title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1480 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Functions of Candida albicans cell wall glycosidases Dfg5p and Dcw1p in biofilm formation and HOG MAPK pathway link: https://peerj.com/articles/5685 last-modified: 2018-09-28 description: BackgroundCandida albicans is a commensal fungus that inhabits the oral mucosal surface and causes oral and systemic candidiasis. Oral candidiasis most commonly occurs in patients with AIDS, denture wearers and newborn children. Systemic candidiasis occurs mainly in immunocompromised patients and patients admitted to hospitals for prolonged periods. C. albicans homologous genes, DFG5 and DCW1, encode for two closely related cell wall proteins with putative glycosyltransferase enzyme activity and C-terminal GPI-anchors. Past studies have shown that individual DFG5 and DCW1 mutations are viable but simultaneous deletion of DFG5 and DCW1 in C. albicans results in lethality. However, the exact functions of these cell wall based enzymes, which represent potential drug targets, are not understood.MethodsC. albicans DFG5/DCW1 heterologous and conditional double mutant strains were assessed for growth and biofilm formation in comparison to wild type and parental strains. Cell wall and heat stress susceptibility of the mutant and control strains were assessed using agar spotting assays. Growth was assessed under normal and osmotic stress conditions along with light microscopy imaging. Biofilm dry weight and microscopic imaging analysis of biofilms was performed. Hypha formation in response to serum was analyzed using light microscopy imaging. Western blot analysis of mutant strains and control strains was performed to assess Hog1 basal levels and phosphorylation status.ResultsAnalysis of the heterologous mutants indicated that Dfg5p is more important for growth while Dcw1p appeared to play a role in cell wall integrity response. The conditional double mutant was observed to be less resistant to cell wall stress. However, growth of the mutants was similar under control and osmotic stress conditions. The mutants were also able to grow similar to wild type under heat stress. Biofilm formation was reduced in the mutants where DFG5 was deleted or suppressed. Hyphal morphogenesis was reduced although germ tube formation was observed in the biofilms of the mutant strains. Basal Hog1 protein levels were reduced or absent in the DFG5 and DCW1 mutants. However, osmotic stress was able to induce Hog1 protein levels comparable to wild type. Hog1 phosphorylation appeared to be slightly reduced although not significantly. In addition to biofilm assays, serum dose response imaging analysis indicated that hyphae formation in DFG5 and DCW1 mutants was defective.ConclusionsThese data indicate that DFG5 and DCW1 are required for hyphal morphogenesis and biofilm formation in C. albicans. These functions may be regulated via basal Hog1 MAPK which is required for transcriptional regulation of chitin synthesis. creator: Ryan Mancuso creator: Jennifer Chinnici creator: Charlene Tsou creator: Sujay Busarajan creator: Raveena Munnangi creator: Abhiram Maddi uri: https://doi.org/10.7717/peerj.5685 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Mancuso et al. title: Meta-analysis of northeast Atlantic marine taxa shows contrasting phylogeographic patterns following post-LGM expansions link: https://peerj.com/articles/5684 last-modified: 2018-09-28 description: BackgroundComparative phylogeography enables the study of historical and evolutionary processes that have contributed to shaping patterns of contemporary genetic diversity across co-distributed species. In this study, we explored genetic structure and historical demography in a range of coastal marine species across the northeast Atlantic to assess whether there are commonalities in phylogeographic patterns across taxa and to evaluate whether the timings of population expansions were linked to the Last Glacial Maximum (LGM).MethodsA literature search was conducted using Web of Science. Search terms were chosen to maximise the inclusion of articles reporting on population structure and phylogeography from the northeast Atlantic; titles and abstracts were screened to identify suitable articles within the scope of this study. Given the proven utility of mtDNA in comparative phylogeography and the availability of these data in the public domain, a meta-analysis was conducted using published mtDNA gene sequences. A standardised methodology was implemented to ensure that the genealogy and demographic history of all mtDNA datasets were reanalysed in a consistent and directly comparable manner.ResultsMitochondrial DNA datasets were built for 21 species. The meta-analysis revealed significant population differentiation in 16 species and four main types of haplotype network were found, with haplotypes in some species unique to specific geographical locations. A signal of rapid expansion was detected in 16 species, whereas five species showed evidence of a stable population size. Corrected mutation rates indicated that the majority of expansions were estimated to have occurred after the earliest estimate for the LGM (∼26.5 Kyr), while few expansions were estimated to have pre-dated the LGM.ConclusionThis study suggests that post-LGM expansion appeared to be common in a range of marine taxa, supporting the concept of rapid expansions after the LGM as the ice sheets started to retreat. However, despite the commonality of expansion patterns in many of these taxa, phylogeographic patterns appear to differ in the species included in this study. This suggests that species-specific evolutionary processes, as well as historical events, have likely influenced the distribution of genetic diversity of marine taxa in the northeast Atlantic. creator: Tom L. Jenkins creator: Rita Castilho creator: Jamie R. Stevens uri: https://doi.org/10.7717/peerj.5684 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Jenkins et al. title: Cellular production of a counterfeit viral protein confers immunity to infection by a related virus link: https://peerj.com/articles/5679 last-modified: 2018-09-28 description: DNA copies of many non-retroviral RNA virus genes or portions thereof (NIRVs) are present in the nuclear genomes of many eukaryotes. These have often been preserved for millions of years of evolution, suggesting that they play an important cellular function. One possible function is resistance to infection by related viruses. In some cases, this appears to occur through the piRNA system, but in others by way of counterfeit viral proteins encoded by NIRVs. In the fungi, NIRVs may be as long as 1,400 uninterrupted codons. In one such case in the yeast Debaryomyces hansenii, one of these genes provides immunity to a related virus by virtue of expression of a counterfeit viral capsid protein, which interferes with assembly of viral capsids by negative complementation. The widespread occurrence of non-retroviral RNA virus genes in eukaryotes may reflect an underappreciated method of host resistance to infection. This work demonstrates for the first time that an endogenous host protein encoded by a gene that has been naturally acquired from a virus and fixed in a eukaryote can interfere with the replication of a related virus and do so by negative complementation. creator: Benjamin E. Warner creator: Matthew J. Ballinger creator: Pradeep Yerramsetty creator: Jennifer Reed creator: Derek J. Taylor creator: Thomas J. Smith creator: Jeremy A. Bruenn uri: https://doi.org/10.7717/peerj.5679 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Warner et al. title: Distinguishing between enduring and dynamic concussion symptoms: applying Generalisability Theory to the Rivermead Post Concussion Symptoms Questionnaire (RPQ) link: https://peerj.com/articles/5676 last-modified: 2018-09-28 description: BackgroundThe Rivermead Post Concussion Symptoms Questionnaire (RPQ) is a widely-used, 16-item measure of concussion symptoms yet its ability to assess change in the symptom experience over time has come under criticism. We applied Generalisability theory to differentiate between dynamic and enduring aspects of post-concussion symptoms and to examine sources of measurement error in the RPQ.Materials and MethodsGeneralisability theory was applied using the longitudinal design with persons as the object of measurement. Patients with a traumatic brain injury (n = 145; aged ≥16 years) were assessed at three time occasions (1, 6 and 12 months post-injury) using the RPQ.ResultsThe RPQ showed overall strong generalisability of scores (G = .98) across persons and occasions with a minor proportion of variance attributed to the dynamic aspect of symptoms reflected by interaction between person and occasion. Items measuring concentration, fatigue, restlessness and irritability reflected more dynamic patterns compared to more enduring patterns of sensitivity to noise, impatience, nausea and sleep disturbance.ConclusionThe RPQ demonstrated strong reliability in assessing enduring post-concussion symptoms but its ability to assess dynamic symptoms is limited. Clinicians should exercise caution in use of the RPQ to track dynamic symptom change over time. Further investigation is necessary to enhance the RPQ’s ability to assess dynamic symptoms and to address measurement error associated with individual items. creator: Oleg N. Medvedev creator: Alice Theadom creator: Suzanne Barker-Collo creator: Valery Feigin uri: https://doi.org/10.7717/peerj.5676 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Medvedev et al. title: Size dimorphism and sexual segregation in pheasants: tests of three competing hypotheses link: https://peerj.com/articles/5674 last-modified: 2018-09-28 description: Fine scale sexual segregation outside of the mating season is common in sexually dimorphic and polygamous species, particularly in ungulates. A number of hypotheses predict sexual segregation but these are often contradictory with no agreement as to a common cause, perhaps because they are species specific. We explicitly tested three of these hypotheses which are commonly linked by a dependence on sexual dimorphism for animals which exhibit fine-scale sexual segregation; the Predation Risk Hypothesis, the Forage Selection Hypothesis, and the Activity Budget Hypothesis, in a single system the pheasant, Phasianus colchicus; a large, sedentary bird that is predominantly terrestrial and therefore analogous to ungulates rather than many avian species which sexually segregate. Over four years we reared 2,400 individually tagged pheasants from one day old and after a period of 8–10 weeks we released them into the wild. We then followed the birds for 7 months, during the period that they sexually segregate, determined their fate and collected behavioural and morphological measures pertinent to the hypotheses. Pheasants are sexually dimorphic during the entire period that they sexually segregate in the wild; males are larger than females in both body size and gut measurements. However, this did not influence predation risk and predation rates (as predicted by the Predation Risk Hypothesis), diet choice (as predicted by the Forage Selection Hypothesis), or the amount of time spent foraging, resting or walking (as predicted by the Activity Budget Hypothesis). We conclude that adult sexual size dimorphism is not responsible for sexual segregation in the pheasant in the wild. Instead, we consider that segregation may be mediated by other, perhaps social, factors. We highlight the importance of studies on a wide range of taxa to help further the knowledge of sexual segregation. creator: Mark A. Whiteside creator: Jayden O. van Horik creator: Ellis J.G. Langley creator: Christine E. Beardsworth creator: Joah R. Madden uri: https://doi.org/10.7717/peerj.5674 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Whiteside et al. title: Biosorption potential of natural, pyrolysed and acid-assisted pyrolysed sugarcane bagasse for the removal of lead from contaminated water link: https://peerj.com/articles/5672 last-modified: 2018-09-28 description: Lead (Pb) is a ubiquitous pollutant which poses serious threats to plants, animals and humans once entered into the food chain via contaminated industrial effluents on their discharge into the surface of water bodies and/or geological materials. This study aimed to examine and compare the biosorption potential of natural sugarcane bagasse (NB), pyrolysed sugarcane bagasse (PB) and acid assisted pyrolysed sugarcane bagasse (APB) for the removal of Pb from contaminated water. To explore this objective, a series of batch experiments were conducted at various adsorbent mass (0.25, 0.5, 0.75, 1.0 g per 100 ml contaminated water), initial Pb concentration (7, 15, 30, 60 and 120 ppm), and contact time (7, 15, 30, 60 and 120 min). Results revealed that all the tested bio-sorbents have potential to adsorb and remove Pb ions from the contaminated water. In this regard, APB proved more effective since it removed 98% of Pb from aqueous solution at initial Pb concentration of 7 ppm and mass of 0.25 g per 100 ml of aqueous solution. The respective values in case of NB and PB were 90 and 95%. For a given adsorbent type, Pb adsorption decreased by increasing the mass from 0.25 to 1.0 g per 100 ml of aqueous solution. However, the greatest Pb removal occurred at adsorbent mass of 1.0 g per 100 ml of aqueous solution. Initial Pb concentration had a great impact on Pb adsorption and removal by adsorbent. The former increased and the latter decreased with the increase in initial Pb concentration from seven to 120 ppm. At seven ppm Pb concentration, maximum Pb removal took place irrespective to the adsorbent type. Out of the total Pb adsorption and removal, maximum contribution occurred within 15 min of contact time between the adsorbate and adsorbent, which slightly increased till 30 min, thereafter, it reached to equilibrium. Application of equilibrium isotherm models revealed that our results were better fitted with Freundlich adsorption isotherm model. Overall, and for the reasons detailed above, it is concluded that sugarcane bagasse has capabilities to adsorb and remove Pb ions from contaminated water. Its bio-sorption potential was considerably increased after pyrolysis and acid treatment. creator: Ghulam Mustafa Shah creator: Muhammad Nasir creator: Muhammad Imran creator: Hafiz Faiq Bakhat creator: Faiz Rabbani creator: Muhammad Sajjad creator: Abu Bakr Umer Farooq creator: Sajjad Ahmad creator: Lifen Song uri: https://doi.org/10.7717/peerj.5672 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Shah et al. title: New mud dragons from Svalbard: three new species of Cristaphyes and the first Arctic species of Pycnophyes (Kinorhyncha: Allomalorhagida: Pycnophyidae) link: https://peerj.com/articles/5653 last-modified: 2018-09-28 description: BackgroundKinorhynchs are marine, microscopic invertebrates inhabiting the seafloors. Their segmented trunk equipped with spines and processes has inspired scientists to give them the common name “mud dragons.” Even though kinorhynchs have been known since the 19th century, less than 300 species are known to science, and it is still considered a largely understudied animal group—in particular in the Arctic, from which only 23 species are known so far.MethodsSamples were collected at eight stations around Svalbard and in the fjords of Spitsbergen. Meiofauna was extracted from the sediment cores with LUDOX centrifugation method, and kinorhynchs were picked up and mounted for light- and scanning electron microscopy.ResultsFour new species of the kinorhynch family Pycnophyidae are described from Svalbard: Cristaphyes dordaidelosensis sp. nov., C. glaurung sp. nov., C. scatha sp. nov., and Pycnophyes ancalagon sp. nov. The new species are generally recognized by their distribution of setae along the trunk segments.DiscussionAfter the discovery of the new species, Pycnophyidae becomes with 14 species the most diverse kinorhynch genus in the Arctic, closely followed by Echinoderidae with 13 species. So far, these are the only kinorhynch families with an Arctic distribution. creator: Martin Vinther Sørensen creator: Katarzyna Grzelak uri: https://doi.org/10.7717/peerj.5653 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Sørensen and Grzelak title: Closing the gap: mixed stock analysis of three foraging populations of green turtles (Chelonia mydas) on the Great Barrier Reef link: https://peerj.com/articles/5651 last-modified: 2018-09-28 description: A solid understanding of the spatial ecology of green turtles (Chelonia mydas) is fundamental to their effective conservation. Yet this species, like many marine migratory species, is challenging to monitor and manage because they utilise a variety of habitats that span wide spatio-temporal scales. To further elucidate the connectivity between green turtle rookeries and foraging populations, we sequenced the mtDNA control region of 278 turtles across three foraging sites from the northern Great Barrier Reef (GBR) spanning more than 330 km: Cockle Bay, Green Island and Low Isles. This was performed with a newly developed assay, which targets a longer fragment of mtDNA than previous studies. We used a mixed stock analysis (MSA), which utilises genetic data to estimate the relative proportion of genetically distinct breeding populations found at a given foraging ground. Haplotype and nucleotide diversity was also assessed. A total of 35 haplotypes were identified across all sites, 13 of which had not been found previously in any rookery. The MSA showed that the northern GBR (nGBR), Coral Sea (CS), southern GBR (sGBR) and New Caledonia (NC) stocks supplied the bulk of the turtles at all three sites, with small contributions from other rookeries in the region. Stock contribution shifted gradually from north to south, although sGBR/CS stock dominated at all three sites. The major change in composition occured between Cockle Bay and Low Isles. Our findings, together with other recent studies in this field, show that stock composition shifts with latitude as a natural progression along a coastal gradient. This phenomenon is likely to be the result of ocean currents influencing both post-hatchling dispersal and subsequent juvenile recruitment to diverse coastal foraging sites. creator: Karina Jones creator: Michael Jensen creator: Graham Burgess creator: Johanna Leonhardt creator: Lynne van Herwerden creator: Julia Hazel creator: Mark Hamann creator: Ian Bell creator: Ellen Ariel uri: https://doi.org/10.7717/peerj.5651 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Jones et al. title: Xeno-miRNet: a comprehensive database and analytics platform to explore xeno-miRNAs and their potential targets link: https://peerj.com/articles/5650 last-modified: 2018-09-28 description: Xeno-miRNAs are microRNAs originating from exogenous species detected in host biofluids. A growing number of studies have suggested that many of these xeno-miRNAs may be involved in cross-species interactions and manipulations. To date, hundreds of xeno-miRNAs have been reported in different hosts at various abundance levels. Based on computational predictions, many more miRNAs could be potentially transferred to human circulation system. There is a clear need for bioinformatics resources and tools dedicated to xeno-miRNA annotations and their potential functions. To address this need, we have systematically curated xeno-miRNAs from multiple sources, performed target predictions using well-established algorithms, and developed a user-friendly web-based tool—Xeno-miRNet—to allow researchers to search and explore xeno-miRNAs and their potential targets within different host species. Xeno-miRNet currently contains 1,702 (including both detected and predicted) xeno-miRNAs from 54 species and 98,053 potential gene targets in six hosts. The web application is freely available at http://xeno.mirnet.ca. creator: Yannan Fan creator: Maria Habib creator: Jianguo Xia uri: https://doi.org/10.7717/peerj.5650 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Fan et al. title: Molecular analysis of oral microflora in patients with primary Sjögren’s syndrome by using high-throughput sequencing link: https://peerj.com/articles/5649 last-modified: 2018-09-28 description: BackgroundThe objective of this study was to characterize the oral microflora profile of primary Sjögren’s syndrome (pSS) patients, thereby revealing the connection between oral bacterial composition and dental caries, and to identify the “core microbiome” in the oral cavities of pSS patients and systemic healthy individuals by using a high-throughput sequencing technique.MethodsTwenty-two pSS patients and 23 healthy controls were enrolled in this study. Their clinical data and oral rinse samples were collected. The V3–V4 hypervariable regions of the bacterial 16S rRNA gene of samples were amplified and analyzed by high-throughput sequencing on the Illumina Miseq PE300 platform.ResultsBoth two groups were age- and sex-matched. There were significantly higher decayed, missing and filled teeth (DMFT) and decayed, missing and filled surfaces (DMFS) in the pSS group than in the control group (p < 0.01). Alpha diversity was depleted in pSS patients, compared with healthy controls (p < 0.01), while beta diversity between the two groups was not significantly different. Seven discriminative genera (LDA > 4) were found between the two groups in LEfSe (LDA Effect Size) analysis. The relative abundance of Veillonella in pSS patients was fourfold higher, while Actinomyces, Haemophilus, Neisseria, Rothia, Porphyromonas and Peptostreptococcus were significantly lower in pSS patients than in healthy controls. However, the correlation between Veillonella and DMFT/DMFS was not significant (p > 0.05). In Venn diagram analysis, nine genera shared by all samples of two groups, which comprised 71.88% and 67.64% in pSS patients and controls, respectively.DiscussionThese findings indicate a microbial dysbiosis in pSS patients; notably, Veillonella might be recognized as a biomarker in pSS patients. The core microbiome in pSS patients was similar to the systemic healthy population. These provide insight regarding advanced microbial prevention and treatment of severe dental caries in pSS patients. This study also provides basic data regarding microbiology in pSS. creator: Zhifang Zhou creator: Guanghui Ling creator: Ning Ding creator: Zhe Xun creator: Ce Zhu creator: Hong Hua creator: Xiaochi Chen uri: https://doi.org/10.7717/peerj.5649 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Zhou et al.