title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1239 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Environmental sampling to assess the bioburden of Mycobacterium avium subspecies paratuberculosis in drylot pens on California dairies link: https://peerj.com/articles/8081 last-modified: 2019-11-19 description: Mycobacterium avium subspecies paratuberculosis (MAP) is a bacterium that can cause substantial economic losses in infected dairy herds due to reduced milk production and increased cow-replacement costs. In order to control MAP in dairies with drylot pens, a standardized environmental sampling protocol to quantify MAP in fecal slurry was developed based on an existing protocol for freestall pens. Specifically, following a 24 h hold of the flush, a grab sample of approximately 10 ml of fecal slurry was collected every 1 m along the flush lane of the drylot pens, avoiding individual cow fecal pats. To determine the reliability and repatability of the new environmental sampling protocol for estimation of MAP bioburden at the pen level, two collectors simultaneously collected fecal slurry samples every day for 3 days from six drylot cow pens on two Central California dairies. During the study period no cow movement between pens was allowed with the exception of sick cows. The study herds had MAP seroprevalence of 5.8% and 3.2%, respectively, based on whole pen serum ELISA results. Variance components models for quantitative real-time PCR (qPCR) results showed samples collected from different pens on different dairies accounted for greater variablitiy in MAP concentration (65%), while samples collected by different collectors had the least variability (0.1%). In contrast, variability in MAP concentration in environmental samples collected on different days had 25% variability. The intraclass correlation coefficient showed high reliability (93%) of environmental sampling simultaneously by different collectors. In contrast, the reliability of environmental sampling at different days was 65%, which was similar to the reliability for sampling by different collectors on different days. Investigators can expect high reliability when employing the new environmental sampling protocol along with qPCR testing of environmental samples from drylot pens. creator: Tapakorn Chamchoy creator: Deneice R. Williams creator: John M. Adaska creator: Randall J. Anderson creator: Sharif S. Aly uri: https://doi.org/10.7717/peerj.8081 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Chamchoy et al. title: The microbiota of Drosophila suzukii influences the larval development of Drosophila melanogaster link: https://peerj.com/articles/8097 last-modified: 2019-11-19 description: Microorganisms play a central role in the biology of vinegar flies such as Drosophila suzukii and Drosophila melanogaster: serving as a food source to both adults and larvae, and influencing a range of traits including nutrition, behavior, and development. The niches utilized by the fly species partially overlap, as do the microbiota that sustain them, and interactions among these players may drive the development of crop diseases. To learn more about how the microbiota of one species may affect the other, we isolated and identified microbes from field-caught D. suzukii, and then characterized their effects on D. melanogaster larval development time in the laboratory. We found that the D. suzukii microbiota consistently included both yeasts and bacteria. It was dominated by yeasts of the genus Hanseniaspora, and bacteria from the families Acetobacteraceae and Enterobacteriaceae. Raising D. melanogaster under gnotobiotic conditions with each microbial isolate individually, we found that some bacteria promoted larval development relative to axenic conditions, but most did not have a significant effect. In contrast, nearly all the yeasts tested significantly accelerated larval development. The one exception was Starmerella bacillaris, which had the opposite effect: significantly slowing larval developmental rate. We investigated the basis for this effect by examining whether S. bacillaris cells could sustain larval growth, and measuring the survival of S. bacillaris and other yeasts in the larval gut. Our results suggest S. bacillaris is not digested by D. melanogaster and therefore cannot serve as a source of nutrition. These findings have interesting implications for possible interactions between the two Drosophilia species and their microbiota in nature. Overall, we found that microbes isolated from D. suzukii promote D. melanogaster larval development, which is consistent with the model that infestation of fruit by D. suzukii can open up habitat for D. melanogaster. We propose that the microbiome is an important dimension of the ecological interactions between Drosophila species. creator: Gabrielle M. Solomon creator: Hiruni Dodangoda creator: Tylea McCarthy-Walker creator: Rita Ntim-Gyakari creator: Peter D. Newell uri: https://doi.org/10.7717/peerj.8097 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Solomon et al. title: Decrease in walking speed increases hip moment impulse in the frontal plane during the stance phase link: https://peerj.com/articles/8110 last-modified: 2019-11-19 description: BackgroundIncreased daily cumulative hip moment in the frontal plane (i.e., the product of hip moment impulse in the frontal plane during the stance phase and mean steps per day) is a risk factor for progression of hip osteoarthritis. Although hip osteoarthritis generally causes a decrease in the walking speed, its effect on hip moment impulse in the frontal plane is unclear. The purpose of this study was to examine the relationship between decrease in walking speed and hip moment impulse in the frontal plane.MethodsWe used a public dataset of treadmill walking in 17 older adults (mean (SD) age: 63.2 (8.0) years). The subjects walked on the treadmill for 30 s under five conditions: (1) 40% of comfortable non-dimensional speed (CNDS), (2) 55% CNDS, (3) 70% CNDS, (4) 85% CNDS, and (5) 100% CNDS. The hip moment impulse in the frontal plane non-normalized (or normalized) to step length (Nm s/kg [or Nm s/(kg m)]) for each condition was calculated. Furthermore, the relationship between walking speed and hip moment impulse in the frontal plane non-normalized (or normalized) to step length was examined using regression analysis based on a previous study.ResultsA decrease in non-dimensional speed (i.e., walking speed) significantly increased the non-normalized (or normalized) hip moment impulse in the frontal plane during the stance phase. The relationship between walking speed and non-normalized (or normalized) hip moment impulse in the frontal plane was fitted by a second-order polynomial.DiscussionThis study revealed that a decrease in walking speed increased the non-normalized (or normalized) hip moment impulse in the frontal plane in healthy older adults. This finding is useful for understanding the relationship between walking speed and hip moment impulse in the frontal plane and suggests that a decrease in walking speed may actually increase the daily cumulative hip moment in the frontal plane of patients with hip osteoarthritis. creator: Takuma Inai creator: Tomoya Takabayashi creator: Mutsuaki Edama creator: Masayoshi Kubo uri: https://doi.org/10.7717/peerj.8110 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Inai et al. title: First palaeoneurological study of a sauropod dinosaur from France and its phylogenetic significance link: https://peerj.com/articles/7991 last-modified: 2019-11-18 description: Despite continuous improvements, our knowledge of the palaeoneurology of sauropod dinosaurs is still deficient. This holds true even for Titanosauria, which is a particularly speciose clade of sauropods with representatives known from numerous Cretaceous sites in many countries on all continents. The data currently available regarding the palaeoneurology of titanosaurs is strongly biased towards Gondwanan forms (Argentina above all, but also India, Malawi and Australia). In contrast, the palaeoneurology of Laurasian titanosaurs is known only from a few taxa from Spain and Uzbekistan, despite the discovery in other countries of Laurasia of a number of neurocranial remains that would lend themselves well to investigations of this kind. To fill in this gap in our knowledge, we subjected a titanosaurian braincase from the uppermost Upper Cretaceous of southern France to X-ray computed tomographic scanning, allowing the generation of 3D renderings of the endocranial cavity enclosing the brain, cranial nerves and blood vessels, as well as the labyrinth of the inner ear. These reconstructions are used to clarify the phylogenetic position of the specimen from the Fox-Amphoux-Métisson site. A combination of characters, including the presence of two hypoglossal rami on the endocast, the average degree of development of the dorsal-head/caudal-middle-cerebral vein system and the relatively short and subequal lengths of the ipsilateral semicircular canals of the labyrinth, are particularly revealing in this respect. They suggest that, compared with the few other Laurasian titanosaurs for which in-depth palaeoneurological data are available, the French taxon is more derived than the distinctly more ancient, possibly non-lithostrotian titanosaur from the Uzbek site of Dzharakuduk but more basal than derived saltasaurids, such as the coeval or slightly more recent forms from the Spanish locality of Lo Hueco. creator: Fabien Knoll creator: Stephan Lautenschlager creator: Xavier Valentin creator: Verónica Díez Díaz creator: Xabier Pereda Suberbiola creator: Géraldine Garcia uri: https://doi.org/10.7717/peerj.7991 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Knoll et al. title: Bibliographic revision of Mesacanthion Filipjev, 1927 (Nematoda: Thoracostomopsidae) with description of a new species from Jeju Island, South Korea link: https://peerj.com/articles/8023 last-modified: 2019-11-18 description: A new species of the genus Mesacanthion Filipjev, 1927 was discovered during a survey of natural beaches of Jeju Island in South Korea. The new species Mesacanthion jejuensissp. nov. shares general morphology of the genus such as the outer labial and cephalic setae being situated at the middle of cephalic capsule, well-developed mandibles with two columns united by a curved bar, and three equally sized and shaped teeth shorter than the mandibles. The new species belongs to a group of Mesacanthion species in which spicules are shorter than two anal body diameters. The new species is most closely related to M. pannosum, first discovered in Puget Sound, Washington, in terms of having enlarged cervical setae flap at the end of cephalic capsule, spicules which are shorter than 2 anal body diameter, both supplementary organ and gubernaculum. It can be distinguished from M. pannosum by its stronger inner labial setae, longer outer labial setae, and difference in the index value of b and c’. Along with the description of Mesacanthion jejuensissp. nov., the genus Mesacanthion Filipjev, 1927 is bibliographically reviewed and revised. Including the new species, a total of 48 species are described within the genus; 39 which are valid; eight which are considered to be species inquirenda due to misplacement of genus and poor description; one which is considered nomen nudum. An updated diagnosis of the genus is provided along with a compiled tabular key comparing different diagnostic morphological characters of all valid species, as well as a pictorial key consisting of 21 species with spicules shorter than two anal body diameters. creator: Raehyuk Jeong creator: Alexei V. Tchesunov creator: Wonchoel Lee uri: https://doi.org/10.7717/peerj.8023 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Jeong et al. title: Host dietary specialization and neutral assembly shape gut bacterial communities of wild dragonflies link: https://peerj.com/articles/8058 last-modified: 2019-11-18 description: Host-associated gut microbiota can have significant impacts on host ecology and evolution and are often host-specific. Multiple factors can contribute to such host-specificity: (1) host dietary specialization passively determining microbial colonization, (2) hosts selecting for specific diet-acquired microbiota, or (3) a combination of both. The latter possibilities indicate a functional association and should produce stable microbiota. We tested these alternatives by analyzing the gut bacterial communities of six species of wild adult dragonfly populations collected across several geographic locations. The bacterial community composition was predominantly explained by sampling location, and only secondarily by host identity. To distinguish the role of host dietary specialization and host-imposed selection, we identified prey in the guts of three dragonfly species. Surprisingly, the dragonflies–considered to be generalist predators–consumed distinct prey; and the prey diversity was strongly correlated with the gut bacterial profile. Such host dietary specialization and spatial variation in bacterial communities suggested passive rather than selective underlying processes. Indeed, the abundance and distribution of 72% of bacterial taxa were consistent with neutral community assembly; and fluorescent in situ hybridization revealed that bacteria only rarely colonized the gut lining. Our results contradict the expectation that host-imposed selection shapes the gut microbiota of most insects, and highlight the importance of joint analyses of diet and gut microbiota of natural host populations. creator: Rittik Deb creator: Ashwin Nair creator: Deepa Agashe uri: https://doi.org/10.7717/peerj.8058 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Deb et al. title: A recombinase polymerase amplification-lateral flow dipstick assay for rapid detection of the quarantine citrus pathogen in China, Phytophthora hibernalis link: https://peerj.com/articles/8083 last-modified: 2019-11-18 description: Phytophthora hibernalis, the causal agent of brown rot of citrus fruit, is an important worldwide pathogen and a quarantine pest in China. Current diagnosis of the disease relies on disease symptoms, pathogen isolation and identification by DNA sequencing. However, symptoms caused by P. hibernalis can be confused with those by other Phytophthora and fungal species. Moreover, pathogen isolation, PCR amplification and sequencing are time-consuming. In this study, a rapid assay including 20-min recombinase polymerase amplification targeting the Ypt1 gene and 5-min visualization using lateral flow dipsticks was developed for detecting P. hibernalis. This assay was able to detect 0.2 ng of P. hibernalis genomic DNA in a 50-µL reaction system. It was specific to P. hibernalis without detection of other tested species including P. citrophthora, P. nicotianae, P. palmivora and P. syringae, four other important citrus pathogens. Using this assay, P. hibernalis was also detected from artificially inoculated orange fruits. Results in this study indicated that this assay has the potential application to detect P. hibernalis at diagnostic laboratories and plant quarantine departments of customs, especially under time- and resource-limited conditions. creator: Tingting Dai creator: Tao Hu creator: Xiao Yang creator: Danyu Shen creator: Binbin Jiao creator: Wen Tian creator: Yue Xu uri: https://doi.org/10.7717/peerj.8083 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Dai et al. title: Acquisition of fungi from the environment modifies ambrosia beetle mycobiome during invasion link: https://peerj.com/articles/8103 last-modified: 2019-11-18 description: Microbial symbionts can play critical roles when their host attempts to colonize a new habitat. The lack of symbiont adaptation can in fact hinder the invasion process of their host. This scenario could change if the exotic species are able to acquire microorganisms from the invaded environment. Understanding the ecological factors that influence the take-up of new microorganisms is thus essential to clarify the mechanisms behind biological invasions. In this study, we tested whether different forest habitats influence the structure of the fungal communities associated with ambrosia beetles. We collected individuals of the most widespread exotic (Xylosandrus germanus) and native (Xyleborinus saxesenii) ambrosia beetle species in Europe in several old-growth and restored forests. We characterized the fungal communities associated with both species via metabarcoding. We showed that forest habitat shaped the community of fungi associated with both species, but the effect was stronger for the exotic X. germanus. Our results support the hypothesis that the direct contact with the mycobiome of the invaded environment might lead an exotic species to acquire native fungi. This process is likely favored by the occurrence of a bottleneck effect at the mycobiome level and/or the disruption of the mechanisms sustaining co-evolved insect-fungi symbiosis. Our study contributes to the understanding of the factors affecting insect-microbes interactions, helping to clarify the mechanisms behind biological invasions. creator: Davide Rassati creator: Lorenzo Marini creator: Antonino Malacrinò uri: https://doi.org/10.7717/peerj.8103 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Rassati et al. title: Angiogenic signaling in the lungs of a metabolically suppressed hibernating mammal (Ictidomys tridecemlineatus) link: https://peerj.com/articles/8116 last-modified: 2019-11-18 description: To conserve energy in times of limited resource availability, particularly during cold winters, hibernators suppress even the most basic of physiologic processes. Breathing rates decrease from 40 breaths/minute to less than 1 breath/min as they decrease body temperature from 37 °C to ambient. Nevertheless, after months of hibernation, these incredible mammals emerge from torpor unscathed. This study was conducted to better understand the protective and possibly anti-inflammatory adaptations that hibernator lungs may use to prevent damage associated with entering and emerging from natural torpor. We postulated that the differential protein expression of soluble protein receptors (decoy receptors that sequester soluble ligands to inhibit signal transduction) would help identify inhibited inflammatory signaling pathways in metabolically suppressed lungs. Instead, the only two soluble receptors that responded to torpor were sVEGFR1 and sVEGFR2, two receptors whose full-length forms are bound by VEGF-A to regulate endothelial cell function and angiogenesis. Decreased sVEGFR1/2 correlated with increased total VEGFR2 protein levels. Maintained or increased levels of key γ-secretase subunits suggested that decreased sVEGFR1/2 protein levels were not due to decreased levels of intramembrane cleavage complex subunits. VEGF-A protein levels did not change, suggesting that hibernators may regulate VEGFR1/2 signaling at the level of the receptor instead of increasing relative ligand abundance. A panel of angiogenic factors used to identify biomarkers of angiogenesis showed a decrease in FGF-1 and an increase in BMP-9. Torpid lungs may use VEGF and BMP-9 signaling to balance angiogenesis and vascular stability, possibly through the activation of SMAD signaling for adaptive tissue remodeling. creator: Samantha M. Logan creator: Kenneth B. Storey uri: https://doi.org/10.7717/peerj.8116 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Logan and Storey title: Single-molecule real-time sequencing identifies massive full-length cDNAs and alternative-splicing events that facilitate comparative and functional genomics study in the hexaploid crop sweet potato link: https://peerj.com/articles/7933 last-modified: 2019-11-15 description: BackgroundSweet potato (Ipomoea batatas (L.) Lam.) is one of the most important crops in many developing countries and provides a candidate source of bioenergy. However, neither a complete reference genome nor large-scale full-length cDNA sequences for this outcrossing hexaploid crop are available, which in turn impedes progress in research studies in I. batatas functional genomics and molecular breeding.MethodsIn this study, we sequenced full-length transcriptomes in I. batatas and its diploid ancestor I. trifida by single-molecule real-time sequencing and Illumina second-generation sequencing technologies. With the generated datasets, we conducted comprehensive intraspecific and interspecific sequence analyses and experimental characterization.ResultsA total of 53,861/51,184 high-quality long-read transcripts were obtained, which covered about 10,439/10,452 loci in the I. batatas/I. trifida genome. These datasets enabled us to predict open reading frames successfully in 96.83%/96.82% of transcripts and identify 34,963/33,637 full-length cDNA sequences, 1,401/1,457 transcription factors, 25,315/27,090 simple sequence repeats, 1,656/1,389 long non-coding RNAs, and 5,251/8,901 alternative splicing events. Approximately, 32.34%/38.54% of transcripts and 46.22%/51.18% multi-exon transcripts underwent alternative splicing in I. batatas/I. trifida. Moreover, we validated one alternative splicing event in each of 10 genes and identified tuberous-root-specific expressed isoforms from a starch-branching enzyme, an alpha-glucan phosphorylase, a neutral invertase, and several ABC transporters. Overall, the collection and analysis of large-scale long-read transcripts generated in this study will serve as a valuable resource for the I. batatas research community, which may accelerate the progress in its structural, functional, and comparative genomics studies. creator: Na Ding creator: Huihui Cui creator: Ying Miao creator: Jun Tang creator: Qinghe Cao creator: Yonghai Luo uri: https://doi.org/10.7717/peerj.7933 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Ding et al.