acids) or damage associated molecular pattern molecules (DAMPs, which are released from dying cells).MethodsSince gene expression and protein synthesis are largely suppressed during torpor, increases in AGE-RAGE pathway proteins relative to a euthermic control could suggest some role for these pro-inflammatory mediators during hibernation. This study determined how the pro-inflammatory AGE-RAGE signaling pathway is regulated at six major time points of the torpor-arousal cycle in brown and white adipose from a model hibernator, Ictidomys tridecemlineatus. Immunoblotting, RT-qPCR, and a competitive ELISA were used to assess the relative gene expression and protein levels of key regulators of the AGE-RAGE pathway during a hibernation bout.ResultsThe results of this study revealed that RAGE is upregulated as animals arouse from torpor in both types of fat, but AGE and DAMP levels either remain unchanged or decrease. Downstream of the AGE-RAGE cascade, nfat5 was more highly expressed during arousal in brown adipose.DiscussionAn increase in RAGE protein levels and elevated mRNA levels of the downstream transcription factor nfat5 during arousal suggest the pro-inflammatory response is upregulated in adipose tissue of the hibernating ground squirrel. It is unlikely that this cascade is activated by AGEs or DAMPs. This research sheds light on how a fat-but-fit organism with highly regulated metabolism may control the pro-inflammatory AGE-RAGE pathway, a signaling cascade that is often dysregulated in other obese organisms. creator: Samantha M. Logan creator: Kenneth B. Storey uri: https://doi.org/10.7717/peerj.4911 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Logan and Storey title: Teleost and elasmobranch eye lenses as a target for life-history stable isotope analyses link: https://peerj.com/articles/4883 last-modified: 2018-06-04 description: Incrementally grown, metabolically inert tissues such as fish otoliths provide biochemical records that can used to infer behavior and physiology throughout the lifetime of the individual. Organic tissues are particularly useful as the stable isotope composition of the organic component can provide information about diet, trophic level and location. Unfortunately, inert, incrementally grown organic tissues are relatively uncommon. The vertebrate eye lens, however, is formed via sequential deposition of protein-filled fiber cells, which are subsequently metabolically inert. Lenses therefore have the potential to serve as biochemical data recorders capturing life-long variations in dietary and spatial ecology. Here we review the state of knowledge regarding the structure and formation of fish eye lenses in the context of using lens tissue for retrospective isotopic analysis. We discuss the relationship between eye lens diameter and body size, describe the successful recovery of expected isotopic gradients throughout ontogeny and between species, and quantify the isotopic offset between lens protein and white muscle tissue. We show that fish eye lens protein is an attractive host for recovery of stable isotope life histories, particularly for juvenile life stages, and especially in elasmobranchs lacking otoliths, but interpretation of lens-based records is complicated by species-specific uncertainties associated with lens growth rates. creator: Katie Quaeck-Davies creator: Victoria A. Bendall creator: Kirsteen M. MacKenzie creator: Stuart Hetherington creator: Jason Newton creator: Clive N. Trueman uri: https://doi.org/10.7717/peerj.4883 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Quaeck-Davies et al. title: Cytotoxicity and antimicrobial action of selected phytochemicals against planktonic and sessile Streptococcus mutans link: https://peerj.com/articles/4872 last-modified: 2018-06-04 description: BackgroundDental caries remains the most prevalent and costly oral infectious disease worldwide, encouraging the search for new and more effective antimicrobials. Therefore, the aim of this work was to study the antimicrobial action of selected phytochemicals (eugenol, citronellol, sabinene hydrate, trans-cinnamaldehyde, terpineol and cinnamic acid) against Streptococcus mutans in planktonic and biofilm states as well as the cytotoxicity of these compounds.MethodsThe antibacterial activity of the selected compounds was evaluated by the determination of the minimal bactericidal concentration. The resazurin assay was used to assess the metabolic activity of sessile S. mutans. The cytotoxicity was determined using a fibroblast cell line.ResultsAmong the tested phytochemicals, citronellol, cinnamic acid and trans-cinnamaldehyde were the most effective against both planktonic and sessile S. mutans, an effect apparently related to their hydrophobic character. Additionally, these three compounds did not compromise fibroblasts cell viability.DiscussionCitronellol, cinnamic acid and trans-cinnamaldehyde demonstrated significant antimicrobial activity and low cytotoxicity proposing their potential as a novel group of therapeutic compounds to control oral infectious diseases. Moreover, their effects are particularly relevant when benchmarked against eugenol, a phytochemical commonly used for prosthodontic applications in dentistry. creator: Marta Ribeiro creator: Joana Malheiro creator: Liliana Grenho creator: Maria Helena Fernandes creator: Manuel Simões uri: https://doi.org/10.7717/peerj.4872 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Ribeiro et al. title: Bullying victimization and child sexual abuse among left-behind and non-left-behind children in China link: https://peerj.com/articles/4865 last-modified: 2018-06-04 description: BackgroundBullying is one of the most important factors associated with child abuse. However, robust tests supporting the assumption that being bullied can contribute to child sexual abuse (CSA) among left-behind children (LBC) remain sparse. This study aims to investigate the association of bullying victimization with CSA among LBC in China.MethodsA cross-sectional study was conducted in six middle schools of Sichuan and Anhui province in 2015. The bullying victimization was assessed by seven items from the Revised Olweus Bully/Victim Questionnaire. The experience of CSA was measured by ten items CSA scale with good consistency.ResultsA total of 1,030 children met the sampling criteria, including 284 LBC and 746 non-LBC. The prevalence of CSA was 22.89% in LBC and 20.19% in non-LBC (p > 0.05). Bullying victimization was related to CSA among both LBC (adjusted Odds Ratio [aOR] = 2.52, 95% CI [1.34–4.73]) and non-LBC (aOR = 2.35, 95% CI [1.58–3.53]). The association between bullying victimization and CSA was much higher among left-behind girls (left-behind girls: aOR = 7.36, 95% CI [2.16–24.99]; non-left-behind girls: aOR = 2.38, 95% CI [1.08–5.27]). Also, LBC of a young age (11–15), children with siblings, living in rural areas and non-traditional family structure who were bullied were more likely to suffer CSA than their non-LBC peers.ConclusionsBullying victimization is associated with a significant increase in CSA among both LBC and non-LBC. Anti-bullying programs should target vulnerable populations including female LBC and LBC with siblings to reduce the risk of CSA. creator: Li Yan creator: Qianqian Zhu creator: Xiaowen Tu creator: Xiayun Zuo creator: Chunyan Yu creator: Chaohua Lou creator: Qiguo Lian uri: https://doi.org/10.7717/peerj.4865 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Yan et al.