title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2017-10 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Water absorption through salivary gland type I acini in the blacklegged tick, Ixodes scapularis link: https://peerj.com/articles/3984 last-modified: 2017-10-31 description: Tick salivary glands play critical roles in maintaining water balance for survival, as they eliminate excess water and ions during blood feeding on hosts. In the long duration of fasting in the off-host period, ticks secrete hygroscopic saliva into the mouth cavity to uptake atmospheric water vapor. Type I acini of tick salivary glands are speculated to be involved in secretion of hygroscopic saliva based on ultrastructure studies. However, we recently proposed that type I acini play a role in resorption of water/ions from the primary saliva produced by other salivary acini (i.e., types II and III) during the tick blood feeding phase. In this study, we tested the function of type I acini in unfed female Ixodes scapularis. The route of ingested water was tracked after forced feeding of water with fluorescent dye rhodamine123. We found that type-I acini of the salivary glands, but not type II and III, are responsible for water uptake. In addition, the ingestion of water through the midgut was also observed. Injection or feeding of ouabain, a Na/K-ATPase inhibitor, suppressed water absorption in type I acini. When I. scapularis was offered a droplet of water, ticks rarely imbibed water directly (5%), while some approached the water droplet to use the high humidity formed in the vicinity of the droplet (23%). We conclude that during both on- and off-host stages, type I acini in salivary glands of female Ixodes scapularis absorb water and ions. creator: Donghun Kim creator: Paulina Maldonado-Ruiz creator: Ludek Zurek creator: Yoonseong Park uri: https://doi.org/10.7717/peerj.3984 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Kim et al. title: Genome size and identification of abundant repetitive sequences in Vallisneria spinulosa link: https://peerj.com/articles/3982 last-modified: 2017-10-31 description: Vallisneria spinulosa is a freshwater aquatic plant of ecological and economic importance. However, there is limited cytogenetic and genomics information on Vallisneria. In this study, we measured the nuclear DNA content of Vallisneria spinulosa by flow cytometry, performed a de novo assembly, and annotated repetitive sequences by using a combination of next-generation sequencing (NGS) and bioinformatics tools. The genome size of Vallisneria spinulosa is approximately 3,595 Mbp, in which nearly 60% of the genome consists of repetitive sequences. The majority of the repetitive sequences are LTR-retrotransposons comprising 43% of the genome. Although the amount of sequencing data used in this study was not sufficient for a whole-genome assembly, it could generate an overview of representative elements in the genome. These results will lay a new foundation for further studies on various species that belong to the Vallisneria genus. creator: RuiJuan Feng creator: Xin Wang creator: Min Tao creator: Guanchao Du creator: Qishuo Wang uri: https://doi.org/10.7717/peerj.3982 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Feng et al. title: Land snails of Leptopoma Pfeiffer, 1847 in Sabah, Northern Borneo (Caenogastropoda: Cyclophoridae): an analysis of molecular phylogeny and geographical variations in shell form link: https://peerj.com/articles/3981 last-modified: 2017-10-31 description: Leptopoma is a species rich genus with approximately 100 species documented. Species-level identification in this group has been based on shell morphology and colouration, as well as some anatomical features based on small sample sizes. However, the implications of the inter- and intra-species variations in shell form to the taxonomy of Leptopoma species and the congruency of its current shell based taxonomy with its molecular phylogeny are still unclear. There are four Leptopoma species found in Sabah, Borneo, and their taxonomy status remains uncertain due to substantial variation in shell forms. This study focuses on the phylogenetic relationships and geographical variation in shell form of three Leptopoma species from Sabah. The phylogenetic relationship of these species was first estimated by performing Maximum Likelihood and Bayesian analysis based on mitochondrial genes (16S rDNA and COI) and nuclear gene (ITS-1). Then, a total of six quantitative shell characters (i.e., shell height, shell width, aperture height, aperture width, shell spire height, and ratio of shell height to width) and three qualitative shell characters (i.e., shell colour patterns, spiral ridges, and dark apertural band) of the specimens were mapped across the phylogenetic tree and tested for phylogenetic signals. Data on shell characters of Leptopoma sericatum and Leptopoma pellucidum from two different locations (i.e., Balambangan Island and Kinabatangan) where both species occurred sympatrically were then obtained to examine the geographical variations in shell form. The molecular phylogenetic analyses suggested that each of the three Leptopoma species was monophyletic and indicated congruence with only one of the shell characters (i.e., shell spiral ridges) in the current morphological-based classification. Although the geographical variation analyses suggested some of the shell characters indicating inter-species differences between the two Leptopoma species, these also pointed to intra-species differences between populations from different locations. This study on Leptopoma species is based on small sample size and the findings appear only applicable to Leptopoma species in Sabah. Nevertheless, we anticipate this study to be a starting point for more detailed investigations to include the other still little-known (ca. 100) Leptopoma species and highlights a need to assess variations in shell characters before they could be used in species classification. creator: Chee-Chean Phung creator: Pooi-San Heng creator: Thor-Seng Liew uri: https://doi.org/10.7717/peerj.3981 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Phung et al. title: Male-male competition and female choice are differentially affected by male call acoustics in the serrate-legged small treefrog, Kurixalus odontotarsus link: https://peerj.com/articles/3980 last-modified: 2017-10-31 description: BackgroundThe evolution of exaggerated vocal signals in anuran species is an important topic. Males and females have both evolved the ability to discriminate communication sounds. However, the nature of sexual dimorphism in cognition and sensory discrimination and in the evolution and limitation of sexual signal exaggeration remain relatively unexplored.MethodsIn the present study, we used male calls of varied complexity in the serrate-legged small treefrog, Kurixalus odontotarsus, as probes to investigate how both sexes respond to variations in call complexity and how sex differences in signal discrimination play a role in the evolution of sexual signal exaggeration. The compound calls of male K. odontotarsus consist of a series of one or more harmonic notes (A notes) which may be followed by one or more short broadband notes (B notes).ResultsMale playback experiments and female phonotaxis tests showed that increasing the number of A notes in stimulus calls elicits increased numbers of response calls by males and increases the attractiveness of the stimulus calls to females. The addition of B notes, however, reduces male calling responses. Moreover, call stimuli which contain only B notes suppress spontaneous male calling responses. Phonotaxis experiments show that females prefer calls with greater numbers of A notes and calls containing both A notes and B notes, but do not prefer calls with only B notes.DiscussionMale-male competition and female choice appear to have played different roles in the evolution and limitation of signal complexity in K. odontotarsus. These results provide new insights into how exaggerated compound signals evolve and how signal complexity may be limited in anurans. creator: Bicheng Zhu creator: Jichao Wang creator: Longhui Zhao creator: Qinghua Chen creator: Zhixin Sun creator: Yue Yang creator: Steven E. Brauth creator: Yezhong Tang creator: Jianguo Cui uri: https://doi.org/10.7717/peerj.3980 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Zhu et al. title: Proteomics research and related functional classification of liquid sclerotial exudates of Sclerotinia ginseng link: https://peerj.com/articles/3979 last-modified: 2017-10-31 description: Sclerotinia ginseng is a necrotrophic soil pathogen that mainly infects the root and basal stem of ginseng, causing serious commercial losses. Sclerotia, which are important in the fungal life cycle, are hard, asexual, resting structures that can survive in soil for several years. Generally, sclerotium development is accompanied by the exudation of droplets. Here, the yellowish droplets of S. ginseng were first examined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and the proteome was identified by a combination of different analytical platforms. A total of 59 proteins were identified and classified into six categories: carbohydrate metabolism (39%), oxidation-reduction process (12%), transport and catabolism (5%), amino acid metabolism (3%), other functions (18%), and unknown protein (23%), which exhibited considerable differences in protein composition compared with droplets of S. sclerotium. In the carbohydrate metabolism group, several proteins were associated with sclerotium development, particularly fungal cell wall formation. The pathogenicity and virulence of the identified proteins are also discussed in this report. The findings of this study may improve our understanding of the function of exudate droplets as well as the life cycle and pathogenesis of S. ginseng. creator: Dan Wang creator: Jun Fan Fu creator: Ru Jun Zhou creator: Zi Bo Li creator: Yu Jiao Xie uri: https://doi.org/10.7717/peerj.3979 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Wang et al. title: Record breaking achievements by spiders and the scientists who study them link: https://peerj.com/articles/3972 last-modified: 2017-10-31 description: Organismal biology has been steadily losing fashion in both formal education and scientific research. Simultaneous with this is an observable decrease in the connection between humans, their environment, and the organisms with which they share the planet. Nonetheless, we propose that organismal biology can facilitate scientific observation, discovery, research, and engagement, especially when the organisms of focus are ubiquitous and charismatic animals such as spiders. Despite being often feared, spiders are mysterious and intriguing, offering a useful foundation for the effective teaching and learning of scientific concepts and processes. In order to provide an entryway for teachers and students—as well as scientists themselves—into the biology of spiders, we compiled a list of 99 record breaking achievements by spiders (the “Spider World Records”). We chose a world-record style format, as this is known to be an effective way to intrigue readers of all ages. We highlighted, for example, the largest and smallest spiders, the largest prey eaten, the fastest runners, the highest fliers, the species with the longest sperm, the most venomous species, and many more. We hope that our compilation will inspire science educators to embrace the biology of spiders as a resource that engages students in science learning. By making these achievements accessible to non-arachnologists and arachnologists alike, we suggest that they could be used: (i) by educators to draw in students for science education, (ii) to highlight gaps in current organismal knowledge, and (iii) to suggest novel avenues for future research efforts. Our contribution is not meant to be comprehensive, but aims to raise public awareness on spiders, while also providing an initial database of their record breaking achievements. creator: Stefano Mammola creator: Peter Michalik creator: Eileen A. Hebets creator: Marco Isaia uri: https://doi.org/10.7717/peerj.3972 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Mammola et al. title: A novel animal model for neuroinflammation and white matter degeneration link: https://peerj.com/articles/3905 last-modified: 2017-10-31 description: Small interference RNA has been widely used to suppress gene expression. Three different short hairpin RNAs (shRNAs) against dopamine D1 receptor (Drd1), driven by mouse U6 promoter in self-complementary AAV8 vector (scAAV8), were used to silence mouse striatal Drd1 expression. Transduction of mouse striatum with all three scAAV8-D1shRNA viruses, but not the control scAAV8 virus, causes extensive neuroinflammation, demyelination, and axon degeneration. RNA interference is known to be coupled to the innate immune system as a host cell defense against virus infection. Activation of the innate immune system may play a causal role in the development of neuroinflammation and white matter degeneration, providing a novel animal model for multiple sclerosis (MS) and other neuroinflammatory diseases. creator: Baohu Ji creator: Kerin Higa creator: Virawudh Soontornniyomkij creator: Atsushi Miyanohara creator: Xianjin Zhou uri: https://doi.org/10.7717/peerj.3905 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Ji et al. title: Comparative genomic analysis of the PKS genes in five species and expression analysis in upland cotton link: https://peerj.com/articles/3974 last-modified: 2017-10-30 description: Plant type III polyketide synthase (PKS) can catalyse the formation of a series of secondary metabolites with different structures and different biological functions; the enzyme plays an important role in plant growth, development and resistance to stress. At present, the PKS gene has been identified and studied in a variety of plants. Here, we identified 11 PKS genes from upland cotton (Gossypium hirsutum) and compared them with 41 PKS genes in Populus tremula, Vitis vinifera, Malus domestica and Arabidopsis thaliana. According to the phylogenetic tree, a total of 52 PKS genes can be divided into four subfamilies (I–IV). The analysis of gene structures and conserved motifs revealed that most of the PKS genes were composed of two exons and one intron and there are two characteristic conserved domains (Chal_sti_synt_N and Chal_sti_synt_C) of the PKS gene family. In our study of the five species, gene duplication was found in addition to Arabidopsis thaliana and we determined that purifying selection has been of great significance in maintaining the function of PKS gene family. From qRT-PCR analysis and a combination of the role of the accumulation of proanthocyanidins (PAs) in brown cotton fibers, we concluded that five PKS genes are candidate genes involved in brown cotton fiber pigment synthesis. These results are important for the further study of brown cotton PKS genes. It not only reveals the relationship between PKS gene family and pigment in brown cotton, but also creates conditions for improving the quality of brown cotton fiber. creator: Xueqiang Su creator: Xu Sun creator: Xi Cheng creator: Yanan Wang creator: Muhammad Abdullah creator: Manli Li creator: Dahui Li creator: Junshan Gao creator: Yongping Cai creator: Yi Lin uri: https://doi.org/10.7717/peerj.3974 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Su et al. title: Early skin-to-skin contact between healthy late preterm infants and their parents: an observational cohort study link: https://peerj.com/articles/3949 last-modified: 2017-10-30 description: BackgroundSkin-to-skin contact (SSC) is an important factor to consider in the care of late preterm infants (born between 34 0/7 and 36 6/7 completed weeks of gestation). The literature suggests that SSC between preterm infants and their mothers facilitates breastfeeding. However, more studies are needed to explore potential dose-response effects between SSC and breastfeeding as well as studies that explicitly investigate SSC by fathers among late preterm infants. The aim was to investigate the duration of healthy late preterm infants’ SSC with the mother and father, respectively, during the first 48 h after birth and the associations with breastfeeding (exclusive/partial at discharged), clinical and demographic variables.MethodsThis was an observational cohort study in which parents to healthy late preterm infants, born between 34 5/7 and 36 6/7 completed weeks of gestation, recorded duration of SSC provided by mother and father, respectively. Demographic and clinical variables were retrieved from the medical records and were used as predictors. Multiple linear regression analysis was used to assess the association between the predictors and the outcome, SSC (hours), separately for mothers and fathers.ResultsThe mean (standard deviation [SD]) time per day spent with SSC with mothers (n = 64) and fathers (n = 64), was 14.7 (5.6) and 4.4 (3.3) hours during the first day (24 h) after birth and 9.2 (7.1) and 3.1 (3.3) hours during the second day (24 h), respectively. Regarding SSC with mothers, no variable was significantly associated with SSC during the first day, while the mean (95% confidence interval [CI]) time of SSC during the second day was 6.9 (1.4–12.4) hours shorter for each additional kg of birthweight (p = 0.014). Concerning SSC with fathers, the mean (95% CI) time of SSC during the first day was 2.1 (0.4–3.7) hours longer for infants born at night (p = 0.015), 1.7 (0.1–3.2) hours longer for boys (p = 0.033), 3.2 (1.2–5.2) hours longer for infants born by caesarean section (p = 0.003), and 1.6 (0.1–3.1) hours longer for infants exclusively breastfed at discharge (p = 0.040). During the second day, the mean (95% CI) time of SSC with fathers was 3.0 (0.6–5.4) hours shorter for each additional kg of birthweight (p = 0.014), 2.0 (0.5–3.6) hours longer for infants born during night-time (p = 0.011), 2.9 (1.4–4.4) hours longer if the mother was primipara (p < 0.001), and 1.9 (0.3–3.5) hours shorter if supplementary artificial milk feeds were given. None of the other predictors, i.e., mother’s age, gestational age, or induction of labor were significantly associated with infants’ SSC with mothers or fathers during any of the first two days after birth.ConclusionFuture studies are warranted that investigate duration of SSC between late preterm infants and their parents separately and the associations with breastfeeding and other variables of clinical importance. creator: Kerstin H. Nyqvist creator: Andreas Rosenblad creator: Helena Volgsten creator: Eva-Lotta Funkquist creator: Elisabet Mattsson uri: https://doi.org/10.7717/peerj.3949 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Nyqvist et al. title: Estimating the potential biodiversity impact of redeveloping small urban spaces: the Natural History Museum’s grounds link: https://peerj.com/articles/3914 last-modified: 2017-10-30 description: BackgroundWith the increase in human population, and the growing realisation of the importance of urban biodiversity for human wellbeing, the ability to predict biodiversity loss or gain as a result of land use change within urban settings is important. Most models that link biodiversity and land use are at too coarse a scale for informing decisions, especially those related to planning applications. Using the grounds of the Natural History Museum, London, we show how methods used in global models can be applied to smaller spatial scales to inform urban planning.MethodsData were extracted from relevant primary literature where species richness had been recorded in more than one habitat type within an urban setting. As within-sample species richness will increase with habitat area, species richness estimates were also converted to species density using theory based on the species–area relationship. Mixed-effects models were used to model the impact on species richness and species density of different habitat types, and to estimate these metrics in the current grounds and under proposed plans for redevelopment. We compared effects of three assumptions on how within-sample diversity scales with habitat area as a sensitivity analysis. A pre-existing database recording plants within the grounds was also used to estimate changes in species composition across different habitats.ResultsAnalysis estimated that the proposed plans would result in an increase of average biodiversity of between 11.2% (when species density was modelled) and 14.1% (when within-sample species richness was modelled). Plant community composition was relatively similar between the habitats currently within the grounds.DiscussionThe proposed plans for change in the NHM grounds are estimated to result in a net gain in average biodiversity, through increased number and extent of high-diversity habitats. In future, our method could be improved by incorporating purposefully collected ecological survey data (if resources permit) and by expanding the data sufficiently to allow modelling of the temporal dynamics of biodiversity change after habitat disturbance and creation. Even in its current form, the method produces transparent quantitative estimates, grounded in ecological data and theory, which can be used to inform relatively small scale planning decisions. creator: Helen R.P. Phillips creator: Sandra Knapp creator: Andy Purvis uri: https://doi.org/10.7717/peerj.3914 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Phillips et al. title: Molecular phylogeny and evolutionary history of Moricandia DC (Brassicaceae) link: https://peerj.com/articles/3964 last-modified: 2017-10-27 description: BackgroundThe phylogeny of tribe Brassiceae (Brassicaceae) has not yet been resolved because of its complex evolutionary history. This tribe comprises economically relevant species, including the genus Moricandia DC. This genus is currently distributed in North Africa, Middle East, Central Asia and Southern Europe, where it is associated with arid and semi-arid environments. Although some species of Moricandia have been used in several phylogenetic studies, the phylogeny of this genus is not well established.MethodsHere we present a phylogenetic analysis of the genus Moricandia using a nuclear (the internal transcribed spacers of the ribosomal DNA) and two plastidial regions (parts of the NADH dehydrogenase subunit F gene and the trnT-trnF region). We also included in the analyses members of their sister genus Rytidocarpus and from the close genus Eruca.ResultsThe phylogenetic analyses showed a clear and robust phylogeny of the genus Moricandia. The Bayesian inference tree was concordant with the maximum likelihood and timing trees, with the plastidial and nuclear trees showing only minor discrepancies. The genus Moricandia appears to be formed by two main lineages: the Iberian clade including three species, and the African clade including the four species inhabiting the Southern Mediterranean regions plus M. arvensis.DiscussionWe dated the main evolutionary events of this genus, showing that the origin of the Iberian clade probably occurred after a range expansion during the Messinian period, between 7.25 and 5.33 Ma. In that period, an extensive African-Iberian floral and faunal interchange occurred due to the existence of land bridges between Africa and Europa in what is, at present-days, the Strait of Gibraltar. We have demonstrated that a Spanish population previously ascribed to Rytidocarpus moricandioides is indeed a Moricandia species, and we propose to name it as M. rytidocarpoides sp. nov. In addition, in all the phylogenetic analyses, M. foleyi appeared outside the Moricandia lineage but within the genus Eruca. Therefore, M. foleyi should be excluded from the genus Moricandia and be ascribed, at least provisionally, to the genus Eruca. creator: Francisco Perfectti creator: José M. Gómez creator: Adela González-Megías creator: Mohamed Abdelaziz creator: Juan Lorite uri: https://doi.org/10.7717/peerj.3964 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Perfectti et al. title: Respiratory syncytial virus genotypes NA1, ON1, and BA9 are prevalent in Thailand, 2012–2015 link: https://peerj.com/articles/3970 last-modified: 2017-10-27 description: Respiratory syncytial virus (RSV) causes acute lower respiratory tract infection in infants and young children worldwide. To investigate the RSV burden in Thailand over four consecutive years (January 2012 to December 2015), we screened 3,306 samples obtained from children ≤5 years old with acute respiratory tract infection using semi-nested reverse-transcription polymerase chain reaction (RT-PCR). In all, 8.4% (277/3,306) of the specimens tested positive for RSV, most of which appeared in the rainy months of July to November. We then genotyped RSV by sequencing the G glycoprotein gene and performed phylogenetic analysis to determine the RSV antigenic subgroup. The majority (57.4%, 159/277) of the RSV belonged to subgroup A (RSV-A), of which NA1 genotype was the most common in 2012 while ON1 genotype became prevalent the following year. Among samples tested positive for RSV-B subgroup B (RSV-B) (42.6%, 118/277), most were genotype BA9 (92.6%, 87/94) with some BA10 and BA-C. Predicted amino acid sequence from the partial G region showed highly conserved N-linked glycosylation site at residue N237 among all RSV-A ON1 strains (68/68), and at residues N296 (86/87) and N310 (87/87) among RSV-B BA9 strains. Positive selection of key residues combined with notable sequence variations on the G gene contributed to the continued circulation of this rapidly evolving virus. creator: Ilada Thongpan creator: John Mauleekoonphairoj creator: Preeyaporn Vichiwattana creator: Sumeth Korkong creator: Rujipat Wasitthankasem creator: Sompong Vongpunsawad creator: Yong Poovorawan uri: https://doi.org/10.7717/peerj.3970 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Thongpan et al. title: Unravelling the ontogeny of a Devonian early gnathostome, the “acanthodian” Triazeugacanthus affinis (eastern Canada) link: https://peerj.com/articles/3969 last-modified: 2017-10-27 description: The study of vertebrate ontogenies has the potential to inform us of shared developmental patterns and processes among organisms. However, fossilised ontogenies of early vertebrates are extremely rare during the Palaeozoic Era. A growth series of the Late Devonian “acanthodian” Triazeugacanthus affinis, from the Miguasha Fossil-Fish Lagerstätte, is identified as one of the best known early vertebrate fossilised ontogenies given the exceptional preservation, the large size range, and the abundance of specimens. Morphological, morphometric, histological and chemical data are gathered on a growth series of Triazeugacanthus ranging from 4 to 52 mm in total length. The developmental trajectory of this Devonian “acanthodian” is characteristic of fishes showing a direct development with alternating steps and thresholds. Larvae show no squamation but a progressive appearance of cartilaginous neurocranial and vertebral elements, and appendicular elements, whereas juveniles progress in terms of ossification and squamation. The presence of cartilaginous and bony tissues, discriminated on histological and chemical signatures, shows a progressive mineralisation of neurocranial and vertebral elements. Comparison among different body proportions for larvae, juveniles and adults suggest allometric growth in juveniles. Because of the phylogenetic position of “acanthodians”, Triazeugacanthus ontogeny informs us about deep time developmental conditions in gnathostomes. creator: Marion Chevrinais creator: Jean-Yves Sire creator: Richard Cloutier uri: https://doi.org/10.7717/peerj.3969 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Chevrinais et al. title: Immunofluorescence characterization of spinal cord dorsal horn microglia and astrocytes in horses link: https://peerj.com/articles/3965 last-modified: 2017-10-27 description: The role of glial cells in pain modulation has recently gathered attention. The objective of this study was to determine healthy spinal microglia and astrocyte morphology and disposition in equine spinal cord dorsal horns using Iba-1 and GFAP/Cx-43 immunofluorescence labeling, respectively. Five adult horses without visible wounds or gait alterations were selected. Spinal cord segments were obtained post-mortem for immunohistochemical and immunocolocalization assays. Immunodetection of spinal cord dorsal horn astrocytes was done using a polyclonal goat antibody raised against Glial Fibrillary Acidic Protein (GFAP) and a polyclonal rabbit antibody against Connexin 43 (Cx-43). For immunodetection of spinal cord dorsal horn microglia, a polyclonal rabbit antibody against a synthetic peptide corresponding to the C-terminus of ionized calcium-binding adaptor molecule 1 (Iba-1) was used. Epifluorescence and confocal images were obtained for the morphological and organizational analysis. Evaluation of shape, area, cell diameter, cell process length and thickness was performed on dorsal horn microglia and astrocyte. Morphologically, an amoeboid spherical shape with a mean cell area of 92.4 + 34 µm2 (in lamina I, II and III) was found in horse microglial cells, located primarily in laminae I, II and III. Astrocyte primary stem branches (and cellular bodies to a much lesser extent) are mainly detected using GFAP. Thus, double GFAP/Cx-43 immunolabeling was needed in order to accurately characterize the morphology, dimension and cell density of astrocytes in horses. Horse and rodent astrocytes seem to have similar dimensions and localization. Horse astrocyte cells have an average diameter of 56 + 14 µm, with a main process length of 28 + 8 µm, and thickness of 1.4 + 0.3 µm, mainly situated in laminae I, II and III. Additionally, a close association between end-point astrocyte processes and microglial cell bodies was found. These results are the first characterization of cell morphology and organizational aspects of horse spinal glia. Iba-1 and GFAP/Cx-43 can successfully immune-label microglia and astrocytes respectively in horse spinal cords, and thus reveal cell morphology and corresponding distribution within the dorsal horn laminae of healthy horses. The conventional hyper-ramified shape that is normally visible in resting microglial cells was not found in horses. Instead, horse microglial cells had an amoeboid spherical shape. Horse protoplasmic astroglia is significantly smaller and structurally less complex than human astrocytes, with fewer main GFAP processes. Instead, horse astrocytes tend to be similar to those found in rodent’s model, with small somas and large cell processes. Microglia and astrocytes were found in the more superficial regions of the dorsal horn, similarly to that previously observed in humans and rodents. Further studies are needed to demonstrate the molecular mechanisms involved in the neuron-glia interaction in horses. creator: Constanza Stefania Meneses creator: Heine Yacob Müller creator: Daniel Eduardo Herzberg creator: Benjamín Uberti creator: Hedie Almagro Bustamante creator: Marianne Patricia Werner uri: https://doi.org/10.7717/peerj.3965 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Meneses et al. title: Genome-wide identification and expression profile analysis of CCH gene family in Populus link: https://peerj.com/articles/3962 last-modified: 2017-10-27 description: Copper plays key roles in plant physiological activities. To maintain copper cellular homeostasis, copper chaperones have important functions in binding and transporting copper to target proteins. Detailed characterization and function analysis of a copper chaperone, CCH, is presently limited to Arabidopsis. This study reports the identification of 21 genes encoding putative CCH proteins in Populus trichocarpa. Besides sharing the conserved metal-binding motif MXCXXC and forming a βαββαβ secondary structure at the N-terminal, all the PtCCHs possessed the plant-exclusive extended C-terminal. Based on their gene structure, conserved motifs, and phylogenetic analysis, the PtCCHs were divided into three subgroups. Our analysis indicated that whole-genome duplication and tandem duplication events likely contributed to expansion of the CCH gene family in Populus. Tissue-specific data from PlantGenIE revealed that PtCCH genes had broad expression patterns in different tissues. Quantitative real-time RT-PCR (qRT-PCR) analysis revealed that PnCCH genes of P. simonii × P. nigra also had different tissue-specific expression traits, as well as different inducible-expression patterns in response to copper stresses (excessive and deficiency). In summary, our study of CCH genes in the Populus genome provides a comprehensive analysis of this gene family, and lays an important foundation for further investigation of their roles in copper homeostasis of poplar. creator: Zhiru Xu creator: Liying Gao creator: Mengquan Tang creator: Chunpu Qu creator: Jiahuan Huang creator: Qi Wang creator: Chuanping Yang creator: Guanjun Liu creator: Chengjun Yang uri: https://doi.org/10.7717/peerj.3962 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Xu et al. title: New Cernotina caddisflies from the Ecuadorian Amazon (Trichoptera: Polycentropodidae) link: https://peerj.com/articles/3960 last-modified: 2017-10-27 description: Two new species of the caddisfly genus CernotinaRoss, 1938 (Polycentropodidae) are described from the lowland Amazon basin of Ecuador, Cernotina tiputini, new species, and Cernotina waorani, new species. These represent the first new species described from this region. We also record from Ecuador for the first time Cernotina hastilis Flint, previously known from Tobago, and present new Ecuadorian locality records for C. cygnea Flint, and C. lobisomem Santos & Nessimian. The homology of the intermediate appendage of the male genitalia of this genus is established. The region surveyed is under severe environmental threat from logging, mining, and crude oil extraction, making the description of the biodiversity of the region imperative. creator: Lucas M. Camargos creator: Blanca Ríos-Touma creator: Ralph W. Holzenthal uri: https://doi.org/10.7717/peerj.3960 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Camargos et al. title: Skin and fur bacterial diversity and community structure on American southwestern bats: effects of habitat, geography and bat traits link: https://peerj.com/articles/3944 last-modified: 2017-10-27 description: Microorganisms that reside on and in mammals, such as bats, have the potential to influence their host’s health and to provide defenses against invading pathogens. However, we have little understanding of the skin and fur bacterial microbiota on bats, or factors that influence the structure of these communities. The southwestern United States offers excellent sites for the study of external bat bacterial microbiota due to the diversity of bat species, the variety of abiotic and biotic factors that may govern bat bacterial microbiota communities, and the lack of the newly emergent fungal disease in bats, white-nose syndrome (WNS), in the southwest. To test these variables, we used 16S rRNA gene 454 pyrosequencing from swabs of external skin and fur surfaces from 163 bats from 13 species sampled from southeastern New Mexico to northwestern Arizona. Community similarity patterns, random forest models, and generalized linear mixed-effects models show that factors such as location (e.g., cave-caught versus surface-netted) and ecoregion are major contributors to the structure of bacterial communities on bats. Bats caught in caves had a distinct microbial community compared to those that were netted on the surface. Our results provide a first insight into the distribution of skin and fur bat bacteria in the WNS-free environment of New Mexico and Arizona. More importantly, it provides a baseline of bat external microbiota that can be explored for potential natural defenses against pathogens. creator: Ara S. Winter creator: Jennifer J.M. Hathaway creator: Jason C. Kimble creator: Debbie C. Buecher creator: Ernest W. Valdez creator: Andrea Porras-Alfaro creator: Jesse M. Young creator: Kaitlyn J.H. Read creator: Diana E. Northup uri: https://doi.org/10.7717/peerj.3944 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: Inferring microevolution from museum collections and resampling: lessons learned from Cepaea link: https://peerj.com/articles/3938 last-modified: 2017-10-27 description: Natural history collections are an important and largely untapped source of long-term data on evolutionary changes in wild populations. Here, we utilize three large geo-referenced sets of samples of the common European land-snail Cepaea nemoralis stored in the collection of Naturalis Biodiversity Center in Leiden, the Netherlands. Resampling of these populations allowed us to gain insight into changes occurring over 95, 69, and 50 years. Cepaea nemoralis is polymorphic for the colour and banding of the shell; the mode of inheritance of these patterns is known, and the polymorphism is under both thermal and predatory selection. At two sites the general direction of changes was towards lighter shells (yellow and less heavily banded), which is consistent with predictions based on on-going climatic change. At one site no directional changes were detected. At all sites there were significant shifts in morph frequencies between years, and our study contributes to the recognition that short-term changes in the states of populations often exceed long-term trends. Our interpretation was limited by the few time points available in the studied collections. We therefore stress the need for natural history collections to routinely collect large samples of common species, to allow much more reliable hind-casting of evolutionary responses to environmental change. creator: Małgorzata Ożgo creator: Thor-Seng Liew creator: Nicole B. Webster creator: Menno Schilthuizen uri: https://doi.org/10.7717/peerj.3938 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Ożgo et al. title: Augmented cartilage regeneration by implantation of cellular versus acellular implants after bone marrow stimulation: a systematic review and meta-analysis of animal studies link: https://peerj.com/articles/3927 last-modified: 2017-10-27 description: Bone marrow stimulation may be applied to regenerate focal cartilage defects, but generally results in transient clinical improvement and formation of fibrocartilage rather than hyaline cartilage. Tissue engineering and regenerative medicine strive to develop new solutions to regenerate hyaline cartilage tissue. This systematic review and meta-analysis provides a comprehensive overview of current literature and assesses the efficacy of articular cartilage regeneration by implantation of cell-laden versus cell-free biomaterials in the knee and ankle joint in animals after bone marrow stimulation. PubMed and EMBASE (via OvidSP) were systematically searched using tissue engineering, cartilage and animals search strategies. Included were primary studies in which cellular and acellular biomaterials were implanted after applying bone marrow stimulation in the knee or ankle joint in healthy animals. Study characteristics were tabulated and outcome data were collected for meta-analysis for studies applying semi-quantitative histology as outcome measure (117 studies). Cartilage regeneration was expressed on an absolute 0–100% scale and random effects meta-analyses were performed. Implantation of cellular biomaterials significantly improved cartilage regeneration by 18.6% compared to acellular biomaterials. No significant differences were found between biomaterials loaded with stem cells and those loaded with somatic cells. Culture conditions of cells did not affect cartilage regeneration. Cartilage formation was reduced with adipose-derived stem cells compared to other cell types, but still improved compared to acellular scaffolds. Assessment of the risk of bias was impaired due to incomplete reporting for most studies. Implantation of cellular biomaterials improves cartilage regeneration compared to acellular biomaterials. creator: Michiel W. Pot creator: Toin H. van Kuppevelt creator: Veronica K. Gonzales creator: Pieter Buma creator: Joanna IntHout creator: Rob B.M. de Vries creator: Willeke F. Daamen uri: https://doi.org/10.7717/peerj.3927 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Pot et al. title: Novel mesostructured inclusions in the epidermal lining of Artemia franciscana ovisacs show optical activity link: https://peerj.com/articles/3923 last-modified: 2017-10-27 description: BackgroundBiomineralization, e.g., in sea urchins or mollusks, includes the assembly of mesoscopic superstructures from inorganic crystalline components and biopolymers. The resulting mesocrystals inspire biophysicists and material scientists alike, because of their extraordinary physical properties. Current efforts to replicate mesocrystal synthesis in vitro require understanding the principles of their self-assembly in vivo. One question, not addressed so far, is whether intracellular crystals of proteins can assemble with biopolymers into functional mesocrystal-like structures. During our electron microscopy studies into Artemia franciscana (Crustacea: Branchiopoda), we found initial evidence of such proteinaceous mesostructures.ResultsEM preparations with high-pressure freezing and accelerated freeze substitution revealed an extraordinary intracellular source of mesostructured inclusions in both the cyto-and nucleoplasm of the epidermal lining of ovisacs of A. franciscana. Confocal reflection microscopy not only confirmed our finding; it also revealed reflective, light dispersing activity of these flake-like structures, their positioning and orientation with respect to the ovisac inside. Both the striation of alternating electron dense and electron-lucent components and the sharp edges of the flakes indicate self-assembly of material of yet unknown origin under supposed participation of crystallization. However, selected area electron diffraction could not verify the status of crystallization. Energy dispersive X-ray analysis measured a marked increase in nitrogen within the flake-like inclusion, and the almost complete absence of elements that are typically involved in inorganic crystallization. This rise in nitrogen could possibility be related to higher package density of proteins, achieved by mesostructure assembly.ConclusionsThe ovisac lining of A. franciscana is endowed with numerous mesostructured inclusions that have not been previously reported. We hypothesize that their self-assembly was from proteinaceous polycrystalline units and carbohydrates. These mesostructured flakes displayed active optical properties, as an umbrella-like, reflective cover of the ovisac, which suggests a functional role in the reproduction of A. franciscana. In turn, studies into ovisac mesostructured inclusions could help to optimizing rearing Artemia as feed for fish farming. We propose Artemia ovisacs as an in vivo model system for studying mesostructure formation. creator: Elena Hollergschwandtner creator: Thomas Schwaha creator: Josef Neumüller creator: Ulrich Kaindl creator: Daniela Gruber creator: Margret Eckhard creator: Michael Stöger-Pollach creator: Siegfried Reipert uri: https://doi.org/10.7717/peerj.3923 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Hollergschwandtner et al. title: Comparative demography of two common scleractinian corals: Orbicella annularis and Porites astreoides link: https://peerj.com/articles/3906 last-modified: 2017-10-27 description: BackgroundStudies directed at understanding the demography and population dynamics of corals are relatively scarce. This limits our understanding of both the dynamics of coral populations and our capacity to develop management and conservation initiatives directed at conserving such ecosystems.MethodsFrom 2012 to 2014, we collected data on the growth, survival, and recruitment rates of two common Caribbean coral species, the stress-tolerant Orbicella annularis and the weedy Porites astreoides. A set of size-based population matrix model was developed for two localities in Northeastern Puerto Rico and used to estimate population growth rates (λ) and determine the life cycle transition(s) that contribute the most to spatiotemporal differences in λs. The model was parameterized by following the fate of 100 colonies of each species at the two sites for two years.ResultsOur data indicate that spatial variability in vital rates of both species was higher than temporal variability. During the first year, populations of O. annularis exhibited λs below equilibrium at Carlos Rosario (0.817) and Palomino (0.694), followed by a considerable decline at both sites during the second year (0.700 and 0.667). Populations of P. astreoides showed higher λs than O. annularis during the first census period at Carlos Rosario (0.898) and Palomino (0.894) with a decline at one of the sites (0.681 and 0.893) during the second census period. Colony fate in both species exhibited a significant interaction with respect to location but not to time (G2 = 20.96; df = 3 for O. annularis and G2 = 9.55; df = 3 for P. astreoides).DiscussionThe similar variability of λs as well as the similar survival rates for both species during the two-year census period (2012–2014) show similar variability on demographic patterns in space and time. Our results suggest that location rather than time is important for the resiliency in coral colonies. Also, P. astreoides will show higher resistance to disturbance in the future than O. annularis. creator: Francisco J. Soto-Santiago creator: Alex Mercado-Molina creator: Koralis Reyes-Maldonado creator: Yaileen Vélez creator: Claudia P. Ruiz-Díaz creator: Alberto Sabat uri: https://doi.org/10.7717/peerj.3906 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Soto-Santiago et al. title: Multivariate ordination identifies vegetation types associated with spider conservation in brassica crops link: https://peerj.com/articles/3795 last-modified: 2017-10-27 description: Conservation biological control emphasizes natural and other non-crop vegetation as a source of natural enemies to focal crops. There is an unmet need for better methods to identify the types of vegetation that are optimal to support specific natural enemies that may colonize the crops. Here we explore the commonality of the spider assemblage—considering abundance and diversity (H)—in brassica crops with that of adjacent non-crop and non-brassica crop vegetation. We employ spatial-based multivariate ordination approaches, hierarchical clustering and spatial eigenvector analysis. The small-scale mixed cropping and high disturbance frequency of southern Chinese vegetation farming offered a setting to test the role of alternate vegetation for spider conservation. Our findings indicate that spider families differ markedly in occurrence with respect to vegetation type. Grassy field margins, non-crop vegetation, taro and sweetpotato harbour spider morphospecies and functional groups that are also present in brassica crops. In contrast, pumpkin and litchi contain spiders not found in brassicas, and so may have little benefit for conservation biological control services for brassicas. Our findings also illustrate the utility of advanced statistical approaches for identifying spatial relationships between natural enemies and the land uses most likely to offer alternative habitats for conservation biological control efforts that generates testable hypotheses for future studies. creator: Hafiz Sohaib Ahmed Saqib creator: Minsheng You creator: Geoff M. Gurr uri: https://doi.org/10.7717/peerj.3795 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Saqib et al. title: Ancient divergence time estimates in Eutropis rugifera support the existence of Pleistocene barriers on the exposed Sunda Shelf link: https://peerj.com/articles/3762 last-modified: 2017-10-27 description: Episodic sea level changes that repeatedly exposed and inundated the Sunda Shelf characterize the Pleistocene. Available evidence points to a more xeric central Sunda Shelf during periods of low sea levels, and despite the broad land connections that persisted during this time, some organisms are assumed to have faced barriers to dispersal between land-masses on the Sunda Shelf. Eutropis rugifera is a secretive, forest adapted scincid lizard that ranges across the Sunda Shelf. In this study, we sequenced one mitochondrial (ND2) and four nuclear (BRCA1, BRCA2, RAG1, and MC1R) markers and generated a time-calibrated phylogeny in BEAST to test whether divergence times between Sundaic populations of E. rugifera occurred during Pleistocene sea-level changes, or if they predate the Pleistocene. We find that E. rugifera shows pre-Pleistocene divergences between populations on different Sundaic land-masses. The earliest divergence within E. rugifera separates the Philippine samples from the Sundaic samples approximately 16 Ma; the Philippine populations thus cannot be considered conspecific with Sundaic congeners. Sundaic populations diverged approximately 6 Ma, and populations within Borneo from Sabah and Sarawak separated approximately 4.5 Ma in the early Pliocene, followed by further cladogenesis in Sarawak through the Pleistocene. Divergence of peninsular Malaysian populations from the Mentawai Archipelago occurred approximately 5 Ma. Separation among island populations from the Mentawai Archipelago likely dates to the Pliocene/Pleistocene boundary approximately 3.5 Ma, and our samples from peninsular Malaysia appear to coalesce in the middle Pleistocene, about 1 Ma. Coupled with the monophyly of these populations, these divergence times suggest that despite consistent land-connections between these regions throughout the Pleistocene E. rugifera still faced barriers to dispersal, which may be a result of environmental shifts that accompanied the sea-level changes. creator: Benjamin R. Karin creator: Indraneil Das creator: Todd R. Jackman creator: Aaron M. Bauer uri: https://doi.org/10.7717/peerj.3762 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Karin et al. title: Inorganic, organic, and encapsulated minerals in vegetable meal based diets for Sparus aurata (Linnaeus, 1758) link: https://peerj.com/articles/3710 last-modified: 2017-10-27 description: Substituting fishmeal (FM) with vegetable meal (VM) can markedly affect the mineral composition of feeds, and may require additional mineral supplementation. Their bioavailability and optimal supplementation levels depend also on the form of delivery of minerals. The aim of the study was to determine the effect of different delivery forms of three major trace elements (Zn, Mn and Se) in a marine teleost. Gilthead sea bream juveniles of 22.5 g were fed a VM-based diet for 12 weeks that was either not supplemented with these minerals or supplemented with inorganic, organic, or encapsulated inorganic forms of minerals in triplicate and compared to a FM-based diet. Our results showed that mineral delivery form significantly affected the biochemical composition and morphology of posterior vertebrae. Supplementation of VM-based diets with inorganic forms of the target minerals significantly promoted growth, increased the vertebral weight and content of ash and Zn, enhanced bone mineralization and affected the vertebral shape. Conversely, encapsulation of inorganic minerals reduced fish growth and vertebral mineral content, whereas supplementation of organic minerals, enhanced bone osteogenesis by upregulating bone morphogenetic protein 2 (bmp2) gene and produced vertebrae with a larger length in relation to height. Furthermore, organic mineral forms of delivery downregulated the expression of oxidative stress related genes, such as Cu/Zn superoxide dismutase (Cu/Zn sod) and glutathione peroxidase 1 (gpx-1), suggesting thus that dietary minerals supplemented in the organic form could be reasonably considered more effective than the inorganic and encapsulated forms of supply. creator: David Domínguez creator: Simona Rimoldi creator: Lidia E. Robaina creator: Silvia Torrecillas creator: Genciana Terova creator: María J. Zamorano creator: Vasileios Karalazos creator: Kristin Hamre creator: Marisol Izquierdo uri: https://doi.org/10.7717/peerj.3710 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Domínguez et al. title: Work-related stress, associated comorbidities and stress causes in French community pharmacies: a nationwide cross-sectional study link: https://peerj.com/articles/3973 last-modified: 2017-10-26 description: BackgroundLike other health professionals, community pharmacists are exposed to stress factors (being efficient, avoiding mistakes and bearing emotional load), but they are also under the pressure of entrepreneurial responsibilities. The main objective was to assess the level of work-related stress in French community pharmacies. The other objectives of the study were to assess the associated comorbidities and causes of work-related stress.MethodsThis observational cross-sectional study was sent to all French community pharmacies by email. The survey was anonymous and designed to collect the following items: socio-demographic factors, professional status, characteristics of community pharmacy, work-related stress (visual analogic scale—VAS), fatigue (VAS), sleep disturbances (questions), anxiety and depression symptoms (hospital anxiety and depression scale), medical consultation for work-related stress, medication use for work related stress, psychoactive drug-use and causes of work-related stress. Participants were included in the survey if they were pharmacists (owner or assistant) or pharmacy technicians working in a community pharmacy at the time of the survey. Exclusion criteria were defined as follows: pharmacy students or other professionals involved in a community pharmacy (e.g. dietician, beautician) and lack of professional status information. There was no age limitation.ResultsAfter three months of data collection, 1,339 participants answered the survey and 1,272 participants were included in conformity with the inclusion and exclusion criteria, and to avoid missing data on the primary endpoint. Work-related stress was detected in 32.8% (417/1,272) of individuals (scores ≥70/100). Men were significantly more affected than women and there was no difference between professional statuses and no relation with the age of the participants. Work-related stress was significantly associated with anxiety, depression, fatigue, sleep disturbances, medical consultations, medication use, alcohol consumption above the WHO recommendations for men and psychoactive drug use. Three causes of stress were clearly identified and related to stress levels, workload, working atmosphere and deterioration of work quality. However, causes of work-related stress were significantly different among professionals, for example: entrepreneurial burden for pharmacists-in-charge and workload for employees (assistant pharmacists and pharmacy technicians).DiscussionWork-related stress has a very strong impact in French community pharmacies. This stress was associated with several comorbidities and induces health resource consumption. Several causes of work-related stress have been identified such as workload, working atmosphere and deterioration of work quality; however, these causes could be detected and managed to improve stress levels. We recommend developing individual and organizational stress management in French community pharmacies. creator: David Balayssac creator: Bruno Pereira creator: Julie Virot creator: Céline Lambert creator: Aurore Collin creator: David Alapini creator: Jean-Marc Gagnaire creator: Nicolas Authier creator: Damien Cuny creator: Brigitte Vennat uri: https://doi.org/10.7717/peerj.3973 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Balayssac et al. title: Constructing stage-structured matrix population models from life tables: comparison of methods link: https://peerj.com/articles/3971 last-modified: 2017-10-26 description: A matrix population model is a convenient tool for summarizing per capita survival and reproduction rates (collectively vital rates) of a population and can be used for calculating an asymptotic finite population growth rate (λ) and generation time. These two pieces of information can be used for determining the status of a threatened species. The use of stage-structured population models has increased in recent years, and the vital rates in such models are often estimated using a life table analysis. However, potential bias introduced when converting age-structured vital rates estimated from a life table into parameters for a stage-structured population model has not been assessed comprehensively. The objective of this study was to investigate the performance of methods for such conversions using simulated life histories of organisms. The underlying models incorporate various types of life history and true population growth rates of varying levels. The performance was measured by comparing differences in λ and the generation time calculated using the Euler-Lotka equation, age-structured population matrices, and several stage-structured population matrices that were obtained by applying different conversion methods. The results show that the discretization of age introduces only small bias in λ or generation time. Similarly, assuming a fixed age of maturation at the mean age of maturation does not introduce much bias. However, aggregating age-specific survival rates into a stage-specific survival rate and estimating a stage-transition rate can introduce substantial bias depending on the organism’s life history type and the true values of λ. In order to aggregate survival rates, the use of the weighted arithmetic mean was the most robust method for estimating λ. Here, the weights are given by survivorship curve after discounting with λ. To estimate a stage-transition rate, matching the proportion of individuals transitioning, with λ used for discounting the rate, was the best approach. However, stage-structured models performed poorly in estimating generation time, regardless of the methods used for constructing the models. Based on the results, we recommend using an age-structured matrix population model or the Euler-Lotka equation for calculating λ and generation time when life table data are available. Then, these age-structured vital rates can be converted into a stage-structured model for further analyses. creator: Masami Fujiwara creator: Jasmin Diaz-Lopez uri: https://doi.org/10.7717/peerj.3971 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Fujiwara and Diaz-Lopez title: Species–specific crab predation on the hydrozoan clinging jellyfish Gonionemus sp. (Cnidaria, Hydrozoa), subsequent crab mortality, and possible ecological consequences link: https://peerj.com/articles/3966 last-modified: 2017-10-26 description: Here we report a unique trophic interaction between the cryptogenic and sometimes highly toxic hydrozoan clinging jellyfish Gonionemus sp. and the spider crab Libinia dubia. We assessed species–specific predation on the Gonionemus medusae by crabs found in eelgrass meadows in Massachusetts, USA. The native spider crab species L. dubia consumed Gonionemus medusae, often enthusiastically, but the invasive green crab Carcinus maenus avoided consumption in all trials. One out of two blue crabs (Callinectes sapidus) also consumed Gonionemus, but this species was too rare in our study system to evaluate further. Libinia crabs could consume up to 30 jellyfish, which was the maximum jellyfish density treatment in our experiments, over a 24-hour period. Gonionemus consumption was associated with Libinia mortality. Spider crab mortality increased with Gonionemus consumption, and 100% of spider crabs tested died within 24 h of consuming jellyfish in our maximum jellyfish density containers. As the numbers of Gonionemus medusae used in our experiments likely underestimate the number of medusae that could be encountered by spider crabs over a 24-hour period in the field, we expect that Gonionemus may be having a negative effect on natural Libinia populations. Furthermore, given that Libinia overlaps in habitat and resource use with Carcinus, which avoids Gonionemus consumption, Carcinus populations could be indirectly benefiting from this unusual crab–jellyfish trophic relationship. creator: Mary R. Carman creator: David W. Grunden creator: Annette F. Govindarajan uri: https://doi.org/10.7717/peerj.3966 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Carman et al. title: Indigenous Australian household structure: a simple data collection tool and implications for close contact transmission of communicable diseases link: https://peerj.com/articles/3958 last-modified: 2017-10-26 description: Households are an important location for the transmission of communicable diseases. Social contact between household members is typically more frequent, of greater intensity, and is more likely to involve people of different age groups than contact occurring in the general community. Understanding household structure in different populations is therefore fundamental to explaining patterns of disease transmission in these populations. Indigenous populations in Australia tend to live in larger households than non-Indigenous populations, but limited data are available on the structure of these households, and how they differ between remote and urban communities. We have developed a novel approach to the collection of household structure data, suitable for use in a variety of contexts, which provides a detailed view of age, gender, and room occupancy patterns in remote and urban Australian Indigenous households. Here we report analysis of data collected using this tool, which quantifies the extent of crowding in Indigenous households, particularly in remote areas. We use these data to generate matrices of age-specific contact rates, as used by mathematical models of infectious disease transmission. To demonstrate the impact of household structure, we use a mathematical model to simulate an influenza-like illness in different populations. Our simulations suggest that outbreaks in remote populations are likely to spread more rapidly and to a greater extent than outbreaks in non-Indigenous populations. creator: Thiripura Vino creator: Gurmeet R. Singh creator: Belinda Davison creator: Patricia T. Campbell creator: Michael J. Lydeamore creator: Andrew Robinson creator: Jodie McVernon creator: Steven Y.C. Tong creator: Nicholas Geard uri: https://doi.org/10.7717/peerj.3958 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Vino et al. title: Phylogenomic analysis of the Chilean clade of Liolaemus lizards (Squamata: Liolaemidae) based on sequence capture data link: https://peerj.com/articles/3941 last-modified: 2017-10-26 description: The genus Liolaemus is one of the most ecologically diverse and species-rich genera of lizards worldwide. It currently includes more than 250 recognized species, which have been subject to many ecological and evolutionary studies. Nevertheless, Liolaemus lizards have a complex taxonomic history, mainly due to the incongruence between morphological and genetic data, incomplete taxon sampling, incomplete lineage sorting and hybridization. In addition, as many species have restricted and remote distributions, this has hampered their examination and inclusion in molecular systematic studies. The aims of this study are to infer a robust phylogeny for a subsample of lizards representing the Chilean clade (subgenus Liolaemus sensu stricto), and to test the monophyly of several of the major species groups. We use a phylogenomic approach, targeting 541 ultra-conserved elements (UCEs) and 44 protein-coding genes for 16 taxa. We conduct a comparison of phylogenetic analyses using maximum-likelihood and several species tree inference methods. The UCEs provide stronger support for phylogenetic relationships compared to the protein-coding genes; however, the UCEs outnumber the protein-coding genes by 10-fold. On average, the protein-coding genes contain over twice the number of informative sites. Based on our phylogenomic analyses, all the groups sampled are polyphyletic. Liolaemus tenuis tenuis is difficult to place in the phylogeny, because only a few loci (nine) were recovered for this species. Topologies or support values did not change dramatically upon exclusion of L. t. tenuis from analyses, suggesting that missing data did not had a significant impact on phylogenetic inference in this data set. The phylogenomic analyses provide strong support for sister group relationships between L. fuscus, L. monticola, L. nigroviridis and L. nitidus, and L. platei and L. velosoi. Despite our limited taxon sampling, we have provided a reliable starting hypothesis for the relationships among many major groups of the Chilean clade of Liolaemus that will help future work aimed at resolving the Liolaemus phylogeny. creator: Alejandra Panzera creator: Adam D. Leaché creator: Guillermo D’Elía creator: Pedro F. Victoriano uri: https://doi.org/10.7717/peerj.3941 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Panzera et al. title: Erwinia amylovora psychrotrophic adaptations: evidence of pathogenic potential and survival at temperate and low environmental temperatures link: https://peerj.com/articles/3931 last-modified: 2017-10-26 description: The fire blight pathogen Erwinia amylovora can be considered a psychrotrophic bacterial species since it can grow at temperatures ranging from 4 °C to 37 °C, with an optimum of 28 °C. In many plant pathogens the expression of virulence determinants is restricted to a certain range of temperatures. In the case of E. amylovora, temperatures above 18 °C are required for blossom blight epidemics under field conditions. Moreover, this bacterium is able to infect a variety of host tissues/organs apart from flowers, but it is still unknown how environmental temperatures, especially those below 18 °C, affect the pathogen ability to cause fire blight disease symptoms in such tissues/organs. There is also scarce information on how temperatures below 18 °C affect the E. amylovora starvation-survival responses, which might determine its persistence in the environment and probably contribute to the seasonal development of fire blight disease, as occurs in other pathogens. To characterize the virulence and survival of E. amylovora at temperate and low temperatures, we evaluated the effect of three temperatures (4 °C, 14 °C, 28 °C) on symptom development, and on different parameters linked to starvation and virulence. E. amylovora was pathogenic at the three assayed temperatures, with a slow-down of symptom development correlating with colder temperatures and slower growth rates. Siderophore secretion and motility also decreased in parallel to incubation temperatures. However, production of the exopolysaccharides amylovoran and levan was enhanced at 4 °C and 14 °C, respectively. Similarly, biofilm formation, and oxidative stress resistance were improved at 14 °C, with this temperature also favoring the maintenance of culturability, together with a reduction in cell size and the acquisition of rounded shapes in E. amylovora cells subjected to long-term starvation. However, starvation at 28 °C and 4 °C induced an enhanced viable but nonculturable (VBNC) response (to a lesser extent at 4 °C). This work reveals E. amylovora as a highly adaptable pathogen that retains its pathogenic potential even at the minimal growth temperatures, with an improved exopolysaccharide synthesis, biofilm formation or oxidative stress resistance at 14 °C, with respect to the optimal growth temperature (28 °C). Finally, our results also demonstrate the thermal modulation of starvation responses in E. amylovora, suggesting that the starvation-survival and the VBNC states are part of its life cycle. These results confirm the particular psychrotrophic adaptations of E. amylovora, revealing its pathogenic potential and survival at temperate and low environmental temperatures, which have probably contributed to its successful spread to countries with different climates. This knowledge might improve integrated control measures against fire blight. creator: Ricardo D. Santander creator: Elena G. Biosca uri: https://doi.org/10.7717/peerj.3931 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Santander and Biosca title: Evaluation of genetic variability among “Early Mature” Juglans regia using microsatellite markers and morphological traits link: https://peerj.com/articles/3834 last-modified: 2017-10-26 description: Limiting the juvenile phase and reducing tree size are the two main challenges for breeders to improve most fruit crops. Early maturation and dwarf cultivars have been reported for many fruit species. “Early mature” and low vigor walnut genotypes were found among seedlings of Persian walnut. Nine microsatellite markers were used to evaluate genetic diversity among “Early Mature” Persian walnut accessions and provide a comparison with “normal growth” accessions. Six maturation related characteristics were also measured in “Early Mature” samples. Phenotypic traits and diversity indices showed relatively high levels of genetic diversity in “Early Mature” seedlings and indicated high differentiation between individuals. Seedling height, the most diverse phenotypic trait, has an important role in the clustering of “Early Mature” accessions. The “Early Mature” type had higher number of alleles, number of effective allele, and Shannon index compared to the “Normal Growth” group. The two types of studied walnuts had different alleles, with more than half of produced alleles specific to a specific group. “Early Mature” and “Normal Growth” walnuts had 27 and 17 private alleles, respectively. Grouping with different methods separated “Early Mature” and “Normal Growth” samples entirely. The presence of moderate to high genetic diversity in “Early Mature” walnuts and high genetic differentiation with “Normal Growth” walnuts, indicated that “Early Mature” walnuts were more diverse and distinct from “Normal Growth” samples. Moreover, our results showed SSR markers were useful for differentiating between “Early Mature” and “Normal Growth” walnuts. A number of identified loci have potential in breeding programs for identification of “Early Mature” walnuts at the germination phase. creator: Aziz Ebrahimi creator: Abdolkarim Zarei creator: Mojtaba Zamani Fardadonbeh creator: Shaneka Lawson uri: https://doi.org/10.7717/peerj.3834 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Ebrahimi et al. title: Knowledge and beliefs regarding cervical cancer screening and HPV vaccination among urban and rural women in León, Nicaragua link: https://peerj.com/articles/3871 last-modified: 2017-10-25 description: BackgroundIn Nicaragua, cervical cancer is the leading cause of cancer-related death for women ages 15–44, yet access to the HPV vaccine is limited to those with financial resources to pay for it. Cervical cytology is provided free of charge in public clinics; however, only 10% of women receive Pap smears at the nationally recommended frequency. Previous studies have not investigated how beliefs regarding cervical cancer screening may differ for urban and rural populations in Nicaragua. Furthermore, no investigation has assessed Nicaraguan women’s beliefs about a potential HPV immunization campaign. Given beliefs’ influence on health behavior, we investigated the structural, sociocultural, and knowledge-based factors influencing women’s beliefs regarding cervical cancer screening among urban and rural women in León, Nicaragua, and assessed acceptance of a potential HPV immunization program.MethodsOur sequential explanatory mixed-methods study consisted of two phases: (1) a close-ended questionnaire, followed by (2) a qualitative, in-depth interview. Our quantitative sample contained 117 urban and 112 rural participants aged 18–49. We assessed beliefs regarding cervical cancer screening using a 22-item scale, with higher scores indicating screening-promoting beliefs in simple linear and multiple linear regressions. Twenty qualitative interviews, exploring the sociocultural dimensions of knowledge and attitudes indicated by our quantitative findings, were conducted with a sample of 13 urban and 7 rural women aged 19–46.ResultsThe multiple linear regression indicates that greater knowledge of Pap smears, HPV, and cervical cancer is significantly associated with screening-promoting beliefs after adjusting for other relevant factors. There was no significant difference in screening knowledge and beliefs for urban and rural women. Four recurrent themes representing determinants of knowledge, beliefs, and attitudes regarding cervical cancer screening arose from interviews and built on quantitative findings: (1) women’s embarrassment due to the intimate nature of the Pap smear and male gender of exam provider discourages screening; (2) women believe Pap smears and cervical cancer are associated with sexual promiscuity, and this association stigmatizes women with the disease; (3) knowledge of cervical cancer prevention is limited to those who regularly attend health centers; and (4) women find screening inconvenient, believing understaffed clinics increase patient wait time, limit time patients spend with clinicians, and delay Pap results. A fifth theme indicates (5) participants’ acceptance of a potential HPV immunization program.DiscussionFuture interventions should focus on increasing access to information about cervical cancer prevention for women who do not regularly attend health centers. Furthermore, our results suggest that if funding were allocated to make the HPV vaccine accessible in Nicaragua, it would be well received. creator: Hannah D. Rees creator: Alexandra R. Lombardo creator: Caroline G. Tangoren creator: Sara J. Meyers creator: Vishnu R. Muppala creator: Linda M. Niccolai uri: https://doi.org/10.7717/peerj.3871 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Rees et al. title: Diversity of fish sound types in the Pearl River Estuary, China link: https://peerj.com/articles/3924 last-modified: 2017-10-24 description: BackgroundRepetitive species-specific sound enables the identification of the presence and behavior of soniferous species by acoustic means. Passive acoustic monitoring has been widely applied to monitor the spatial and temporal occurrence and behavior of calling species.MethodsUnderwater biological sounds in the Pearl River Estuary, China, were collected using passive acoustic monitoring, with special attention paid to fish sounds. A total of 1,408 suspected fish calls comprising 18,942 pulses were qualitatively analyzed using a customized acoustic analysis routine.ResultsWe identified a diversity of 66 types of fish sounds. In addition to single pulse, the sounds tended to have a pulse train structure. The pulses were characterized by an approximate 8 ms duration, with a peak frequency from 500 to 2,600 Hz and a majority of the energy below 4,000 Hz. The median inter-pulsepeak interval (IPPI) of most call types was 9 or 10 ms. Most call types with median IPPIs of 9 ms and 10 ms were observed at times that were exclusive from each other, suggesting that they might be produced by different species. According to the literature, the two section signal types of 1 + 1 and 1 + N10 might belong to big-snout croaker (Johnius macrorhynus), and 1 + N19 might be produced by Belanger’s croaker (J. belangerii).DiscussionCategorization of the baseline ambient biological sound is an important first step in mapping the spatial and temporal patterns of soniferous fishes. The next step is the identification of the species producing each sound. The distribution pattern of soniferous fishes will be helpful for the protection and management of local fishery resources and in marine environmental impact assessment. Since the local vulnerable Indo-Pacific humpback dolphin (Sousa chinensis) mainly preys on soniferous fishes, the fine-scale distribution pattern of soniferous fishes can aid in the conservation of this species. Additionally, prey and predator relationships can be observed when a database of species-identified sounds is completed. creator: Zhi-Tao Wang creator: Douglas P. Nowacek creator: Tomonari Akamatsu creator: Ke-Xiong Wang creator: Jian-Chang Liu creator: Guo-Qin Duan creator: Han-Jiang Cao creator: Ding Wang uri: https://doi.org/10.7717/peerj.3924 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Wang et al. title: Norwegian honey bees surviving Varroa destructor mite infestations by means of natural selection link: https://peerj.com/articles/3956 last-modified: 2017-10-24 description: BackgroundManaged, feral and wild populations of European honey bee subspecies, Apis mellifera, are currently facing severe colony losses globally. There is consensus that the ectoparasitic mite Varroa destructor, that switched hosts from the Eastern honey bee Apis cerana to the Western honey bee A. mellifera, is a key factor driving these losses. For >20 years, breeding efforts have not produced European honey bee colonies that can survive infestations without the need for mite control. However, at least three populations of European honey bees have developed this ability by means of natural selection and have been surviving for >10 years without mite treatments. Reduced mite reproductive success has been suggested as a key factor explaining this natural survival. Here, we report a managed A. mellifera population in Norway, that has been naturally surviving consistent V. destructor infestations for >17 years.MethodsSurviving colonies and local susceptible controls were evaluated for mite infestation levels, mite reproductive success and two potential mechanisms explaining colony survival: grooming of adult worker bees and Varroa Sensitive Hygiene (VSH): adult workers specifically detecting and removing mite-infested brood.ResultsMite infestation levels were significantly lower in surviving colonies and mite reproductive success was reduced by 30% when compared to the controls. No significant differences were found between surviving and control colonies for either grooming or VSH.DiscussionOur data confirm that reduced mite reproductive success seems to be a key factor for natural survival of infested A. mellifera colonies. However, neither grooming nor VSH seem to explain colony survival. Instead, other behaviors of the adult bees seem to be sufficient to hinder mite reproductive success, because brood for this experiment was taken from susceptible donor colonies only. To mitigate the global impact of V. destructor, we suggest learning more from nature, i.e., identifying the obviously efficient mechanisms favored by natural selection. creator: Melissa A.Y. Oddie creator: Bjørn Dahle creator: Peter Neumann uri: https://doi.org/10.7717/peerj.3956 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Oddie et al. title: A massive update of non-indigenous species records in Mediterranean marinas link: https://peerj.com/articles/3954 last-modified: 2017-10-24 description: The Mediterranean Sea is home to over 2/3 of the world’s charter boat traffic and hosts an estimated 1.5 million recreational boats. Studies elsewhere have demonstrated marinas as important hubs for the stepping-stone transfer of non-indigenous species (NIS), but these unique anthropogenic, and typically artificial habitats have largely gone overlooked in the Mediterranean as sources of NIS hot-spots. From April 2015 to November 2016, 34 marinas were sampled across the following Mediterranean countries: Spain, France, Italy, Malta, Greece, Turkey and Cyprus to investigate the NIS presence and richness in the specialized hard substrate material of these marina habitats. All macroinvertebrate taxa were collected and identified. Additionally, fouling samples were collected from approximately 600 boat-hulls from 25 of these marinas to determine if boats host diverse NIS not present in the marina. Here, we present data revealing that Mediterranean marinas indeed act as major hubs for the transfer of marine NIS, and we also provide evidence that recreational boats act as effective vectors of spread. From this wide-ranging geographical study, we report here numerous new NIS records at the basin, subregional, country and locality level. At the basin level, we report three NIS new to the Mediterranean Sea (Achelia sawayai sensu lato, Aorides longimerus, Cymodoce aff. fuscina), and the re-appearance of two NIS previously known but currently considered extinct in the Mediterranean (Bemlos leptocheirus, Saccostrea glomerata). We also compellingly update the distributions of many NIS in the Mediterranean Sea showing some recent spreading; we provide details for 11 new subregional records for NIS (Watersipora arcuata, Hydroides brachyacantha sensu lato and Saccostrea glomerata now present in the Western Mediterranean; Symplegma brakenhielmi, Stenothoe georgiana, Spirobranchus tertaceros sensu lato, Dendostrea folium sensu lato and Parasmittina egyptiaca now present in the Central Mediterranean, and W. arcuata, Bemlos leptocheirus and Dyspanopeus sayi in the Eastern Mediterranean). We also report 51 new NIS country records from recreational marinas: 12 for Malta, 10 for Cyprus, nine for Greece, six for Spain and France, five for Turkey and three for Italy, representing 32 species. Finally, we report 20 new NIS records (representing 17 species) found on recreational boat-hulls (mobile habitats), not yet found in the same marina, or in most cases, even the country. For each new NIS record, their native origin and global and Mediterranean distributions are provided, along with details of the new record. Additionally, taxonomic characters used for identification and photos of the specimens are also provided. These new NIS records should now be added to the relevant NIS databases compiled by several entities. Records of uncertain identity are also discussed, to assess the probability of valid non-indigenous status. creator: Aylin Ulman creator: Jasmine Ferrario creator: Anna Occhpinti-Ambrogi creator: Christos Arvanitidis creator: Ada Bandi creator: Marco Bertolino creator: Cesare Bogi creator: Giorgos Chatzigeorgiou creator: Burak Ali Çiçek creator: Alan Deidun creator: Alfonso Ramos-Esplá creator: Cengiz Koçak creator: Maurizio Lorenti creator: Gemma Martinez-Laiz creator: Guenda Merlo creator: Elisa Princisgh creator: Giovanni Scribano creator: Agnese Marchini uri: https://doi.org/10.7717/peerj.3954 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Ulman et al. title: Statins: antimicrobial resistance breakers or makers? link: https://peerj.com/articles/3952 last-modified: 2017-10-24 description: IntroductionThe repurposing of non-antibiotic drugs as adjuvant antibiotics may help break antimicrobial resistance (AMR). Statins are commonly prescribed worldwide to lower cholesterol. They also possess qualities of AMR “breakers”, namely direct antibacterial activity, synergism with antibiotics, and ability to stimulate the host immune system. However, statins’ role as AMR breakers may be limited. Their current extensive use for cardiovascular protection might result in selective pressures for resistance, ironically causing statins to be AMR “makers” instead. This review examines statins’ potential as AMR breakers, probable AMR makers, and identifies knowledge gaps in a statin-bacteria-human-environment continuum. The most suitable statin for repurposing is identified, and a mechanism of antibacterial action is postulated based on structure-activity relationship analysis.MethodsA literature search using keywords “statin” or “statins” combined with “minimum inhibitory concentration” (MIC) was performed in six databases on 7th April 2017. After screening 793 abstracts, 16 relevant studies were identified. Unrelated studies on drug interactions; antifungal or antiviral properties of statins; and antibacterial properties of mevastatin, cerivastatin, antibiotics, or natural products were excluded. Studies involving only statins currently registered for human use were included.ResultsAgainst Gram-positive bacteria, simvastatin generally exerted the greatest antibacterial activity (lowest MIC) compared to atorvastatin, rosuvastatin, and fluvastatin. Against Gram-negative bacteria, atorvastatin generally exhibited similar or slightly better activity compared to simvastatin, but both were more potent than rosuvastatin and fluvastatin.DiscussionStatins may serve as AMR breakers by working synergistically with existing topical antibiotics, attenuating virulence factors, boosting human immunity, or aiding in wound healing. It is probable that statins’ mechanism of antibacterial activity involves interference of bacterial cell regulatory functions via binding and disrupting cell surface structures such as wall teichoic acids, lipoteichoic acids, lipopolysaccharides, and/or surface proteins. The widespread use of statins for cardiovascular protection may favor selective pressures or co-selection for resistance, including dysbiosis of the human gut microbiota, sublethal plasma concentrations in bacteremic patients, and statin persistence in the environment, all possibly culminating in AMR.ConclusionSimvastatin appears to be the most suitable statin for repurposing as a novel adjuvant antibiotic. Current evidence better supports statins as potential AMR breakers, but their role as plausible AMR makers cannot be excluded. Elucidating the mechanism of statins’ antibacterial activity is perhaps the most important knowledge gap to address as this will likely clarify statins’ role as AMR breakers or makers. creator: Humphrey H.T. Ko creator: Ricky R. Lareu creator: Brett R. Dix creator: Jeffery D. Hughes uri: https://doi.org/10.7717/peerj.3952 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Ko et al. title: Measuring language lateralisation with different language tasks: a systematic review link: https://peerj.com/articles/3929 last-modified: 2017-10-24 description: Language lateralisation refers to the phenomenon in which one hemisphere (typically the left) shows greater involvement in language functions than the other. Measurement of laterality is of interest both to researchers investigating the neural organisation of the language system and to clinicians needing to establish an individual’s hemispheric dominance for language prior to surgery, as in patients with intractable epilepsy. Recently, there has been increasing awareness of the possibility that different language processes may develop hemispheric lateralisation independently, and to varying degrees. However, it is not always clear whether differences in laterality across language tasks with fMRI are reflective of meaningful variation in hemispheric lateralisation, or simply of trivial methodological differences between paradigms. This systematic review aims to assess different language tasks in terms of the strength, reliability and robustness of the laterality measurements they yield with fMRI, to look at variability that is both dependent and independent of aspects of study design, such as the baseline task, region of interest, and modality of the stimuli. Recommendations are made that can be used to guide task design; however, this review predominantly highlights that the current high level of methodological variability in language paradigms prevents conclusions as to how different language functions may lateralise independently. We conclude with suggestions for future research using tasks that engage distinct aspects of language functioning, whilst being closely matched on non-linguistic aspects of task design (e.g., stimuli, task timings etc); such research could produce more reliable and conclusive insights into language lateralisation. This systematic review was registered as a protocol on Open Science Framework: https://osf.io/5vmpt/. creator: Abigail R. Bradshaw creator: Paul A. Thompson creator: Alexander C. Wilson creator: Dorothy V.M. Bishop creator: Zoe V.J. Woodhead uri: https://doi.org/10.7717/peerj.3929 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Bradshaw et al. title: The head turn paradigm to assess auditory laterality in cats: influence of ear position and repeated sound presentation link: https://peerj.com/articles/3925 last-modified: 2017-10-24 description: In most humans, speech is predominantly processed by the left hemisphere. This auditory laterality was formerly thought to be an exclusive human characteristic, but is now suggested to have pre-human origins. In studies on auditory laterality in nonhuman animals, the head turn paradigm has become very popular due to its non-invasive character. Although there are implications that the head turn direction indicates functional dominance of the contralateral hemisphere in processing a given sound, the validity of the paradigm is under debate. To validate the paradigm via comparison with imaging or electrophysiological methods, it is first necessary to establish turning biases at the individual level. Recently, the domestic cat, a common model in hearing research, has been found to show turning biases at the group level. To assess individual turning asymmetries in cats, we repeatedly presented kitten isolation calls and assessed whether differences in conveyed arousal changed the previously described left-wards lateralisation of conspecific vocalizations. Based on responses to 50 playback presentations (25 of high and 25 of low arousal), we calculated individual head turn indices. Based on the total data set, we found no consistent individual turning bias, irrespective of call category or sex of the receiver. Although the playback paradigm was chosen carefully to reduce any effects of lateralized loudness perception or changes in motivation due to habituation, individual head turn biases changed significantly in concordance with habituation to repeated playback-presentations and was predictable by small deflections in ear position prior to listening. When splitting the data set according to a decline in responsiveness after seven playback presentations, we revealed an initial left turning bias for most of our subjects (i.e., significant at the group level). We propose that this left turning bias is related to right hemisphere dominance in processes like vigilance behaviour or general arousal rather than on auditory processing, as such. Our findings suggest that both the experimental sequence and sound level differences, induced by asymmetric ear positions, strongly influence the outcome of the head turn paradigm and should be taken into account when evaluating auditory laterality at the behavioural level. creator: Wiebke S. Konerding creator: Elke Zimmermann creator: Eva Bleich creator: Hans-Jürgen Hedrich creator: Marina Scheumann uri: https://doi.org/10.7717/peerj.3925 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Konerding et al. title: Glycaspis brimblecombei (Hemiptera: Psyllidae) attack patterns on different Eucalyptus genotypes link: https://peerj.com/articles/3864 last-modified: 2017-10-24 description: BackgroundThe red gum lerp psyllid, Glycaspis brimblecombei Moore (Hemiptera: Psyllidae), an eucalypt insect pest from Australia, was reported in Brazil in 2003. This study evaluated damage patterns of this pest on Eucalyptus camaldulensis Dehn (Myrtaceae) and its hybrids E. urophylla X E. camaldulensis (urocam) and E. urophylla X E. grandis (urograndis). In addition, parasitism rates of Psyllaephagus bliteus Riek (Hymenoptera: Encyrtidae) on G. brimblecombei collected on different eucalypt genotypes are reported.MethodsPlantation plots of three eucalypt genotypes were evaluated over one year. The eucalypt leaves were collected and examined for attack by G. brimblecombei. Nymph parasitism of G. brimblecombei by P. bliteus was recorded.ResultsDamage by G. brimblecombei was lower on the hybrid genotypes and on the adaxial surface of the eucalypt leaves. G. brimblecombei egg and nymph density were negatively correlated with monthly rainfall. Nymph parasitism of G. brimblecombei by P. bliteus was low (2.9%) independent of genotype and did not vary throughout the year.DiscussionOur data indicate the use of less susceptible eucalypt genotypes (e.g., hybrids) as an alternative to G. brimblecombei management. Because of the current low mortality rates for G. brimblecombei resulting from P. bliteus parasitism, biological control with this natural enemy is not recommended as a management strategy for G. brimblecombei. creator: Juliana Tuller creator: Karla Nunes Oliveira creator: Jhonathan Oliveira Silva creator: Maurício Lopes de Faria creator: Mario Marcos do Espírito-Santo creator: José Eduardo Serrão creator: José Cola Zanuncio uri: https://doi.org/10.7717/peerj.3864 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Tuller et al. title: The comparison of molecular and morphology-based phylogenies of trichaline net-winged beetles (Coleoptera: Lycidae: Metriorrhynchini) with description of a new subgenus link: https://peerj.com/articles/3963 last-modified: 2017-10-23 description: Separate morphological and molecular phylogenetic analyses are presented and the classification of trichaline net-winged beetles is revised. The clade, earlier given a subfamily, tribe or subtribe rank, is a terminal lineage in Metriorrhynchina and contains DiatrichalusKleine, 1926, EniclasesWaterhouse, 1879, Flabellotrichalus Pic, 1921, Lobatang Bocak, 1998, Microtrichalus Pic, 1921, SchizotrichalusKleine, 1926, and TrichalusWaterhouse, 1877. Maibrius subgen. nov. is proposed in Flabellotrichalus with the type-species Flabellotrichalus (Maibrius) horaki sp. nov. Unlike previous studies, Lobatang is included in the trichaline clade. Further, SpinotrichalusKazantsev, 2010, stat. nov. is down-ranked to the subgenus in Lobatang Bocak, 1998 and a new combination, Lobatang (Spinotrichalus) telnovi (Kazantsev, 2010) comb. nov., is proposed. The morphology does not provide a sufficient support for robust phylogeny due to the intrageneric variability of most phenotypic traits and the limited number of characters supporting deep relationships. Most morphological generic diagnoses must be based on the shape of male genitalia. Other characters, such as the shapes of pronotum and antennae are commonly variable within genera. The fronto-lateral pronotal ridges of Eniclases + Schizotrichalus resemble the ancestral condition in Metriorrhynchini and they re-evolved in the terminal clade and do not indicate the early split of Eniclases + Schizotrichalus from other trichaline genera. The evolution of morphological traits and the conflict in the morphological and molecular phylogenetic signal are discussed in details. We suggest that the general appearance is affected by the evolution of mimetic complexes, the patterns of elytral costae by their strengthening function, and the presence of flabellate antennae by their role in sexual communication. Then, similar phenotypic traits evolve in unrelated lineages. The results demonstrate that phylogenetic classification must be based on all available information because neither morphological traits nor DNA data robustly support all recovered relationships. creator: Matej Bocek creator: Ladislav Bocak uri: https://doi.org/10.7717/peerj.3963 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Bocek and Bocak title: Self-efficacy, relationship satisfaction, and social support: the quality of life of maternal caregivers of children with type 1 diabetes link: https://peerj.com/articles/3961 last-modified: 2017-10-23 description: ObjectivesTo examine maternal functioning and wellbeing as important aspects of a family’s adaptation to chronic paediatric conditions, in particular, children with diabetes.MethodThis cross-sectional study investigated the difference between the perceived quality of life of mothers of children with diabetes (n = 63) and mothers of children without diabetes (n = 114). The study also examined the role of self-efficacy, relationship satisfaction, number of social support providers, and satisfaction with social support in predicting quality of life.ResultsMothers who had a child with diabetes had lower quality of life measured by general health, vitality, social functioning, role-emotional, and mental health than mothers that did not have a child with diabetes. Self-efficacy, relationship satisfaction, and social support were significant predictors of quality of life (mental health domain).ConclusionIn order to enhance their psychological wellbeing, mothers of children with diabetes require adequate psychosocial support. Other implications for research and potential interventions are discussed. creator: Einar B. Thorsteinsson creator: Natasha M. Loi creator: Kylie Rayner uri: https://doi.org/10.7717/peerj.3961 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Thorsteinsson et al. title: Pheromones of three ambrosia beetles in the Euwallacea fornicatus species complex: ratios and preferences link: https://peerj.com/articles/3957 last-modified: 2017-10-23 description: Three cryptic species in the Euwallacea fornicatus species complex were reared in laboratory colonies and investigated for the presence of pheromones. Collections of volatiles from combinations of diet, fungus, beetles, and galleries from polyphagous shot hole borer (Euwallacea sp. #1) revealed the presence of 2-heneicosanone and 2-tricosanone only in the presence of beetles, regardless of sex. Subsequent examination of volatiles from the other two species, tea shot hole borer (Euwallacea sp. #2) and Kuroshio shot hole borer (Euwallacea sp. #5), revealed these two ketones were present in all three species but in different ratios. In dual choice olfactometer behavioral bioassays, mature mated females were strongly attracted to a synthetic binary blend of ketones matching their own natural ratios. However, females in each species were repelled by ketone blends in ratios corresponding to the other two species. Males of each species responded similarly to females when presented with ratios matching their own or the other two species. The presence of these compounds in the three beetle species, in ratios unique to each species, and their strong species-specific attraction and repellency, suggests they are pheromones. The ecological function of these pheromones is discussed. In addition to the pheromones, the previously known attractant (1S,4R)-p-menth-2-en-1-ol (also known as quercivorol) was discovered in the presence of the fungal symbionts, but not in association with the beetles. Quercivorol was tested in a dual-choice olfactometer and was strongly attractive to all three species. This evidence suggests quercivorol functions as a kairomone for members of the E. fornicatus species complex, likely produced by the symbiotic fungi. creator: Miriam F. Cooperband creator: Allard A. Cossé creator: Tappey H. Jones creator: Daniel Carrillo creator: Kaitlin Cleary creator: Isaiah Canlas creator: Richard Stouthamer uri: https://doi.org/10.7717/peerj.3957 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Cooperband et al. title: Learning performance and brain structure of artificially-reared honey bees fed with different quantities of food link: https://peerj.com/articles/3858 last-modified: 2017-10-23 description: BackgroundArtificial rearing of honey bee larvae is an established method which enables to fully standardize the rearing environment and to manipulate the supplied diet to the brood. However, there are no studies which compare learning performance or neuroanatomic differences of artificially-reared (in-lab) bees in comparison with their in-hive reared counterparts.MethodsHere we tested how different quantities of food during larval development affect body size, brain morphology and learning ability of adult honey bees. We used in-lab rearing to be able to manipulate the total quantity of food consumed during larval development. After hatching, a subset of the bees was taken for which we made 3D reconstructions of the brains using confocal laser-scanning microscopy. Learning ability and memory formation of the remaining bees was tested in a differential olfactory conditioning experiment. Finally, we evaluated how bees reared with different quantities of artificial diet compared to in-hive reared bees.ResultsThorax and head size of in-lab reared honey bees, when fed the standard diet of 160 µl or less, were slightly smaller than hive bees. The brain structure analyses showed that artificially reared bees had smaller mushroom body (MB) lateral calyces than their in-hive counterparts, independently of the quantity of food they received. However, they showed the same total brain size and the same associative learning ability as in-hive reared bees. In terms of mid-term memory, but not early long-term memory, they performed even better than the in-hive control.DiscussionWe have demonstrated that bees that are reared artificially (according to the Aupinel protocol) and kept in lab-conditions perform the same or even better than their in-hive sisters in an olfactory conditioning experiment even though their lateral calyces were consistently smaller at emergence. The applied combination of experimental manipulation during the larval phase plus subsequent behavioral and neuro-anatomic analyses is a powerful tool for basic and applied honey bee research. creator: Karin Steijven creator: Johannes Spaethe creator: Ingolf Steffan-Dewenter creator: Stephan Härtel uri: https://doi.org/10.7717/peerj.3858 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Steijven et al. title: Oxygen-limited metabolism in the methanotroph Methylomicrobium buryatense 5GB1C link: https://peerj.com/articles/3945 last-modified: 2017-10-20 description: The bacteria that grow on methane aerobically (methanotrophs) support populations of non-methanotrophs in the natural environment by excreting methane-derived carbon. One group of excreted compounds are short-chain organic acids, generated in highest abundance when cultures are grown under O2-starvation. We examined this O2-starvation condition in the methanotroph Methylomicrobium buryatense 5GB1. The M. buryatense 5GB1 genome contains homologs for all enzymes necessary for a fermentative metabolism, and we hypothesize that a metabolic switch to fermentation can be induced by low-O2 conditions. Under prolonged O2-starvation in a closed vial, this methanotroph increases the amount of acetate excreted about 10-fold, but the formate, lactate, and succinate excreted do not respond to this culture condition. In bioreactor cultures, the amount of each excreted product is similar across a range of growth rates and limiting substrates, including O2-limitation. A set of mutants were generated in genes predicted to be involved in generating or regulating excretion of these compounds and tested for growth defects, and changes in excretion products. The phenotypes and associated metabolic flux modeling suggested that in M. buryatense 5GB1, formate and acetate are excreted in response to redox imbalance. Our results indicate that even under O2-starvation conditions, M. buryatense 5GB1 maintains a metabolic state representing a combination of fermentation and respiration metabolism. creator: Alexey Gilman creator: Yanfen Fu creator: Melissa Hendershott creator: Frances Chu creator: Aaron W. Puri creator: Amanda Lee Smith creator: Mitchell Pesesky creator: Rose Lieberman creator: David A.C. Beck creator: Mary E. Lidstrom uri: https://doi.org/10.7717/peerj.3945 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Gilman et al. title: The benefits of Tai Chi and brisk walking for cognitive function and fitness in older adults link: https://peerj.com/articles/3943 last-modified: 2017-10-20 description: The purpose of this study was to investigate the benefits of exercises with different cognitive demands for cognitive functions (Executive and non-Executive) in healthy older adults. A cross-sectional design was adopted. In total, 84 healthy older adults were enrolled in the study. They were categorized into the Tai Chi group (TG), the brisk walking group (BG) or the control group (CG). Each participant performed the Stroop task and a digit comparison task. The Stroop task included the following three conditions: a naming condition, an inhibition condition and an executive condition. There were two experimental conditions in the digit comparison task: the non-delay condition and the delay condition. The results indicated that participants of the TG and BG revealed significant better performance than the CG in the executive condition of cognitive tasks and fitness. There was no significant difference of reaction time (RT) and accuracy rate in the inhibition and delay conditions of cognitive tasks and fitness between the TG and BG. The TG showed shorter reaction time in the naming and the executive conditions, and more accurate in the inhibition conditions than the BG. These findings demonstrated that regular participation in brisk walking and Tai Chi have significant beneficial effects on executive function and fitness. However, due to the high cognitive demands of the exercise, Tai Chi benefit cognitive functions (Executive and non-Executive) in older adults more than brisk walking does. Further studies should research the underlying mechanisms at the behavioural and neuroelectric levels, providing more evidence to explain the effect of high-cognitive demands exercise on different processing levels of cognition. creator: Zhiguang Ji creator: Anmin Li creator: Tian Feng creator: Xiaolei Liu creator: Yihong You creator: Fanying Meng creator: Ruoqing Wang creator: Jialing Lu creator: Chunhua Zhang uri: https://doi.org/10.7717/peerj.3943 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Ji et al. title: Influence of current climate, historical climate stability and topography on species richness and endemism in Mesoamerican geophyte plants link: https://peerj.com/articles/3932 last-modified: 2017-10-20 description: BackgroundA number of biotic and abiotic factors have been proposed as drivers of geographic variation in species richness. As biotic elements, inter-specific interactions are the most widely recognized. Among abiotic factors, in particular for plants, climate and topographic variables as well as their historical variation have been correlated with species richness and endemism. In this study, we determine the extent to which the species richness and endemism of monocot geophyte species in Mesoamerica is predicted by current climate, historical climate stability and topography.MethodsUsing approximately 2,650 occurrence points representing 507 geophyte taxa, species richness (SR) and weighted endemism (WE) were estimated at a geographic scale using grids of 0.5 × 0.5 decimal degrees resolution using Mexico as the geographic extent. SR and WE were also estimated using species distributions inferred from ecological niche modeling for species with at least five spatially unique occurrence points. Current climate, current to Last Glacial Maximum temperature, precipitation stability and topographic features were used as predictor variables on multiple spatial regression analyses (i.e., spatial autoregressive models, SAR) using the estimates of SR and WE as response variables. The standardized coefficients of the predictor variables that were significant in the regression models were utilized to understand the observed patterns of species richness and endemism.ResultsOur estimates of SR and WE based on direct occurrence data and distribution modeling generally yielded similar results, though estimates based on ecological niche modeling indicated broader distribution areas for SR and WE than when species richness was directly estimated using georeferenced coordinates. The SR and WE of monocot geophytes were highest along the Trans-Mexican Volcanic Belt, in both cases with higher levels in the central area of this mountain chain. Richness and endemism were also elevated in the southern regions of the Sierra Madre Oriental and Occidental mountain ranges, and in the Tehuacán Valley. Some areas of the Sierra Madre del Sur and Sierra Madre Oriental had high levels of WE, though they are not the areas with the highest SR. The spatial regressions suggest that SR is mostly influenced by current climate, whereas endemism is mainly affected by topography and precipitation stability.ConclusionsBoth methods (direct occurrence data and ecological niche modeling) used to estimate SR and WE in this study yielded similar results and detected a key area that should be considered in plant conservation strategies: the central region of the Trans-Mexican Volcanic Belt. Our results also corroborated that species richness is more closely correlated with current climate factors while endemism is related to differences in topography and to changes in precipitation levels compared to the LGM climatic conditions. creator: Victoria Sosa creator: Israel Loera uri: https://doi.org/10.7717/peerj.3932 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Sosa and Loera title: Effects of GnRHa treatment during vitellogenesis on the reproductive physiology of thermally challenged female Atlantic salmon (Salmo salar) link: https://peerj.com/articles/3898 last-modified: 2017-10-20 description: Tasmanian Atlantic salmon (S. salar) broodstock can experience temperatures above 20 °C, which impairs reproductive development and inhibits ovulation. The present study investigated the prolonged use of gonadotropin releasing hormone analogue (GnRHa) during vitellogenesis as a means of maintaining endocrine function and promoting egg quality at elevated temperature in maiden and repeat spawning S. salar. GnRHa-treatment during vitellogenesis did not compensate for the negative effects of thermal challenge on the timing of ovulation, egg size, egg fertility or embryo survival in any fish maintained at 22 °C relative to 14 °C. The lack of effectiveness was reflected by the endocrine data, as plasma follicle stimulating hormone and luteinising hormone levels were not different between treated and untreated groups at 22 °C. Furthermore, plasma testosterone and E2 levels were unchanged in GnRHa-treated fish at 22 °C, and plasma levels were generally lower in both groups maintained at 22 °C relative to 14 °C. Transcription of vitellogenin, and zona pellucida B and C was not enhanced in GnRHa-treated fish relative to untreated fish at 22 °C, presumably due to observed suppression of plasma E2. These results indicate that thermal impairment of reproduction is likely to occur on multiple levels, and is difficult to overcome via hormonal manipulation. creator: Kelli Anderson creator: Ned Pankhurst creator: Harry King creator: Abigail Elizur uri: https://doi.org/10.7717/peerj.3898 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Anderson et al. title: First record of the family Sphyrapodidae Guţu, 1980 (Crustacea: Peracarida: Apseudomorpha) with the description of a new species of Sphyrapus from the Colombian Caribbean link: https://peerj.com/articles/3947 last-modified: 2017-10-19 description: A new sphyrapodid tanaidacean, Sphyrapus caribensis sp. nov. is described and a new record of Kudinopasternakia siegi is reported for the Colombian Caribbean based on samples collected during cruises in 2014–2015. The new species appears to be most closely related to the northeast Atlantic species, Sphyrapus malleolus. Sphyrapus caribensis can be distinguished from Sphyrapus malleolus by a combination of characters, including the maxillipedal basis without long distal seta, the number of setae on the distoventral margin of pereopods 1 and 2, and the number of plumose seta on the pleopod basis. A key for the separation of Sphyrapus species is presented. creator: Andrés G. Morales-Núñez creator: Catalina Morales-Ruiz creator: Néstor E. Ardila uri: https://doi.org/10.7717/peerj.3947 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Morales-Núñez et al. title: The neuroprotective effect of nicotine in Parkinson’s disease models is associated with inhibiting PARP-1 and caspase-3 cleavage link: https://peerj.com/articles/3933 last-modified: 2017-10-19 description: Clinical evidence points to neuroprotective effects of smoking in Parkinson’s disease (PD), but the molecular mechanisms remain unclear. We investigated the pharmacological pathways involved in these neuroprotective effects, which could provide novel ideas for developing targeted neuroprotective treatments for PD. We used the ETC complex I inhibitor methylpyridinium ion (MPP+) to induce cell death in SH-SY5Y cells as a cellular model for PD and found that nicotine inhibits cell death. Using choline as a nicotinic acetylcholine receptor (nAChR) agonist, we found that nAChR stimulation was sufficient to protect SH-SY5Y cells against cell death from MPP+. Blocking α7 nAChR with methyllycaconitine (MLA) prevented the protective effects of nicotine, demonstrating that these receptors are necessary for the neuroprotective effects of nicotine. The neuroprotective effect of nicotine involves other pathways relevant to PD. Cleaved Poly (ADP-ribose) polymerase-1 (PARP-1) and cleaved caspase-3 were decreased by nicotine in 6-hydroxydopamine (6-OHDA) lesioned mice and in MPP+-treated SH-SY5Y cells. In conclusion, our data indicate that nicotine likely exerts neuroprotective effects in PD through the α7 nAChR and downstream pathways including PARP-1 and caspase-3. This knowledge could be pursued in future research to develop neuroprotective treatments for PD. creator: Justin Y.D. Lu creator: Ping Su creator: James E.M. Barber creator: Joanne E. Nash creator: Anh D. Le creator: Fang Liu creator: Albert H.C. Wong uri: https://doi.org/10.7717/peerj.3933 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Lu et al. title: Range expansion of a fouling species indirectly impacts local species interactions link: https://peerj.com/articles/3911 last-modified: 2017-10-19 description: We investigated how recent changes in the distribution and abundance of a fouling organism affected the strength of interactions between a commercially important foundation species and a common predator. Increases in the abundance of boring sponges that bioerode the calcified shells of oysters and other shelled organisms have been attributed to increased salinization of estuarine ecosystems. We tested the hypothesis that fouling by boring sponges will change the interaction strength between oysters and a common predator (stone crabs). We generated five oyster density treatments crossed with two sponge treatments (sponge and no sponge). We contrasted the interaction strength between stone crabs and fouled and non-fouled oysters by comparing the parameters of fitted functional response curves based on Rogers random predation model. We found that fouled oysters suffered higher predation from stone crabs, and that the increased predation risk stemmed from a reduction in the handling time needed to consume the fouled oysters. These findings highlight the importance of understanding the effects of abiotic changes on both the composition of ecological communities, and on the strengths of direct and indirect interactions among species. Global climate change is altering local ecosystems in complex ways, and the success of restoration, management, and mitigation strategies for important species requires a better appreciation for how these effects cascade through ecosystems. creator: Cori J. Speights creator: Michael W. McCoy uri: https://doi.org/10.7717/peerj.3911 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Speights and McCoy title: Decreased quality of life and treatment satisfaction in patients with latent autoimmune diabetes of the adult link: https://peerj.com/articles/3928 last-modified: 2017-10-18 description: ObjectivesOur main aim was to assess the quality of life (QoL) and treatment satisfaction (TS) of subjects with LADA (latent autoimmune diabetes of the adult) and compare these measures with those of patients with other diabetes types, i.e., type 1 (T1DM) and type 2 diabetes mellitus (T2DM).MethodsThis was a cross-sectional study with a total of 48 patients with LADA, 297 patients with T2DM and 124 with T1DM. The Audit of Diabetes-Dependent Quality of Life (ADDQoL-19) questionnaire and the Diabetes Treatment Satisfaction Questionnaire (DTSQ) were administered. Relevant clinical variables were also assessed. The data analysis included comparisons between groups and multivariate linear models.ResultsThe LADA patients presented lower diabetes-specific QoL (p = 0.045) and average weighted impact scores (p = 0.007) than the T2DM patients. The subgroup of LADA patients with diabetic retinopathy (DR) who were treated with insulin had a lower ADDQoL average weighted impact score than the other diabetic groups. Although the overall measure of TS was not different between the LADA and T2DM (p = 0.389) and T1DM (p = 0.091) groups, the patients with LADA showed a poorer hyperglycemic frequency perception than the T2DM patients (p < 0.001) and an improved frequency of hypoglycemic perception compared with the T1DM patients (p = 0.021).ConclusionsThe current findings suggest a poorer quality of life, especially in terms of DR and insulin treatment, among patients with LADA compared with those with T1DM and T2DM. Hyperglycemia frequency perception was also poorer in the LADA patients than in the T1DM and T2DM patients. Further research with prospective studies and a large number of patients is necessary. creator: Minerva Granado-Casas creator: Montserrat Martínez-Alonso creator: Nuria Alcubierre creator: Anna Ramírez-Morros creator: Marta Hernández creator: Esmeralda Castelblanco creator: Joan Torres-Puiggros creator: Didac Mauricio uri: https://doi.org/10.7717/peerj.3928 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Granado-Casas et al. title: Ongoing removals of invasive lionfish in Honduras and their effect on native Caribbean prey fishes link: https://peerj.com/articles/3818 last-modified: 2017-10-18 description: The invasion of Indo-Pacific lionfish is one of the most pressing concerns in the context of coral reef conservation throughout the Caribbean. Invasive lionfish threaten Caribbean fish communities by feeding on a wide range of native prey species, some of which have high ecological and economic value. In Roatan (Honduras) a local non-governmental organisation (i.e. Roatan Marine Park) trains residents and tourists in the use of spears to remove invasive lionfish. Here, we assess the effectiveness of local removal efforts in reducing lionfish populations. We ask whether reefs subject to relatively frequent removals support more diverse and abundant native fish assemblages compared to sites were no removals take place. Lionfish biomass, as well as density and diversity of native prey species were quantified on reefs subject to regular and no removal efforts. Reefs subject to regular lionfish removals (two to three removals month−1) with a mean catch per unit effort of 2.76 ± 1.72 lionfish fisher−1 h−1 had 95% lower lionfish biomass compared to non-removal sites. Sites subject to lionfish removals supported 30% higher densities of native prey-sized fishes compared to sites subject to no removal efforts. We found no evidence that species richness and diversity of native fish communities differ between removal and non-removal sites. We conclude that opportunistic voluntary removals are an effective management intervention to reduce lionfish populations locally and might alleviate negative impacts of lionfish predation. We recommend that local management and the diving industry cooperate to cost-effectively extend the spatial scale at which removal regimes are currently sustained. creator: Friederike Peiffer creator: Sonia Bejarano creator: Giacomo Palavicini de Witte creator: Christian Wild uri: https://doi.org/10.7717/peerj.3818 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Peiffer et al. title: lncRNA H19 is involved in TGF-β1-induced epithelial to mesenchymal transition in bovine epithelial cells through PI3K/AKT Signaling Pathway link: https://peerj.com/articles/3950 last-modified: 2017-10-17 description: Increased levels of long noncoding RNA H19 (H19) have been observed in many inflammatory and organ fibrosis diseases including ulcerative colitis, osteoarthritis, liver fibrosis, renal fibrosis and pulmonary fibrosis. However, the role of H19 in bovine mastitis and mastitis-caused fibrosis is still unclear. In our study, H19 was characterized as a novel regulator of EMT induced by transforming growth factor-β1 (TGF-β1) in bovine mammary alveolar cell-T (MAC-T) cell line. We found that H19 was highly expressed in bovine mastitis tissues and inflammatory MAC-T cells induced by virulence factors of pathogens. TGF-β1 was also highly expressed in inflammatory MAC-T cells, and exogenous TGF-β1 could induce EMT, enhance extracellular matrix protein expression, and upregulate H19 expression in epithelial cells. Stable expression of H19 significantly promotes EMT progression and expression of ECM protein induced by TGF-β1 in MAC-T cells. Furthermore, by using a specific inhibitor of the PI3K/AKT pathway, we demonstrated that TGF-β1 upregulated H19 expression through PI3K/AKT pathway. All these observations imply that the lncRNA H19 modulated TGF-β1-induced epithelial to mesenchymal transition in bovine epithelial cells through PI3K/AKT signaling pathway, which suggests that mammary epithelial cells might be one source for myofibroblasts in vivo in the mammary glands under an inflammatory condition, thereby contributing to mammary gland fibrosis. creator: Wei Yang creator: Xuezhong Li creator: Shaopei Qi creator: Xueru Li creator: Kun Zhou creator: Suzhu Qing creator: Yong Zhang creator: Ming-Qing Gao uri: https://doi.org/10.7717/peerj.3950 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Yang et al. title: MGST2 and WNT2 are candidate genes for comitant strabismus susceptibility in Japanese patients link: https://peerj.com/articles/3935 last-modified: 2017-10-17 description: Background/AimStrabismus is a common condition with misalignment between two eyes that may lead to decrease of visual acuity, lack of binocularity, and diplopia. It is caused by heterogeneous environmental and genetic risk factors. Our previous research has identified new chromosomal susceptibility loci in 4q28.3 and 7q31.2 regions for comitant strabismus in Japanese families. We conducted a verification study by linkage analysis to narrow the chromosomal loci down to a single gene.MethodsFrom Japanese and U.S. databases, 24 rsSNPs and 233 rsSNPs were chosen from the 4q28.3 and 7q31.2 region, respectively, and were typed in 108 affected subjects and 96 unaffected subjects of 58 families with primary and non-syndromic comitant strabismus. Three major analytical methods were used: transmission disequilibrium test (TDT), TDT allowing for errors (TDTae), and linkage analysis under dominant and recessive inheritance.ResultsThe SNPs with significant P values in TDT and TDTae were located solely at the gene, microsomal glutathione S-transferase 2 (MGST2), on chromosome 4q28.3 locus. In contrast, significant SNPs were dispersed in a few genes, containing wingless-type MMTV integration site family member 2 (WNT2), on chromosome 7q31.2 locus. The distribution of significant SNPs on the 7q31.2 locus showed that only the ST7 to WNT2 region in the same big haplotype block contained significant SNPs for all three methods of linkage analysis.ConclusionsThis study suggests that MGST2 and WNT2 are potential candidates for comitant strabismus in Japanese population. creator: Jingjing Zhang creator: Toshihiko Matsuo uri: https://doi.org/10.7717/peerj.3935 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Zhang and Matsuo title: Bacterial and fungal communities respond differently to varying tillage depth in agricultural soils link: https://peerj.com/articles/3930 last-modified: 2017-10-17 description: In arable cropping systems, reduced or conservation tillage practices are linked with improved soil quality, C retention and higher microbial biomass, but most long-term studies rarely focus on depths greater than 15 cm nor allow comparison of microbial community responses to agricultural practices. We investigated microbial community structure in a long-term field trial (12-years, Lincoln, New Zealand) established in a silt-loam soil over four depth ranges down to 30 cm. Our objectives were to investigate the degree of homogenisation of soil biological and chemical properties with depth, and to determine the main drivers of microbial community response to tillage. We hypothesised that soil microbiological responses would depend on tillage depth, observed by a homogenisation of microbial community composition within the tilled zone. Tillage treatments were mouldboard plough and disc harrow, impacting soil to ∼20 and ∼10 cm depth, respectively. These treatments were compared to a no-tillage treatment and two control treatments, both permanent pasture and permanent fallow. Bacterial and fungal communities collected from the site were not impacted by the spatial location of sampling across the study area but were affected by physicochemical changes associated with tillage induced soil homogenisation and plant presence. Tillage treatment effects on both species richness and composition were more evident for bacterial communities than fungal communities, and were greater at depths <15 cm. Homogenisation of soil and changing land management appears to redistribute both microbiota and nutrients deeper in the soil profile while consequences for soil biogeochemical functioning remain poorly understood. creator: Craig Anderson creator: Mike Beare creator: Hannah L. Buckley creator: Gavin Lear uri: https://doi.org/10.7717/peerj.3930 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Anderson et al. title: How to normalize metatranscriptomic count data for differential expression analysis link: https://peerj.com/articles/3859 last-modified: 2017-10-17 description: BackgroundDifferential expression analysis on the basis of RNA-Seq count data has become a standard tool in transcriptomics. Several studies have shown that prior normalization of the data is crucial for a reliable detection of transcriptional differences. Until now it has not been clear whether and how the transcriptomic approach can be used for differential expression analysis in metatranscriptomics.MethodsWe propose a model for differential expression in metatranscriptomics that explicitly accounts for variations in the taxonomic composition of transcripts across different samples. As a main consequence the correct normalization of metatranscriptomic count data under this model requires the taxonomic separation of the data into organism-specific bins. Then the taxon-specific scaling of organism profiles yields a valid normalization and allows us to recombine the scaled profiles into a metatranscriptomic count matrix. This matrix can then be analyzed with statistical tools for transcriptomic count data. For taxon-specific scaling and recombination of scaled counts we provide a simple R script.ResultsWhen applying transcriptomic tools for differential expression analysis directly to metatranscriptomic data with an organism-independent (global) scaling of counts the resulting differences may be difficult to interpret. The differences may correspond to changing functional profiles of the contributing organisms but may also result from a variation of taxonomic abundances. Taxon-specific scaling eliminates this variation and therefore the resulting differences actually reflect a different behavior of organisms under changing conditions. In simulation studies we show that the divergence between results from global and taxon-specific scaling can be drastic. In particular, the variation of organism abundances can imply a considerable increase of significant differences with global scaling. Also, on real metatranscriptomic data, the predictions from taxon-specific and global scaling can differ widely. Our studies indicate that in real data applications performed with global scaling it might be impossible to distinguish between differential expression in terms of transcriptomic changes and differential composition in terms of changing taxonomic proportions.ConclusionsAs in transcriptomics, a proper normalization of count data is also essential for differential expression analysis in metatranscriptomics. Our model implies a taxon-specific scaling of counts for normalization of the data. The application of taxon-specific scaling consequently removes taxonomic composition variations from functional profiles and therefore provides a clear interpretation of the observed functional differences. creator: Heiner Klingenberg creator: Peter Meinicke uri: https://doi.org/10.7717/peerj.3859 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Klingenberg and Meinicke title: Exploring the psychological health of emergency dispatch centre operatives: a systematic review and narrative synthesis link: https://peerj.com/articles/3735 last-modified: 2017-10-17 description: BackgroundThe study objective was to investigate and synthesize available evidence relating to the psychological health of Emergency Dispatch Centre (EDC) operatives, and to identify key stressors experienced by EDC operatives.MethodsEight electronic databases (Embase, PubMed, Medline, CINAHL, PsycInfo, PsycArticles, The Psychology and Behavioural Sciences Collection, and Google Scholar) were searched. All study designs were included, and no date limits were set. Studies were included if they were published in English, and explored the psychological health of any EDC operatives, across fire, police, and emergency medical services. Studies were excluded if they related solely to other emergency workers, such as police officers or paramedics. Methodological quality of included studies was assessed using checklists adapted from the Critical Appraisal Skills Programme. A narrative synthesis was conducted, using thematic analysis.ResultsA total of 16 articles were included in the review. Two overarching themes were identified during the narrative synthesis: ‘Organisational and Operational Factors’ and ‘Interactions with Others’. Stressors identified included being exposed to traumatic calls, lacking control over high workload, and working in under-resourced and pressured environments. Lack of support from management and providing an emotionally demanding service were additional sources of stress. Peer support and social support from friends and family were helpful in managing work-related stress.DiscussionEDC operatives experience stress as a result of their work, which appears to be related to negative psychological health outcomes. Future research should explore the long-term effects of this stress, and the potential for workplace interventions to alleviate the negative impacts on psychological health.PROSPERO Registration NumberCRD42014010806. creator: Sarah E. Golding creator: Claire Horsfield creator: Annette Davies creator: Bernadette Egan creator: Martyn Jones creator: Mary Raleigh creator: Patricia Schofield creator: Allison Squires creator: Kath Start creator: Tom Quinn creator: Mark Cropley uri: https://doi.org/10.7717/peerj.3735 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Golding et al. title: Microbial community diversity patterns are related to physical and chemical differences among temperate lakes near Beaver Island, MI link: https://peerj.com/articles/3937 last-modified: 2017-10-16 description: Lakes are dynamic and complex ecosystems that can be influenced by physical, chemical, and biological processes. Additionally, individual lakes are often chemically and physically distinct, even within the same geographic region. Here we show that differences in physicochemical conditions among freshwater lakes located on (and around) the same island, as well as within the water column of each lake, are significantly related to aquatic microbial community diversity. Water samples were collected over time from the surface and bottom-water within four freshwater lakes located around Beaver Island, MI within the Laurentian Great Lakes region. Three of the sampled lakes experienced seasonal lake mixing events, impacting either O2, pH, temperature, or a combination of the three. Microbial community alpha and beta diversity were assessed and individual microbial taxa were identified via high-throughput sequencing of the 16S rRNA gene. Results demonstrated that physical and chemical variability (temperature, dissolved oxygen, and pH) were significantly related to divergence in the beta diversity of surface and bottom-water microbial communities. Despite its correlation to microbial community structure in unconstrained analyses, constrained analyses demonstrated that dissolved organic carbon (DOC) concentration was not strongly related to microbial community structure among or within lakes. Additionally, several taxa were correlated (either positively or negatively) to environmental variables, which could be related to aerobic and anaerobic metabolisms. This study highlights the measurable relationships between environmental conditions and microbial communities within freshwater temperate lakes around the same island. creator: Miranda H. Hengy creator: Dean J. Horton creator: Donald G. Uzarski creator: Deric R. Learman uri: https://doi.org/10.7717/peerj.3937 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Hengy et al. title: Tolerance: the forgotten child of plant resistance link: https://peerj.com/articles/3934 last-modified: 2017-10-16 description: Plant resistance against insect herbivory has greatly focused on antibiosis, whereby the plant has a deleterious effect on the herbivore, and antixenosis, whereby the plant is able to direct the herbivore away from it. Although these two types of resistance may reduce injury and yield loss, they can produce selection pressures on insect herbivores that lead to pest resistance. Tolerance, on the other hand, is a more sustainable pest management strategy because it involves only a plant response and therefore does not cause evolution of resistance in target pest populations. Despite its attractive attributes, tolerance has been poorly studied and understood. In this critical, interpretive review, we discuss tolerance to insect herbivory and the biological and socioeconomic factors that have limited its use in plant resistance and integrated pest management. First, tolerance is difficult to identify, and the mechanisms conferring it are poorly understood. Second, the genetics of tolerance are mostly unknown. Third, several obstacles hinder the establishment of high-throughput phenotyping methods for large-scale screening of tolerance. Fourth, tolerance has received little attention from entomologists because, for most, their primary interest, research training, and funding opportunities are in mechanisms which affect pest biology, not plant biology. Fifth, the efforts of plant resistance are directed at controlling pest populations rather than managing plant stress. We conclude this paper by discussing future research and development activities. creator: Robert K.D. Peterson creator: Andrea C. Varella creator: Leon G. Higley uri: https://doi.org/10.7717/peerj.3934 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Peterson et al. title: L1 and L2 reading skills in Dutch adolescents with a familial risk of dyslexia link: https://peerj.com/articles/3895 last-modified: 2017-10-16 description: BackgroundThe present study investigated differences in reading and spelling outcomes in Dutch and English as a second language (ESL) in adolescents with a high familial risk of dyslexia, of whom some have developed dyslexia (HRDys) while others have not (HRnonDys), in comparison to a low familial risk control group without dyslexia (LRnonDys). This allowed us to investigate the persistence of dyslexia in the first language (L1) and the effect of dyslexia on the second language (L2), which has, in this case, a lower orthographic transparency. Furthermore, the inclusion of the HRnonDys group allowed us to investigate the continuity of the familial risk of dyslexia, as previous studies observed that the HRnonDys group often scores in between the HRDys and LRnonDys group, and whether these readers without reading deficits in Dutch, have more reading difficulties in ESL.MethodsThe data of three groups of adolescents were analyzed; 27 LRnonDys, 25 HRdys 25 HRnonDys. The mean age was 14;1 years; months, and 37 were male. All were native speakers of Dutch, attended regular secondary education (grade 7–10), and were non-native speakers of English. Using MANOVA the groups were compared on Dutch and English word reading fluency (WRF), spelling and vocabulary, Dutch pseudoword and loanword reading fluency, phonological awareness (PA), rapid automatized naming (RAN), and verbal short term and working memory. A repeated measures ANOVA was used to compare English and Dutch WRF, spelling and vocabulary directly within the three groups.ResultsThe analyses revealed that the HRDys group had a deficit in both reading and spelling in Dutch and ESL. They also performed poorer than the LRnonDys group on all other measures. Effect sizes were especially large for pseudoword reading and the reaction times during the PA task. The HRnonDys group scored generally poorer than the LRnonDys group but this difference was only significant for Dutch pseudoword reading, PA reaction times and verbal short term memory. In general the HRDys and HRnonDys group scored similar in Dutch and English, except for English WRF where the HRDys group scored slightly better than expected based on their Dutch WRF.DiscussionThere was a high persistence of dyslexia. Adolescents with dyslexia had large impairments in reading and spelling, and reading related measures, both in Dutch and ESL. Despite high inter-individual differences, an overall three-step pattern was observed. Adolescents in the HRnonDys group scored in between the HRDys and LRnonDys group, supporting the polygenetic origin of dyslexia and the continuity of the familial risk of dyslexia. The lower orthographic transparency did not have a negative effect on L2 reading, spelling and vocabulary, both in the HRnonDys and HRDys group. The latter group performed slightly better than expected in L2, which may be a result of the massive exposure to English and high motivation to use English by adolescents. creator: Ellie R.H. van Setten creator: Wim Tops creator: Britt E. Hakvoort creator: Aryan van der Leij creator: Natasha M. Maurits creator: Ben A.M. Maassen uri: https://doi.org/10.7717/peerj.3895 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 van Setten et al. title: Investigating the level of agreement of two positioning protocols when using dual energy X-ray absorptiometry in the assessment of body composition link: https://peerj.com/articles/3880 last-modified: 2017-10-16 description: BackgroundDual energy X-ray absorptiometry (DXA) is a commonly used instrument for analysing segmental body composition (BC). The information from the scan guides the clinician in the treatment of conditions such as obesity and can be used to monitor recovery of lean mass following injury. Two commonly used DXA positioning protocols have been identified—the Nana positioning protocol and the National Health and Nutrition Examination Survey (NHANES). Both protocols have been shown to be reliable. However, only one study has assessed the level of agreement between the protocols and ascertained the participants’ preference of protocol based upon comfort. Given the paucity of research in the field and the growing use of DXA in both healthy and pathological populations further research determining the most appropriate positioning protocol is warranted. Therefore, the aims of this study were to assess the level of agreement between results from the NHANES protocol and Nana protocol, and the participants’ preference of protocol based on comfort.MethodsThirty healthy participants (15 males, 15 females, aged 23–59 years) volunteered to participate in this study. These participants underwent two whole body DXA scans in a single morning (Nana positioning protocol and NHANES positioning protocol), in a randomised order. Each participant attended for scanning wearing minimal clothing and having fasted overnight, refrained from exercise in the past 24 h and voided their bladders. Level of agreement, comparing NAHNES to Nana protocol was assessed using an intra-class correlation coefficient (ICC), concordance correlation coefficient (CCC) and percentage change in mean. Limit of agreement comparing the two protocols were assessed using plots, mean difference and confidence limits. Participants were asked to indicate the protocol they found most comfortable.ResultsWhen assessing level of agreement between protocols both the ICC and CCC scores were very high and ranged from 0.987 to 0.997 for whole body composition, indicating excellent agreement between the Nana and NHANES protocols. Regional analysis (arms, legs, trunk) ICC scores, ranged between 0.966 and 0.996, CCC ranged between 0.964 and 0.997, change in mean percentage ranged between −0.58% and 0.37% which indicated a very high level of agreement. Limit of agreement analysis using mean difference ranged between −0.223 and 0.686 kg and 95% CL produced results ranging between −1.262 kg and 1.630 kg. The majority (80%) of participants found the NHANES positioning protocol more comfortable.DiscussionThis study reveals a strong level of agreement as illustrated by high ICC’s and CCC’s between the positioning protocols, however systematic bias within limit of agreement plot and a large difference in 95% confidence limits indicates that the protocols should not be interchanged when assessing an individual. The NHANES protocol affords greater participant comfort. creator: Flinn Shiel creator: Carl Persson creator: Vini Simas creator: James Furness creator: Mike Climstein creator: Ben Schram uri: https://doi.org/10.7717/peerj.3880 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Shiel et al. title: Tumor-infiltrating CD8+ lymphocytes predict different clinical outcomes in organ- and non-organ-confined urothelial carcinoma of the bladder following radical cystectomy link: https://peerj.com/articles/3921 last-modified: 2017-10-13 description: Tumor-infiltrating lymphocytes (TILs) are associated with better clinical outcomes in many tumors. TILs represent a cell-mediated immune response against the carcinoma. CD8+ TILs are a crucial component of cell-mediated immunity. The significance of CD8+ TILs has not been reported respectively in organ- and non-organ-confined urothelial carcinoma (UC) of the bladder. We explored the prognostic value of CD8+ TILs in the two groups. The presence of CD8+ TILs was assessed by immunohistochemical staining of whole tissue sections from 75 organ and 51 non-organ-confined disease patients with long-term follow-up, and its correlation with clinicopathological features and overall survival (OS) was determined. The CD8+ TIL immunohistochemical staining score was 0 (<1%), 1 (≥1%), 2 (≥5%), or 3 (≥10%) based on the percentage of positively stained cells out of total cells. A patient was considered CD8 negative if the score was 0. There were no associations between CD8+ TILs and age, sex, nuclear grade, and adjuvant or neoadjuvant chemotherapy in organ- and non-organ-confined disease. The presence of CD8+ TILs was seen more frequently in pTa-1 than pT2 stage (p = 0.033) in organ-confined disease. No associations between CD8+ TILs and pT stage, pN stage were found in non-organ-confined disease. CD8+ TILs were associated with better OS (log-rank test, P = 0.036) in non-organ-confined disease, but with poorer OS (log-rank test, P = 0.040) in organ-confined disease by the Kaplan–Meier method. In multivariate analysis, CD8+ TILs were an independent favorable prognostic factor in non-organ-confined disease, but were an independent unfavorable prognostic factor in organ-confined disease. These results suggest that CD8+ TILs have clinically significant anti-tumor activity in non-organ-confined disease, but may have pro-tumor activity in organ-confined disease. Therefore, we should be cautious if CD8+ TILs are aimed to be exploited in the treatment of bladder cancer. creator: Shiqiang Zhang creator: Jun Wang creator: Xinyu Zhang creator: Fangjian Zhou uri: https://doi.org/10.7717/peerj.3921 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Zhang et al. title: A retrospective study: does upper airway morphology differ between non-positional and positional obstructive sleep apnea? link: https://peerj.com/articles/3918 last-modified: 2017-10-13 description: ObjectiveThe objective of this study was to explore the differences in upper airway morphology between positional (POSA) and non-positional (NPOSA) obstructive sleep apnea.MethodsThis retrospective study enrolled 75 patients (45 NPOSA and 30 POSA) who underwent polysomnography (PSG) and computed tomography (CT). The differences in, and relationships of, the PSG values and CT data between POSA and NPOSA were analyzed.ResultsSignificant (p < 0.05) differences between the two groups were found in the apnea/hypopnea index (AHI), lateral-AHI (L-AHI), soft palate length (SPL), cross-sectional palatopharyngeal area, and the coronal diameter (CD) of the palatopharyngeal area at the narrowest part of the glossopharynx, which were all higher in POSA, except for SPL, AHI, and L-AHI. L-AHI was correlated with the cross-sectional area (r =  − 0.306, p = 0.008) and CD (r =  − 0.398, p < 0.001) of the palatopharyngeal area, the cross-sectional area (r =  − 0.241, p = 0.038) and CD (r =  − 0.297, p = 0.010) of the narrowest level of the glossopharynx, the CD of the glossopharynx (r = 0.284, p = 0.013), body mass index (BMI, r = 0.273, p = 0.018), SPL (r = 0.284, p = 0.014), and vallecula-tip of tongue (r = 0.250, p = 0.030). The SPL and CD at the narrowest part of the glossopharynx were included in the simplified screening model.ConclusionsIn NPOSA, the CD of the upper airway was smaller, and the soft palate was longer, than in POSA. These differences may play significant roles in explaining the main differences between NPOSA and POSA. creator: Xiao Jiao creator: Jianyin Zou creator: Suru Liu creator: Jian Guan creator: Hongliang Yi creator: Shankai Yin uri: https://doi.org/10.7717/peerj.3918 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Jiao et al. title: Neurodynamic mobilization and foam rolling improved delayed-onset muscle soreness in a healthy adult population: a randomized controlled clinical trial link: https://peerj.com/articles/3908 last-modified: 2017-10-13 description: ObjectivesCompare the immediate effects of a Neurodynamic Mobilization (NM) treatment or foam roller (FR) treatment after DOMS.DesignDouble blind randomised clinical trial.SettingThe participants performed 100 drop jumps (5 sets of 20 repetitions, separated by 2 min rests) from a 0.5-m high box in a University biomechanics laboratory to induce muscle soreness. The participants were randomly assigned in a counter-balanced fashion to either a FR or NM treatment group.ParticipantsThirty-two healthy subjects (21 males and 11 females, mean age 22.6 ± 2.2 years) were randomly assigned into the NM group (n = 16) or the FR group (n = 16).Main Outcome MeasuresThe numeric pain rating scale (NPRS; 0–10), isometric leg strength with dynamometry, surface electromyography at maximum voluntary isometric contraction (MVIC) and muscle peak activation (MPA) upon landing after a test jump were measured at baseline, 48 h after baseline before treatment, and immediately after treatment.ResultsBoth groups showed significant reduction in NPRS scores after treatment (NM: 59%, p < .01; FR: 45%, p < .01), but no difference was found between them (p > .05). The percentage change improvement in the MVIC for the rectus femoris was the only significant difference between the groups (p < 0.05) at post-treatment. After treatment, only the FR group had a statistically significant improvement (p < 0.01) in strength compared to pre-treatment.ConclusionOur results illustrate that both treatments are effective in reducing pain perception after DOMS whereas only FR application showed differences for the MVIC in the rectus femoris and strength. creator: Blanca Romero-Moraleda creator: Roy La Touche creator: Sergio Lerma-Lara creator: Raúl Ferrer-Peña creator: Víctor Paredes creator: Ana Belén Peinado creator: Daniel Muñoz-García uri: https://doi.org/10.7717/peerj.3908 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Romero-Moraleda et al. title: Multigene phylogeny of the scyphozoan jellyfish family Pelagiidae reveals that the common U.S. Atlantic sea nettle comprises two distinct species (Chrysaora quinquecirrha and C. chesapeakei) link: https://peerj.com/articles/3863 last-modified: 2017-10-13 description: BackgroundSpecies of the scyphozoan family Pelagiidae (e.g., Pelagia noctiluca, Chrysaora quinquecirrha) are well-known for impacting fisheries, aquaculture, and tourism, especially for the painful sting they can inflict on swimmers. However, historical taxonomic uncertainty at the genus (e.g., new genus Mawia) and species levels hinders progress in studying their biology and evolutionary adaptations that make them nuisance species, as well as ability to understand and/or mitigate their ecological and economic impacts.MethodsWe collected nuclear (28S rDNA) and mitochondrial (cytochrome c oxidase I and 16S rDNA) sequence data from individuals of all four pelagiid genera, including 11 of 13 currently recognized species of Chrysaora. To examine species boundaries in the U.S. Atlantic sea nettle Chrysaora quinquecirrha, specimens were included from its entire range along the U.S. Atlantic and Gulf of Mexico coasts, with representatives also examined morphologically (macromorphology and cnidome).ResultsPhylogenetic analyses show that the genus Chrysaora is paraphyletic with respect to other pelagiid genera. In combined analyses, Mawia, sampled from the coast of Senegal, is most closely related to Sanderia malayensis, and Pelagia forms a close relationship to a clade of Pacific Chrysaora species (Chrysaora achlyos, Chrysaora colorata, Chrysaora fuscescens, and Chrysaora melanaster). Chrysaora quinquecirrha is polyphyletic, with one clade from the U.S. coastal Atlantic and another in U.S. Atlantic estuaries and Gulf of Mexico. These genetic differences are reflected in morphology, e.g., tentacle and lappet number, oral arm length, and nematocyst dimensions. Caribbean sea nettles (Jamaica and Panama) are genetically similar to the U.S. Atlantic estuaries and Gulf of Mexico clade of Chrysaora quinquecirrha.DiscussionOur phylogenetic hypothesis for Pelagiidae contradicts current generic definitions, revealing major disagreements between DNA-based and morphology-based phylogenies. A paraphyletic Chrysaora raises systematic questions at the genus level for Pelagiidae; accepting the validity of the recently erected genus Mawia, as well as past genera, will require the creation of additional pelagiid genera. Historical review of the species-delineating genetic and morphological differences indicates that Chrysaora quinquecirrha Desor 1848 applies to the U.S. Coastal Atlantic Chrysaora species (U.S. Atlantic sea nettle), while the name C. chesapeakei Papenfuss 1936 applies to the U.S. Atlantic estuarine and Gulf of Mexico Chrysaora species (Atlantic bay nettle). We provide a detailed redescription, with designation of a neotype for Chrysaora chesapeakei, and clarify the description of Chrysaora quinquecirrha. Since Caribbean Chrysaora are genetically similar to Chrysaora chesapeakei, we provisionally term them Chrysaora c.f. chesapeakei. The presence of Mawia benovici off the coast of Western Africa provides a potential source region for jellyfish introduced into the Adriatic Sea in 2013. creator: Keith M. Bayha creator: Allen G. Collins creator: Patrick M. Gaffney uri: https://doi.org/10.7717/peerj.3863 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Bayha et al. title: Mysterious inhibitory cell regulator investigated and found likely to be secretogranin II related link: https://peerj.com/articles/3833 last-modified: 2017-10-13 description: In the context of a hunt for a postulated hormone that is tissue-mass inhibiting and reproductively associated, there is described probable relatedness to a granin protein. A 7–8 kDa polypeptide candidate (gels/MS) appeared in a bioassay-guided fractionation campaign involving sheep plasma. An N-terminal sequence of 14 amino acids was obtained for the polypeptide by Edman degradation. Bioinformatics and molecular biology failed to illuminate any ovine or non-ovine protein which might relate to this sequence. The N-terminal sequence was synthesized as the 14mer EPL001 peptide and surprisingly found to be inhibitory in an assay in vivo of compensatory renal growth in the rat and modulatory of nematode fecundity, in line with the inhibitory hormone hypothesis. Antibodies were raised to EPL001 and their deployment upheld the hypothesis that the EPL001 amino acid sequence is meaningful and relevant, notwithstanding bioinformatic obscurity. Immunohistochemistry (IHC) in sheep, rodents and humans yielded staining of seeming endocrine relevance (e.g. hypothalamus, gonads and neuroendocrine cells in diverse tissues), with apparent upregulation in certain human tumours (e.g. pheochromocytoma). Discrete IHC staining in Drosophila melanogaster embryo brain was seen in glia and in neuroendocrine cells, with staining likely in the corpus cardiacum. The search for the endogenous antigen involved immunoprecipitation (IP) followed by liquid chromatography and mass spectrometry (LC–MS). Feedstocks were PC12 conditioned medium and aqueous extract of rat hypothalamus—both of which had anti-proliferative and pro-apoptotic effects in an assay in vitro involving rat bone marrow cells, which inhibition was subject to prior immunodepletion with an anti-EPL001 antibody—together with fruit fly embryo material. It is concluded that the mammalian antigen is likely secretogranin II (SgII) related. The originally seen 7–8 kDa polypeptide is suggested to be a new proteoform of secretogranin II of ∼70 residues, SgII-70, with the anti-EPL001 antibody seeing a discontinuous epitope. The fly antigen is probably Q9W2X8 (UniProt), an uncharacterised protein newly disclosed as a granin and provisionally dubbed macrogranin I (MgI). SgII and Q9W2X8 merit further investigation in the context of tissue-mass inhibition. creator: John E. Hart creator: Iain J. Clarke creator: Gail P. Risbridger creator: Ben Ferneyhough creator: Mónica Vega-Hernández uri: https://doi.org/10.7717/peerj.3833 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Hart et al. title: The intervals method: a new approach to analyse finite element outputs using multivariate statistics link: https://peerj.com/articles/3793 last-modified: 2017-10-13 description: BackgroundIn this paper, we propose a new method, named the intervals’ method, to analyse data from finite element models in a comparative multivariate framework. As a case study, several armadillo mandibles are analysed, showing that the proposed method is useful to distinguish and characterise biomechanical differences related to diet/ecomorphology.MethodsThe intervals’ method consists of generating a set of variables, each one defined by an interval of stress values. Each variable is expressed as a percentage of the area of the mandible occupied by those stress values. Afterwards these newly generated variables can be analysed using multivariate methods.ResultsApplying this novel method to the biological case study of whether armadillo mandibles differ according to dietary groups, we show that the intervals’ method is a powerful tool to characterize biomechanical performance and how this relates to different diets. This allows us to positively discriminate between specialist and generalist species.DiscussionWe show that the proposed approach is a useful methodology not affected by the characteristics of the finite element mesh. Additionally, the positive discriminating results obtained when analysing a difficult case study suggest that the proposed method could be a very useful tool for comparative studies in finite element analysis using multivariate statistical approaches. creator: Jordi Marcé-Nogué creator: Soledad De Esteban-Trivigno creator: Thomas A. Püschel creator: Josep Fortuny uri: https://doi.org/10.7717/peerj.3793 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Marcé-Nogué et al. title: Sediment microbial taxonomic and functional diversity in a natural salinity gradient challenge Remane’s “species minimum” concept link: https://peerj.com/articles/3687 last-modified: 2017-10-13 description: Several models have been developed for the description of diversity in estuaries and other brackish habitats, with the most recognized being Remane’s Artenminimum (“species minimum”) concept. It was developed for the Baltic Sea, one of the world’s largest semi-enclosed brackish water body with a unique permanent salinity gradient, and it argues that taxonomic diversity of macrobenthic organisms is lowest within the horohalinicum (5 to 8 psu). The aim of the present study was to investigate the relationship between salinity and sediment microbial diversity at a freshwater-marine transect in Amvrakikos Gulf (Ionian Sea, Western Greece) and assess whether species composition and community function follow a generalized concept such as Remane’s. DNA was extracted from sediment samples from six stations along the aforementioned transect and sequenced for the 16S rRNA gene using high-throughput sequencing. The metabolic functions of the OTUs were predicted and the most abundant metabolic pathways were extracted. Key abiotic variables, i.e., salinity, temperature, chlorophyll-a and oxygen concentration etc., were measured and their relation with diversity and functional patterns was explored. Microbial communities were found to differ in the three habitats examined (river, lagoon and sea) with certain taxonomic groups being more abundant in the freshwater and less in the marine environment, and vice versa. Salinity was the environmental factor with the highest correlation to the microbial community pattern, while oxygen concentration was highly correlated to the metabolic functional pattern. The total number of OTUs showed a negative relationship with increasing salinity, thus the sediment microbial OTUs in this study area do not follow Remane’s concept. creator: Christina Pavloudi creator: Jon B. Kristoffersen creator: Anastasis Oulas creator: Marleen De Troch creator: Christos Arvanitidis uri: https://doi.org/10.7717/peerj.3687 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Pavloudi et al. title: Evaluation of plasma cytokines in patients with cocaine use disorders in abstinence identifies transforming growth factor alpha (TGFα) as a potential biomarker of consumption and dual diagnosis link: https://peerj.com/articles/3926 last-modified: 2017-10-12 description: BackgroundCocaine use disorder (CUD) is a complex health condition, especially when it is accompanied by comorbid psychiatric disorders (dual diagnosis). Dual diagnosis is associated with difficulties in the stratification and treatment of patients. One of the major challenges in clinical practice of addiction psychiatry is the lack of objective biological markers that indicate the degree of consumption, severity of addiction, level of toxicity and response to treatment in patients with CUD. These potential biomarkers would be fundamental players in the diagnosis, stratification, prognosis and therapeutic orientation in addiction. Due to growing evidence of the involvement of the immune system in addiction and psychiatric disorders, we tested the hypothesis that patients with CUD in abstinence might have altered circulating levels of signaling proteins related to systemic inflammation.MethodsThe study was designed as a cross-sectional study of CUD treatment-seeking patients. These patients were recruited from outpatient programs in the province of Malaga (Spain). The study was performed with a total of 160 white Caucasian subjects, who were divided into the following groups: patients diagnosed with CUD in abstinence (N = 79, cocaine group) and matched control subjects (N = 81, control group). Participants were clinically evaluated with the diagnostic interview PRISM according to the DSM-IV-TR, and blood samples were collected for the determination of chemokine C-C motif ligand 11 (CCL11, eotaxin-1), interferon gamma (IFNγ), interleukin-4 (IL-4), interleukin-8 (IL-8), interleukin-17α (IL-17α), macrophage inflammatory protein 1α (MIP-1α) and transforming growth factor α (TGFα) levels in the plasma. Clinical and biochemical data were analyzed in order to find relationships between variables.ResultsWhile 57% of patients with CUD were diagnosed with dual diagnosis, approximately 73% of patients had other substance use disorders. Cocaine patients displayed greater cocaine symptom severity when they were diagnosed with psychiatric comorbidity. Regarding inflammatory factors, we observed significantly lower plasma levels of IL-17α (p < 0.001), MIP-1α (p < 0.001) and TGFα (p < 0.05) in the cocaine group compared with the levels in the control group. Finally, there was a significant primary effect of dual diagnosis on the plasma concentrations of TGFα (p < 0.05) in the cocaine group, and these levels were lower in patients with dual diagnosesDiscussionIL-17α, MIP-1α and TGFα levels are different between the cocaine and control groups, and TGFα levels facilitate the identification of patients with dual diagnosis. Because TGFα reduction is associated with enhanced responses to cocaine in preclinical models, we propose TGFα as a potential biomarker of complex CUD in humans. creator: Rosa Maza-Quiroga creator: Nuria García-Marchena creator: Pablo Romero-Sanchiz creator: Vicente Barrios creator: María Pedraz creator: Antonia Serrano creator: Raquel Nogueira-Arjona creator: Juan Jesus Ruiz creator: Maribel Soria creator: Rafael Campos creator: Julie Ann Chowen creator: Jesus Argente creator: Marta Torrens creator: Meritxell López-Gallardo creator: Eva María Marco creator: Fernando Rodríguez de Fonseca creator: Francisco Javier Pavón creator: Pedro Araos uri: https://doi.org/10.7717/peerj.3926 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Maza-Quiroga et al. title: External validation of cut-off points for foveal thickness taking into account the intraretinal fluid using optical coherence tomography to diagnose diabetic macular oedema link: https://peerj.com/articles/3922 last-modified: 2017-10-12 description: BackgroundIn late 2015, cut-off points were published for foveal thickness to diagnose diabetic macular oedema taking into account the presence of intraretinal fluid using optical coherence tomography (OCT) in primary care patients (90 µm in the presence of intraretinal fluid and 310 µm otherwise).MethodsThis cross-sectional observational study was carried out on 134 eyes of diabetic patients treated in specialised ophthalmology services in a Spanish region in 2012–2013, to externally validate the aforementioned cut-off points. The main variable (Clinical Standard) was the diagnosis of macular oedema through indirect ophthalmoscopy and posterior segment slit-lamp biomicroscopy. As validation variables, both the foveal thickness and the presence of intraretinal fluid obtained by OCT were used. Validation was performed using bootstrapping by calculating the area under the ROC curve (AUC), sensitivity, specificity, positive likelihood ratio (PLR) and negative likelihood ratio (NLR).ResultsForty-one eyes presented diabetic macular oedema (30.6%). The bootstrapping validation parameters were: AUC, 0.88; sensitivity, 0.75; specificity, 0.95; PLR, 14.31; NLR, 0.26. These values were very similar to those of the original publication.ConclusionWe have externally validated in specialised care patients the cut-off points published for the diagnosis of diabetic macular oedema. We suggest that others carry out validation studies in their communities. creator: Carmen Hernández-Martínez creator: Antonio Palazón-Bru creator: Cesar Azrak creator: Aída Navarro-Navarro creator: Manuel Vicente Baeza-Díaz creator: José Juan Martínez-Toldos creator: Vicente Francisco Gil-Guillén uri: https://doi.org/10.7717/peerj.3922 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Hernández-Martínez et al. title: The complete chloroplast genome sequence of strawberry (Fragaria  × ananassa Duch.) and comparison with related species of Rosaceae link: https://peerj.com/articles/3919 last-modified: 2017-10-12 description: Compared with other members of the family Rosaceae, the chloroplast genomes of Fragaria species exhibit low variation, and this situation has limited phylogenetic analyses; thus, complete chloroplast genome sequencing of Fragaria species is needed. In this study, we sequenced the complete chloroplast genome of F. × ananassa ‘Benihoppe’ using the Illumina HiSeq 2500-PE150 platform and then performed a combination of de novo assembly and reference-guided mapping of contigs to generate complete chloroplast genome sequences. The chloroplast genome exhibits a typical quadripartite structure with a pair of inverted repeats (IRs, 25,936 bp) separated by large (LSC, 85,531 bp) and small (SSC, 18,146 bp) single-copy (SC) regions. The length of the F. × ananassa ‘Benihoppe’ chloroplast genome is 155,549 bp, representing the smallest Fragaria chloroplast genome observed to date. The genome encodes 112 unique genes, comprising 78 protein-coding genes, 30 tRNA genes and four rRNA genes. Comparative analysis of the overall nucleotide sequence identity among ten complete chloroplast genomes confirmed that for both coding and non-coding regions in Rosaceae, SC regions exhibit higher sequence variation than IRs. The Ka/Ks ratio of most genes was less than 1, suggesting that most genes are under purifying selection. Moreover, the mVISTA results also showed a high degree of conservation in genome structure, gene order and gene content in Fragaria, particularly among three octoploid strawberries which were F. × ananassa ‘Benihoppe’, F. chiloensis (GP33) and F. virginiana (O477). However, when the sequences of the coding and non-coding regions of F. × ananassa ‘Benihoppe’ were compared in detail with those of F. chiloensis (GP33) and F. virginiana (O477), a number of SNPs and InDels were revealed by MEGA 7. Six non-coding regions (trnK-matK, trnS-trnG, atpF-atpH, trnC-petN, trnT-psbD and trnP-psaJ) with a percentage of variable sites greater than 1% and no less than five parsimony-informative sites were identified and may be useful for phylogenetic analysis of the genus Fragaria. creator: Hui Cheng creator: Jinfeng Li creator: Hong Zhang creator: Binhua Cai creator: Zhihong Gao creator: Yushan Qiao creator: Lin Mi uri: https://doi.org/10.7717/peerj.3919 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Cheng et al. title: Mouse spermatozoa with higher fertilization rates have thinner nuclei link: https://peerj.com/articles/3913 last-modified: 2017-10-12 description: BackgroundAlthough spermatozoa with normal morphology are assumed to have uniform fertilization ability, recent data show that even normal spermatozoa have considerable variation in their head shape which is associated with differences in fertilization ability. Appropriate quantitative indicators for good sperm morphology, however, remain unidentified.MethodsTherefore, in an effort to identify such an indicator, we compared the nuclear contour of normal mouse spermatozoa by quantitative multivariate analysis using elliptic Fourier descriptors combined with principal component analysis. The spermatozoa were obtained from different strains and collection sites which have been shown to be associated with different fertilization abilities.ResultsWe found that the head was 5.7% thinner in spermatozoa from the B6D2F1 (BDF1) strain, known to have a higher fertilization rate, than in those from the C57BL/6N (B6N) strain, which has a lower fertilization rate. Moreover, zona-penetrated spermatozoa in the perivitelline space consistently had 5.4% thinner heads than those isolated from the epididymis before ejaculation. The aspect ratio, which represents the sperm head thinness, uniquely distinguished these sperm populations, confirming its validity as a morphological indicator.DiscussionBecause aspect ratio has also been shown to characterize human spermatozoa, this unique morphometric indicator might be applicable to compare normal spermatozoa among multiple patients, which will greatly facilitate and enhance current reproductive technologies. creator: Daisuke Mashiko creator: Masahito Ikawa creator: Koichi Fujimoto uri: https://doi.org/10.7717/peerj.3913 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Mashiko et al. title: Cellobiohydrolase B of Aspergillus niger over-expressed in Pichia pastoris stimulates hydrolysis of oil palm empty fruit bunches link: https://peerj.com/articles/3909 last-modified: 2017-10-12 description: BackgroundAspergillus niger, along with many other lignocellulolytic fungi, has been widely used as a commercial workhorse for cellulase production. A fungal cellulase system generally includes three major classes of enzymes i.e., β-glucosidases, endoglucanases and cellobiohydrolases. Cellobiohydrolases (CBH) are vital to the degradation of crystalline cellulose present in lignocellulosic biomass. However, A. niger naturally secretes low levels of CBH. Hence, recombinant production of A. niger CBH is desirable to increase CBH production yield and also to allow biochemical characterisation of the recombinant CBH from A. niger.MethodsIn this study, the gene encoding a cellobiohydrolase B (cbhB) from A. niger ATCC 10574 was cloned and expressed in the methylotrophic yeast Pichia pastoris X-33. The recombinant CBHB was purified and characterised to study its biochemical and kinetic characteristics. To evaluate the potential of CBHB in assisting biomass conversion, CBHB was supplemented into a commercial cellulase preparation (Cellic® CTec2) and was used to hydrolyse oil palm empty fruit bunch (OPEFB), one of the most abundant lignocellulosic waste from the palm oil industry. To attain maximum saccharification, enzyme loadings were optimised by response surface methodology and the optimum point was validated experimentally. Hydrolysed OPEFB samples were analysed using attenuated total reflectance FTIR spectroscopy (ATR-FTIR) to screen for any compositional changes upon enzymatic treatment.ResultsRecombinant CBHB was over-expressed as a hyperglycosylated protein attached to N-glycans. CBHB was enzymatically active towards soluble substrates such as 4-methylumbelliferyl-β-D-cellobioside (MUC), p-nitrophenyl-cellobioside (pNPC) and p-nitrophenyl-cellobiotrioside (pNPG3) but was not active towards crystalline substrates like Avicel® and Sigmacell cellulose. Characterisation of purified CBHB using MUC as the model substrate revealed that optimum catalysis occurred at 50 °C and pH 4 but the enzyme was stable between pH 3 to 10 and 30 to 80 °C. Although CBHB on its own was unable to digest crystalline substrates, supplementation of CBHB (0.37%) with Cellic® CTec2 (30%) increased saccharification of OPEFB by 27%. Compositional analyses of the treated OPEFB samples revealed that CBHB supplementation reduced peak intensities of both crystalline cellulose Iα and Iβ in the treated OPEFB samples.DiscussionSince CBHB alone was inactive against crystalline cellulose, these data suggested that it might work synergistically with other components of Cellic® CTec2. CBHB supplements were desirable as they further increased hydrolysis of OPEFB when the performance of Cellic® CTec2 was theoretically capped at an enzyme loading of 34% in this study. Hence, A. niger CBHB was identified as a potential supplementary enzyme for the enzymatic hydrolysis of OPEFB. creator: James Sy-Keen Woon creator: Mukram M. Mackeen creator: Rosli M. Illias creator: Nor M. Mahadi creator: William J. Broughton creator: Abdul Munir Abdul Murad creator: Farah Diba Abu Bakar uri: https://doi.org/10.7717/peerj.3909 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Woon et al. title: Nests of red wood ants (Formica rufa-group) are positively associated with tectonic faults: a double-blind test link: https://peerj.com/articles/3903 last-modified: 2017-10-12 description: Ecological studies often are subjected to unintentional biases, suggesting that improved research designs for hypothesis testing should be used. Double-blind ecological studies are rare but necessary to minimize sampling biases and omission errors, and improve the reliability of research. We used a double-blind design to evaluate associations between nests of red wood ants (Formica rufa, RWA) and the distribution of tectonic faults. We randomly sampled two regions in western Denmark to map the spatial distribution of RWA nests. We then calculated nest proximity to the nearest active tectonic faults. Red wood ant nests were eight times more likely to be found within 60 m of known tectonic faults than were random points in the same region but without nests. This pattern paralleled the directionality of the fault system, with NNE–SSW faults having the strongest associations with RWA nests. The nest locations were collected without knowledge of the spatial distribution of active faults thus we are confident that the results are neither biased nor artefactual. This example highlights the benefits of double-blind designs in reducing sampling biases, testing controversial hypotheses, and increasing the reliability of the conclusions of research. creator: Israel Del Toro creator: Gabriele M. Berberich creator: Relena R. Ribbons creator: Martin B. Berberich creator: Nathan J. Sanders creator: Aaron M. Ellison uri: https://doi.org/10.7717/peerj.3903 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Del Toro et al. title: Seasonal and year-round use of the Kushiro Wetland, Hokkaido, Japan by sika deer (Cervus nippon yesoensis) link: https://peerj.com/articles/3869 last-modified: 2017-10-12 description: The sika deer (Cervus nippon yesoensis) population in the Ramsar-listed Kushiro Wetland has increased in recent years, and the Ministry of the Environment of Japan has decided to take measures to reduce the impact of deer on the ecosystem. However, seasonal movement patterns of the deer (i.e., when and where the deer inhabit the wetland) remain unclear. We examined the seasonal movement patterns of sika deer in the Kushiro Wetland from 2013 to 2015 by analyzing GPS location data for 28 hinds captured at three sites in the wetland. Seasonal movement patterns were quantitatively classified as seasonal migration, mixed, dispersal, nomadic, resident, or atypical, and the degree of wetland utilization for each individual was estimated. The area of overlap for each individual among intra-capture sites and inter-capture sites was calculated for the entire year and for each season. Our results showed that the movement patterns of these deer were classified not only as resident but also as seasonal migration, dispersal, and atypical. Approximately one-third of the individuals moved into and out of the wetland during the year as either seasonal migrants or individuals with atypical movement. Some of the individuals migrated to farmland areas outside the wetland (the farthest being 69.9 km away). Half of the individuals inhabited the wetland all or most of the year, i.e., 81–100% of their annual home range was within the wetland area. Even among individuals captured at the same site, different seasonal movement patterns were identified. The overlap areas of the home ranges of individuals from the same capture sites were larger than those for individuals from different capture sites (e.g., mean of annual home range overlap with intra-capture sites: 47.7% vs. inter-sites: 1.3%). To achieve more effective ecosystem management including deer management in the wetland, management plans should cover inside and outside of the wetland and separate the population into multiple management units to address the different movement patterns and wetland utilization of the population. creator: Hino Takafumi creator: Tatsuya Kamii creator: Takunari Murai creator: Ryoto Yoshida creator: Atsuki Sato creator: Yasuyuki Tachiki creator: Rika Akamatsu creator: Tsuyoshi Yoshida uri: https://doi.org/10.7717/peerj.3869 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Takafumi et al. title: Combining graph and flux-based structures to decipher phenotypic essential metabolites within metabolic networks link: https://peerj.com/articles/3860 last-modified: 2017-10-12 description: BackgroundThe emergence of functions in biological systems is a long-standing issue that can now be addressed at the cell level with the emergence of high throughput technologies for genome sequencing and phenotyping. The reconstruction of complete metabolic networks for various organisms is a key outcome of the analysis of these data, giving access to a global view of cell functioning. The analysis of metabolic networks may be carried out by simply considering the architecture of the reaction network or by taking into account the stoichiometry of reactions. In both approaches, this analysis is generally centered on the outcome of the network and considers all metabolic compounds to be equivalent in this respect. As in the case of genes and reactions, about which the concept of essentiality has been developed, it seems, however, that some metabolites play crucial roles in system responses, due to the cell structure or the internal wiring of the metabolic network.ResultsWe propose a classification of metabolic compounds according to their capacity to influence the activation of targeted functions (generally the growth phenotype) in a cell. We generalize the concept of essentiality to metabolites and introduce the concept of the phenotypic essential metabolite (PEM) which influences the growth phenotype according to sustainability, producibility or optimal-efficiency criteria. We have developed and made available a tool, Conquests, which implements a method combining graph-based and flux-based analysis, two approaches that are usually considered separately. The identification of PEMs is made effective by using a logical programming approach.ConclusionThe exhaustive study of phenotypic essential metabolites in six genome-scale metabolic models suggests that the combination and the comparison of graph, stoichiometry and optimal flux-based criteria allows some features of the metabolic network functionality to be deciphered by focusing on a small number of compounds. By considering the best combination of both graph-based and flux-based techniques, the Conquests python package advocates for a broader use of these compounds both to facilitate network curation and to promote a precise understanding of metabolic phenotype. creator: Julie Laniau creator: Clémence Frioux creator: Jacques Nicolas creator: Caroline Baroukh creator: Maria-Paz Cortes creator: Jeanne Got creator: Camille Trottier creator: Damien Eveillard creator: Anne Siegel uri: https://doi.org/10.7717/peerj.3860 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Laniau et al. title: Is geography an accurate predictor of evolutionary history in the millipede family Xystodesmidae? link: https://peerj.com/articles/3854 last-modified: 2017-10-12 description: For the past several centuries, millipede taxonomists have used the morphology of male copulatory structures (modified legs called gonopods), which are strongly variable and suggestive of species-level differences, as a source to understand taxon relationships. Millipedes in the family Xystodesmidae are blind, dispersal-limited and have narrow habitat requirements. Therefore, geographical proximity may instead be a better predictor of evolutionary relationship than morphology, especially since gonopodal anatomy is extremely divergent and similarities may be masked by evolutionary convergence. Here we provide a phylogenetics-based test of the power of morphological versus geographical character sets for resolving phylogenetic relationships in xystodesmid millipedes. Molecular data from 90 species-group taxa in the family were included in a six-gene phylogenetic analysis to provide the basis for comparing trees generated from these alternative character sets. The molecular phylogeny was compared to topologies representing three hypotheses: (1) a prior classification formulated using morphological and geographical data, (2) hierarchical groupings derived from Euclidean geographical distance, and (3) one based solely on morphological data. Euclidean geographical distance was not found to be a better predictor of evolutionary relationship than the prior classification, the latter of which was the most similar to the molecular topology. However, all three of the alternative topologies were highly divergent (Bayes factor >10) from the molecular topology, with the tree inferred exclusively from morphology being the most divergent. The results of this analysis show that a high degree of morphological convergence from substantial gonopod shape divergence generated spurious phylogenetic relationships. These results indicate the impact that a high degree of morphological homoplasy may have had on prior treatments of the family. Using the results of our phylogenetic analysis, we make several changes to the classification of the family, including transferring the rare state-threatened species Sigmoria whiteheadi Shelley, 1986 to the genus Apheloria Chamberlin, 1921—a relationship not readily apparent based on morphology alone. We show that while gonopod differences are a premier source of taxonomic characters to diagnose species pairwise, the traits should be viewed critically as taxonomic features uniting higher levels. creator: Jackson C. Means creator: Paul E. Marek uri: https://doi.org/10.7717/peerj.3854 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Means and Marek title: Pulmonary transcriptomic responses indicate a dual role of inflammation in pneumonia development and viral clearance during 2009 pandemic influenza infection link: https://peerj.com/articles/3915 last-modified: 2017-10-11 description: BackgroundThe interaction between influenza virus and the host response to infection clearly plays an important role in determining the outcome of infection. While much is known on the participation of inflammation on the pathogenesis of severe A (H1N1) pandemic 09-influenza virus, its role in the course of non-fatal pneumonia has not been fully addressed.MethodsA systems biology approach was used to define gene expression profiles, histology and viral dynamics in the lungs of healthy immune-competent mice with pneumonia caused by a human influenza A (H1N1) pdm09 virus, which successfully resolved the infection.ResultsViral infection activated a marked pro-inflammatory response at the lung level paralleling the emergence of histological changes. Cellular immune response and cytokine signaling were the two signaling pathway categories more representative of our analysis. This transcriptome response was associated to viral clearance, and its resolution was accompanied by resolution of histopathology.DiscussionThese findings suggest a dual role of pulmonary inflammation in viral clearance and development of pneumonia during non-fatal infection caused by the 2009 pandemic influenza virus. Understanding the dynamics of the host’s transcriptomic and virological changes over the course of the infection caused by A (H1N1) pdm09 virus may help identifying the immune response profiles associated with an effective response against influenza virus. creator: Raquel Almansa creator: Pamela Martínez-Orellana creator: Lucía Rico creator: Verónica Iglesias creator: Alicia Ortega creator: Beatriz Vidaña creator: Jorge Martínez creator: Ana Expósito creator: María Montoya creator: Jesús F. Bermejo-Martin uri: https://doi.org/10.7717/peerj.3915 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Almansa et al. title: The effects of familiarity on escape responses in the Trinidadian guppy (Poecilia reticulata) link: https://peerj.com/articles/3899 last-modified: 2017-10-11 description: Predation is the main cause of mortality during early life stages. The ability to avoid and evade potential threats is, therefore, favoured to evolve during the early stages of life. It is also during these early stages that the process of familiarization occurs. It has long been recognized that associating with familiar individuals confers antipredator benefits. Yet gaps in our knowledge remain about how predator evasion is affected by social experience during early stages. In this study, we test the hypothesis that familiarization acquired during early life stages improves escape responses. Using the guppy Poecilia reticulata, we examine the effect of different recent social conditions in the three main components of predator evasion. Using high-speed motion analysis, we compared the number of individuals in each test group that responded to a visual stimulus, their reactive distance and magnitude of their response (maximum speed, maximum acceleration and distance) in groups composed either of familiar or non-familiar individuals. Contrary to the prediction, groups composed of familiar individuals were less responsive than groups of unfamiliar individuals. Reactive distance and magnitude of response were more dependent on individual size rather than on familiarity. Larger individuals reached higher maximum speeds and total distances in their escape response. Our result indicates that familiarity is likely to affect behaviour earlier in a predator-prey interaction, which then affects the behavioural component of the response. Taken together, our study contributes to previous ones by distinguishing which components of an escape response are modulated by familiarity. creator: Hayley L. Wolcott creator: Alfredo F. Ojanguren creator: Miguel Barbosa uri: https://doi.org/10.7717/peerj.3899 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Wolcott et al. title: Evidence for continual hybridization rather than hybrid speciation between Ligularia duciformis and L. paradoxa (Asteraceae) link: https://peerj.com/articles/3884 last-modified: 2017-10-11 description: BackgroundHybrids possess phenotypic traits that are often intermediate between their parental taxa, which commonly serves as evidence of hybridization in morphological analyses. Natural hybridization has been shown to occur frequently in Ligularia (Asteraceae). In a previous study, Ligularia ×maoniushanensis was demonstrated as a natural hybrid species between L. duciformis and L. paradoxa based on morphological and reproductive traits.MethodsWe used three chloroplast (cpDNA) fragments (psbA-trnH, trnL-rpl32 and trnQ-5′rps16), the nuclear ribosomal internal transcribed spacer (nrITS), and co-dominant SSR and dominant ISSR markers to study natural hybridization between L. duciformis and L. paradoxa growing sympatrically in two locations. Parental taxa were inferred using network analyses of cpDNA and nrITS haplotypes. Admixture among individuals was examined using the Bayesian clustering programs STRUCTURE and NewHybrids based on the SSR and ISSR data; and potential introgression in the SSR loci was assessed using the INTROGRESS package.ResultsThe putative parental species were clearly distinguished from other sympatric Ligularia species by nrITS data, and L. ×maoniushanensis individuals were confirmed to be the hybrid offspring of L. duciformis and L. paradoxa. Moreover, introgression was detected among several individuals morphologically identified as L. duciformis or L. paradoxa. Analyses of the cpDNA data revealed primarily unidirectional hybridization between L. duciformis and L. paradoxa, with L. paradoxa as the maternal parent in Mt. Maoniu, whereas bidirectional but asymmetrical hybridization was inferred to occur in Heihai Lake. The STRUCTURE analyses based on the SSR data detected two distinct clusters among the three taxa. The NewHybrids analyses showed that individuals circumscribed as L. ×maoniushanensis were dominated by early- and later-generation and backcrossing hybrids. The NewHybrids results based on the ISSR data were congruent with SSR results. In addition, introgression was detected in some SSR loci, and heterogeneity among loci was found in terms of detected patterns of introgression.ConclusionsOur data provide strong evidence for hybridization and introgression between L. duciformis and L. paradoxa. Ligularia ×maoniushanensis was demonstrated to be of hybrid origin. Since no evident reproductive isolation was found between the two parental species, detected hybrids appear to be part of hybrid swarms resulting from frequent and ongoing gene flow, which might impede the formation of a new hybrid species. creator: Rong Zhang creator: Xun Gong creator: Ryan Folk uri: https://doi.org/10.7717/peerj.3884 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Zhang et al. title: Light induced intraspecific variability in response to thermal stress in the hard coral Stylophora pistillata link: https://peerj.com/articles/3802 last-modified: 2017-10-11 description: Recent research suggests that prior exposure of several months to elevated irradiance induces enhanced thermal tolerance in scleractinian corals. While this tolerance has been reported at the species level, individual coral colonies may react differently due to individual variability in thermal tolerance. As thermal anomalies are predicted to become common in the upcoming future, intraspecific variation may be key to the survival of coral populations. In order to study light-history based thermal stress responses on individual colonies, we developed a preliminary microcosm experiment where three randomly chosen, aquacultured colonies of the model coral Stylophora pistillata were exposed to two irradiance treatments (200 and 400 μmol photons m−2 s−1) for 31 days, followed by artificially induced heat stress (∼33.4 °C). We found different responses to occur at both the intraspecific and the intracolonial levels, as indicated by either equal, less severe, delayed, and/or even non-necrotic responses of corals previously exposed to the irradiance of 400 compared to 200 μmol photons m−2 s−1. In addition, all individual colonies revealed light-enhanced calcification. Finally, elevated irradiance resulted in a lower chlorophyll a concentration in one colony compared to the control treatment, and the same colony displayed more rapid bleaching compared to the other ones. Taken together, this study highlights the potential importance of intra-individual variability in physiological responses of scleractinian corals and provides recommendations for improving methodological designs for future studies. creator: Arjen Tilstra creator: Tim Wijgerde creator: Francisco Dini-Andreote creator: Britas Klemens Eriksson creator: Joana Falcão Salles creator: Ido Pen creator: Ronald Osinga creator: Christian Wild uri: https://doi.org/10.7717/peerj.3802 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Tilstra et al. title: Illegal use of natural resources in federal protected areas of the Brazilian Amazon link: https://peerj.com/articles/3902 last-modified: 2017-10-10 description: BackgroundThe Brazilian Amazon is the world’s largest rainforest regions and plays a key role in biodiversity conservation as well as climate adaptation and mitigation. The government has created a network of protected areas (PAs) to ensure long-term conservation of the region. However, despite the importance of and positive advances in the establishment of PAs, natural resource depletion in the Brazilian Amazon is pervasive.MethodsWe evaluated a total of 4,243 official law enforcement records generated between 2010 and 2015 to understand the geographical distribution of the illegal use of resources in federal PAs in the Brazilian Amazon. We classified illegal activities into ten categories and used generalized additive models (GAMs) to evaluate the relationship between illegal use of natural resources inside PAs with management type, age of PAs, population density, and accessibility.ResultsWe found 27 types of illegal use of natural resources that were grouped into 10 categories of illegal activities. Most infractions were related to suppression and degradation of vegetation (37.40%), followed by illegal fishing (27.30%) and hunting activities (18.20%). The explanatory power of the GAMs was low for all categories of illegal activity, with a maximum explained variation of 41.2% for illegal activities as a whole, and a minimum of 14.6% for hunting activities.DiscussionThese findings demonstrate that even though PAs are fundamental for nature conservation in the Brazilian Amazon, the pressures and threats posed by human activities include a broad range of illegal uses of natural resources. Population density up to 50 km from a PA is a key variable, influencing illegal activities. These threats endanger long-term conservation and many efforts are still needed to maintain PAs that are large enough and sufficiently intact to maintain ecosystem functions and protect biodiversity. creator: Érico E. Kauano creator: Jose M.C. Silva creator: Fernanda Michalski uri: https://doi.org/10.7717/peerj.3902 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Kauano et al. title: Complete mitochondrial genome sequences of the northern spotted owl (Strix occidentalis caurina) and the barred owl (Strix varia; Aves: Strigiformes: Strigidae) confirm the presence of a duplicated control region link: https://peerj.com/articles/3901 last-modified: 2017-10-10 description: We report here the successful assembly of the complete mitochondrial genomes of the northern spotted owl (Strix occidentalis caurina) and the barred owl (S. varia). We utilized sequence data from two sequencing methodologies, Illumina paired-end sequence data with insert lengths ranging from approximately 250 nucleotides (nt) to 9,600 nt and read lengths from 100–375 nt and Sanger-derived sequences. We employed multiple assemblers and alignment methods to generate the final assemblies. The circular genomes of S. o. caurina and S. varia are comprised of 19,948 nt and 18,975 nt, respectively. Both code for two rRNAs, twenty-two tRNAs, and thirteen polypeptides. They both have duplicated control region sequences with complex repeat structures. We were not able to assemble the control regions solely using Illumina paired-end sequence data. By fully spanning the control regions, Sanger-derived sequences enabled accurate and complete assembly of these mitochondrial genomes. These are the first complete mitochondrial genome sequences of owls (Aves: Strigiformes) possessing duplicated control regions. We searched the nuclear genome of S. o. caurina for copies of mitochondrial genes and found at least nine separate stretches of nuclear copies of gene sequences originating in the mitochondrial genome (Numts). The Numts ranged from 226–19,522 nt in length and included copies of all mitochondrial genes except tRNAPro, ND6, and tRNAGlu. Strix occidentalis caurina and S. varia exhibited an average of 10.74% (8.68% uncorrected p-distance) divergence across the non-tRNA mitochondrial genes. creator: Zachary R. Hanna creator: James B. Henderson creator: Anna B. Sellas creator: Jérôme Fuchs creator: Rauri C.K. Bowie creator: John P. Dumbacher uri: https://doi.org/10.7717/peerj.3901 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Hanna et al. title: Infection of army ant pupae by two new parasitoid mites (Mesostigmata: Uropodina) link: https://peerj.com/articles/3870 last-modified: 2017-10-10 description: A great variety of parasites and parasitoids exploit ant societies. Among them are the Mesostigmata mites, a particularly common and diverse group of ant-associated arthropods. While parasitism is ubiquitous in Mesostigmata, parasitoidism has only been described in the genus Macrodinychus. Yet information about the basic biology of most Macrodinychus species is lacking. Out of 24 formally described species, information about basic life-history traits is only available for three species. Here we formally describe two new Macrodinychus species, i.e. Macrodinychus hilpertae and Macrodinychus derbyensis. In both species, immature stages developed as ecto-parasitoids on ant pupae of the South-East Asian army ant Leptogenys distinguenda. By piercing the developing ant with their chelicera, the mites apparently suck ant hemolymph, ultimately killing host individuals. We compare infection rates among all studied Macrodinychus species and discuss possible host countermeasures against parasitoidism. The cryptic lifestyle of living inside ant nests has certainly hampered the scientific discovery of Macrodinychus mites and we expect that many more macrodinychid species await scientific discovery and description. creator: Adrian Brückner creator: Hans Klompen creator: Andrew Iain Bruce creator: Rosli Hashim creator: Christoph von Beeren uri: https://doi.org/10.7717/peerj.3870 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Brückner et al. title: Extending SEQenv: a taxa-centric approach to environmental annotations of 16S rDNA sequences link: https://peerj.com/articles/3827 last-modified: 2017-10-10 description: Understanding how the environment selects a given taxon and the diversity patterns that emerge as a result of environmental filtering can dramatically improve our ability to analyse any environment in depth as well as advancing our knowledge on how the response of different taxa can impact each other and ecosystem functions. Most of the work investigating microbial biogeography has been site-specific, and logical environmental factors, rather than geographical location, may be more influential on microbial diversity. SEQenv, a novel pipeline aiming to provide environmental annotations of sequences emerged to provide a consistent description of the environmental niches using the ENVO ontology. While the pipeline provides a list of environmental terms on the basis of sample datasets and, therefore, the annotations obtained are at the dataset level, it lacks a taxa centric approach to environmental annotation. The work here describes an extension developed to enhance the SEQenv pipeline, which provided the means to directly generate environmental annotations for taxa under different contexts. 16S rDNA amplicon datasets belonging to distinct biomes were selected to illustrate the applicability of the extended SEQenv pipeline. A literature survey of the results demonstrates the immense importance of sequence level environmental annotations by illustrating the distribution of both taxa across environments as well as the various environmental sources of a specific taxon. Significantly enhancing the SEQenv pipeline in the process, this information would be valuable to any biologist seeking to understand the various taxa present in the habitat and the environment they originated from, enabling a more thorough analysis of which lineages are abundant in certain habitats and the recovery of patterns in taxon distribution across different habitats and environmental gradients. creator: Ali Z. Ijaz creator: Thomas C. Jeffries creator: Umer Z. Ijaz creator: Kelly Hamonts creator: Brajesh K. Singh uri: https://doi.org/10.7717/peerj.3827 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Ijaz et al. title: Virulence test using nematodes to prescreen Nocardia species capable of inducing neurodegeneration and behavioral disorders link: https://peerj.com/articles/3823 last-modified: 2017-10-10 description: BackgroundParkinson’s disease (PD) is a disorder characterized by dopaminergic neuron programmed cell death. The etiology of PD remains uncertain—some cases are due to selected genes associated with familial heredity, others are due to environmental exposure to toxic components, but over 90% of cases have a sporadic origin. Nocardia are Actinobacteria that can cause human diseases like nocardiosis. This illness can lead to lung infection or central nervous system (CNS) invasion in both immunocompromised and immunocompetent individuals. The main species involved in CNS are N. farcinica, N. nova, N. brasiliensis and N. cyriacigeorgica. Some studies have highlighted the ability of N. cyriacigeorgica to induce Parkinson’s disease-like symptoms in animals. Actinobacteria are known to produce a large variety of secondary metabolites, some of which can be neurotoxic. We hypothesized that neurotoxic secondary metabolite production and the onset of PD-like symptoms in animals could be linked.MethodsHere we used a method to screen bacteria that could induce dopaminergic neurodegeneration before performing mouse experiments.ResultsThe nematode Caenorhabditis elegans allowed us to demonstrate that Nocardia strains belonging to N. cyriacigeorgica and N. farcinica species can induce dopaminergic neurodegeneration. Strains of interest involved with the nematodes in neurodegenerative disorders were then injected in mice. Infected mice had behavioral disorders that may be related to neuronal damage, thus confirming the ability of Nocardia strains to induce neurodegeneration. These behavioral disorders were induced by N. cyriacigeorgica species (N. cyriacigeorgica GUH-2 and N. cyriacigeorgica 44484) and N. farcinica 10152.DiscussionWe conclude that C. elegans is a good model for detecting Nocardia strains involved in neurodegeneration. This model allowed us to detect bacteria with high neurodegenerative effects and which should be studied in mice to characterize the induced behavioral disorders and bacterial dissemination. creator: Claire Bernardin Souibgui creator: Anthony Zoropogui creator: Jeremy Voisin creator: Sebastien Ribun creator: Valentin Vasselon creator: Petar Pujic creator: Veronica Rodriguez-Nava creator: Patrick Belly creator: Benoit Cournoyer creator: Didier Blaha uri: https://doi.org/10.7717/peerj.3823 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Bernardin Souibgui et al. title: Clinical outcomes of residual or recurrent nasopharyngeal carcinoma treated with endoscopic nasopharyngectomy plus chemoradiotherapy or with chemoradiotherapy alone: a retrospective study link: https://peerj.com/articles/3912 last-modified: 2017-10-09 description: BackgroundLocal residual and recurrent nasopharyngeal carcinoma (NPC) generally shows treatment failure after standard radiotherapy with or without concurrent chemotherapy. Whether endoscopic nasopharyngectomy might provide an additional therapeutic advantage remains controversial. Therefore, we retrospectively compared the clinical prognoses of patients with residual or recurrent NPC treated with endoscopic nasopharyngectomy combined with chemoradiotherapy (CRT) with those of patients treated with CRT alone.Methods and MaterialsA total of sixty-two patients with local residual or recurrent NPC were studied retrospectively: 36 patients received endoscopic nasopharyngectomy combined with CRT, whereas 26 patients who refused the surgery or had surgical contraindications received CRT alone. Serum Epstein-Barr virus (EBV) DNA levels were measured pre- and post-treatment. The differences in prognosis between the two treatment regimens and the pre- and post-treatment changes in EBV-DNA levels were analyzed.ResultsThe median follow-up time was 31 months, with a 3-year overall survival (OS) of 51.40% and a 3-year disease-free survival (DFS) of 46.86%. The surgery + CRT group had a better OS than the CRT alone group did (χ2 = 4.054, P = 0.044). The pretreatment EBV-DNA levels showed a positive correlation with the clinical staging of recurrent NPC (χ2 = 11.674, P = 0.009). Patients with negative pretreatment serum EBV-DNA levels showed a superior OS to those of patients who tested positive for EBV-DNA (>0 copy/mL) (χ2 = 9.833, P = 0.002). The post-treatment EBV-DNA levels, compared with the pretreatment levels, decreased significantly in the surgery + CRT group (Z =  − 3.484, P = 0.000). In contrast, the EBV-DNA levels after CRT alone did not decrease significantly (Z =  − 1.956, P = 0.051). Multivariate analysis indicated that local staging, pretreatment EBV-DNA load, and the treatment method were independent risk factors for OS. Subgroup analysis indicated that the patients who tested negative for EBV-DNA before the treatment and those who received surgery + CRT showed a better OS than those who received CRT alone.ConclusionsThe pretreatment serum EBV-DNA level was associated with disease prognosis. The combination therapy preceded by surgery can effectively decrease the copy number of EBV-DNA. Patients with local intermediate- and late-stage NPC, especially those negative for EBV-DNA, may consider opting for surgery followed by post-operative adjuvant radiotherapy or chemotherapy. creator: Jingjin Weng creator: Jiazhang Wei creator: Jinyuan Si creator: Yangda Qin creator: Min Li creator: Fei Liu creator: Yongfeng Si creator: Jiping Su uri: https://doi.org/10.7717/peerj.3912 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Weng et al. title: Comparison of human papillomavirus (HPV) detection in urine and cervical swab samples using the HPV GenoArray Diagnostic assay link: https://peerj.com/articles/3910 last-modified: 2017-10-09 description: Human papillomavirus (HPV) is the leading cause of cervical cancer. Urine-based HPV testing offers a simple and non-invasive method because of its increasing acceptance. A total of 164 pairs of cervical swab and urine samples from Thai women who underwent cervical cancer screening were used for HPV testing with HPV GenoArray Diagnostic Kits. The overall concordance percentage for HPV detection in the cervical swab and urine samples was 65.2%. The HPV genotypes most commonly detected were HPV16 and HPV18. An analysis of the urine samples and a second analysis of the cervical swab samples showed that the differences in the overall HPV detection rate between women with normal and abnormal cytology were not significant (p > 0.05). Urine samples processed with the GenoArray assay is an alternative for women who decline to undergo Pap smear even though it is not ideal as the first-line screening option. creator: Pornjarim Nilyanimit creator: Jira Chansaenroj creator: Anant Karalak creator: Piyawat Laowahutanont creator: Pairoj Junyangdikul creator: Yong Poovorawan uri: https://doi.org/10.7717/peerj.3910 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Nilyanimit et al. title: Histamine-2 receptor antagonist famotidine modulates cardiac stem cell characteristics in hypertensive heart disease link: https://peerj.com/articles/3882 last-modified: 2017-10-09 description: BackgroundCardiac stem cells (CSCs) play a vital role in cardiac homeostasis. A decrease in the efficiency of cardiac stem cells is speculated in various cardiac abnormalities. The maintenance of a healthy stem cell population is essential for the prevention of adverse cardiac remodeling leading to cardiac failure. Famotidine, a histamine-2 receptor antagonist, is currently used to treat ulcers of the stomach and intestines. In repurposing the use of the drug, reduction of cardiac hypertrophy and improvement in cardiac function of spontaneously hypertensive rats (SHR) was reported by our group. Given that stem cells are affected in cardiac pathologies, the effect of histamine-2 receptor antagonism on CSC characteristics was investigated.MethodsTo examine whether famotidine has a positive effect on CSCs, spontaneously hypertensive rats (SHR) treated with the drug were sacrificed; and CSCs isolated from atrial appendages was evaluated. Six-month-old male SHRs were treated with famotidine (30 mg/kg/day) for two months. The effect of famotidine treatment on migration, proliferation and survival of CSCs was compared with untreated SHRs and normotensive Wistar rats.ResultsFunctional efficiency of CSCs from SHR was compromised relative to that in Wistar rat. Famotidine increased the migration and proliferation potential, along with retention of stemness of CSCs in treated SHRs. Cellular senescence and oxidative stress were also reduced. The expression of H2R was unaffected by the treatment.DiscussionAs anticipated, CSCs from SHRs were functionally impaired. Stem cell attributes of famotidine-treated SHRs was comparable to that of Wistar rats. Therefore, in addition to being cardioprotective, the histamine 2 receptor antagonist modulated cardiac stem cells characteristics. Restoration of stem cell efficiency by famotidine is possibly mediated by reduction of oxidative stress as the expression of H2R was unaffected by the treatment. Maintenance of healthy stem cell population is suggested as a possible mechanism underlying the cardioprotective effect of famotidine. creator: Sherin Saheera creator: Ajay G. Potnuri creator: Renuka Nair uri: https://doi.org/10.7717/peerj.3882 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Saheera et al. title: Influence of exercise duration on cardiorespiratory responses, energy cost and tissue oxygenation within a 6 hour treadmill run link: https://peerj.com/articles/3694 last-modified: 2017-10-09 description: PurposeThe physiological mechanisms for alterations in oxygen utilization ($\dot {\mathrm{V }}{\mathrm{O}}_{2}$V ̇O2) and the energy cost of running (Cr) during prolonged running are not completely understood, and could be linked with alterations in muscle and cerebral tissue oxygenation.MethodsEight trained ultramarathon runners (three women; mean ± SD; age 37 ± 7 yr; maximum $\dot {\mathrm{V }}{\mathrm{O}}_{2}$V ̇O2 60 ± 15 mL min−1 kg−1) completed a 6 hr treadmill run (6TR), which consisted of four modules, including periods of moderate (3 min at 10 km h−1, 10-CR) and heavy exercise intensities (6 min at 70% of maximum $\dot {\mathrm{V }}{\mathrm{O}}_{2}$V ̇O2, HILL), separated by three, 100 min periods of self-paced running (SP). We measured $\dot {\mathrm{V }}{\mathrm{O}}_{2}$V ̇O2, minute ventilation (${\dot {\mathrm{V }}}_{\mathrm{E}}$V ̇E), ventilatory efficiency (${\dot {\mathrm{V }}}_{\mathrm{E}}:\dot {\mathrm{V }}{\mathrm{O}}_{2}$V ̇E:V ̇O2), respiratory exchange ratio (RER), Cr, muscle and cerebral tissue saturation index (TSI) during the modules, and heart rate (HR) and perceived exertion (RPE) during the modules and SP.ResultsParticipants ran 58.3 ± 10.5 km during 6TR. Speed decreased and HR and RPE increased during SP. Across the modules, HR and $\dot {\mathrm{V }}{\mathrm{O}}_{2}$V ̇O2 increased (10-CR), and RER decreased (10-CR and HILL). There were no significant changes in ${\dot {\mathrm{V }}}_{\mathrm{E}}$V ̇E, ${\dot {\mathrm{V }}}_{\mathrm{E}}:\dot {\mathrm{V }}{\mathrm{O}}_{2}$V ̇E:V ̇O2, Cr, TSI and RPE across the modules.ConclusionsIn the context of positive pacing (decreasing speed), increased cardiac drift and perceived exertion over the 6TR, we observed increased RER and increased HR at moderate and heavy exercise intensity, increased $\dot {\mathrm{V }}{\mathrm{O}}_{2}$V ̇O2 at moderate intensity, and no effect of exercise duration on ventilatory efficiency, energy cost of running and tissue oxygenation. creator: Hugo A. Kerhervé creator: Scott McLean creator: Karen Birkenhead creator: David Parr creator: Colin Solomon uri: https://doi.org/10.7717/peerj.3694 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Kerhervé et al. title: Independent evolution of tetraloop in enterovirus oriL replicative element and its putative binding partners in virus protein 3C link: https://peerj.com/articles/3896 last-modified: 2017-10-06 description: BackgroundEnteroviruses are small non-enveloped viruses with a (+) ssRNA genome with one open reading frame. Enterovirus protein 3C (or 3CD for some species) binds the replicative element oriL to initiate replication. The replication of enteroviruses features a low-fidelity process, which allows the virus to adapt to the changing environment on the one hand, and requires additional mechanisms to maintain the genome stability on the other. Structural disturbances in the apical region of oriL domain d can be compensated by amino acid substitutions in positions 154 or 156 of 3C (amino acid numeration corresponds to poliovirus 3C), thus suggesting the co-evolution of these interacting sequences in nature. The aim of this work was to understand co-evolution patterns of two interacting replication machinery elements in enteroviruses, the apical region of oriL domain d and its putative binding partners in the 3C protein.MethodsTo evaluate the variability of the domain d loop sequence we retrieved all available full enterovirus sequences (>6, 400 nucleotides), which were present in the NCBI database on February 2017 and analysed the variety and abundance of sequences in domain d of the replicative element oriL and in the protein 3C.ResultsA total of 2,842 full genome sequences was analysed. The majority of domain d apical loops were tetraloops, which belonged to consensus YNHG (Y = U/C, N = any nucleotide, H = A/C/U). The putative RNA-binding tripeptide 154–156 (Enterovirus C 3C protein numeration) was less diverse than the apical domain d loop region and, in contrast to it, was species-specific.DiscussionDespite the suggestion that the RNA-binding tripeptide interacts with the apical region of domain d, they evolve independently in nature. Together, our data indicate the plastic evolution of both interplayers of 3C-oriL recognition. creator: Maria A. Prostova creator: Andrei A. Deviatkin creator: Irina O. Tcelykh creator: Alexander N. Lukashev creator: Anatoly P. Gmyl uri: https://doi.org/10.7717/peerj.3896 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Prostova et al. title: Cryptic biodiversity and phylogeographic patterns of Seychellois Ligia isopods link: https://peerj.com/articles/3894 last-modified: 2017-10-06 description: Ligia isopods are conspicuous inhabitants of rocky intertidal habitats exhibiting several biological traits that severely limit their dispersal potential. Their presence in patchy habitats and low vagility may lead to long term isolation, allopatric isolation and possible cryptic speciation. Indeed, various species of Ligia have been suggested to represent instead cryptic species complexes. Past studies; however, have largely focused in Eastern Pacific and Atlantic species of Ligia, leaving in doubt whether cryptic diversity occurs in other highly biodiverse areas. The Seychelles consists of 115 islands of different ages and geological origins spread across the western Indian Ocean. They are well known for their rich biodiversity with recent reports of cryptic species in terrestrial Seychellois organisms. Despite these studies, it is unclear whether coastal invertebrates from the Seychelles harbor any cryptic diversity. In this study, we examined patterns of genetic diversity and isolation within Ligia isopods across the Seychelles archipelago by characterizing individuals from locations across both inner and outer islands of the Seychelles using mitochondrial and nuclear markers. We report the presence of highly divergent lineages of independent origin. At Aldabra Atoll, we uncovered a lineage closely related to the Ligia vitiensis cryptic species complex. Within the inner islands of Cousine, Silhouette, and Mahé we detected the presence of two moderately divergent and geographically disjunct lineages most closely related to Ligia dentipes. Our findings suggest that the Seychelles may harbor at least three novel species of Ligia in need of description and that these species may have originated independently. creator: Carlos A. Santamaria creator: Joanna K. Bluemel creator: Nancy Bunbury creator: Melinda Curran uri: https://doi.org/10.7717/peerj.3894 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Santamaria et al. title: Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance link: https://peerj.com/articles/3893 last-modified: 2017-10-06 description: BackgroundAs next generation sequence technology has advanced, there have been parallel advances in genome-scale analysis programs for determining evolutionary relationships as proxies for epidemiological relationship in public health. Most new programs skip traditional steps of ortholog determination and multi-gene alignment, instead identifying variants across a set of genomes, then summarizing results in a matrix of single-nucleotide polymorphisms or alleles for standard phylogenetic analysis. However, public health authorities need to document the performance of these methods with appropriate and comprehensive datasets so they can be validated for specific purposes, e.g., outbreak surveillance. Here we propose a set of benchmark datasets to be used for comparison and validation of phylogenomic pipelines.MethodsWe identified four well-documented foodborne pathogen events in which the epidemiology was concordant with routine phylogenomic analyses (reference-based SNP and wgMLST approaches). These are ideal benchmark datasets, as the trees, WGS data, and epidemiological data for each are all in agreement. We have placed these sequence data, sample metadata, and “known” phylogenetic trees in publicly-accessible databases and developed a standard descriptive spreadsheet format describing each dataset. To facilitate easy downloading of these benchmarks, we developed an automated script that uses the standard descriptive spreadsheet format.ResultsOur “outbreak” benchmark datasets represent the four major foodborne bacterial pathogens (Listeria monocytogenes, Salmonella enterica, Escherichia coli, and Campylobacter jejuni) and one simulated dataset where the “known tree” can be accurately called the “true tree”. The downloading script and associated table files are available on GitHub: https://github.com/WGS-standards-and-analysis/datasets.DiscussionThese five benchmark datasets will help standardize comparison of current and future phylogenomic pipelines, and facilitate important cross-institutional collaborations. Our work is part of a global effort to provide collaborative infrastructure for sequence data and analytic tools—we welcome additional benchmark datasets in our recommended format, and, if relevant, we will add these on our GitHub site. Together, these datasets, dataset format, and the underlying GitHub infrastructure present a recommended path for worldwide standardization of phylogenomic pipelines. creator: Ruth E. Timme creator: Hugh Rand creator: Martin Shumway creator: Eija K. Trees creator: Mustafa Simmons creator: Richa Agarwala creator: Steven Davis creator: Glenn E. Tillman creator: Stephanie Defibaugh-Chavez creator: Heather A. Carleton creator: William A. Klimke creator: Lee S. Katz uri: https://doi.org/10.7717/peerj.3893 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: Hearing assessment during deep brain stimulation of the central nucleus of the inferior colliculus and dentate cerebellar nucleus in rat link: https://peerj.com/articles/3892 last-modified: 2017-10-06 description: BackgroundRecently it has been shown in animal studies that deep brain stimulation (DBS) of auditory structures was able to reduce tinnitus-like behavior. However, the question arises whether hearing might be impaired when interfering in auditory-related network loops with DBS.MethodsThe auditory brainstem response (ABR) was measured in rats during high frequency stimulation (HFS) and low frequency stimulation (LFS) in the central nucleus of the inferior colliculus (CIC, n = 5) or dentate cerebellar nucleus (DCBN, n = 5). Besides hearing thresholds using ABR, relative measures of latency and amplitude can be extracted from the ABR. In this study ABR thresholds, interpeak latencies (I–III, III–V, I–V) and V/I amplitude ratio were measured during off-stimulation state and during LFS and HFS.ResultsIn both the CIC and the CNBN groups, no significant differences were observed for all outcome measures.DiscussionDBS in both the CIC and the CNBN did not have adverse effects on hearing measurements. These findings suggest that DBS does not hamper physiological processing in the auditory circuitry. creator: Jasper V. Smit creator: Ali Jahanshahi creator: Marcus L.F. Janssen creator: Robert J. Stokroos creator: Yasin Temel uri: https://doi.org/10.7717/peerj.3892 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Smit et al. title: Genome methylation and regulatory functions for hypoxic adaptation in Tibetan chicken embryos link: https://peerj.com/articles/3891 last-modified: 2017-10-06 description: Tibetan chickens have unique adaptations to the extreme high-altitude environment that they inhabit. Epigenetic DNA methylation affects many biological processes, including hypoxic adaptation; however, the regulatory genes for DNA methylation in hypoxic adaptation remain unknown. In this study, methylated DNA immunoprecipitation with high-throughput sequencing (MeDIP-seq) was used to provide an atlas of the DNA methylomes of the heart tissue of hypoxic highland Tibetan and lowland Chahua chicken embryos. A total of 31.2 gigabases of sequence data were generated from six MeDIP-seq libraries. We identified 1,049 differentially methylated regions (DMRs) and 695 related differentially methylated genes (DMGs) between the two chicken breeds. The DMGs are involved in vascular smooth muscle contraction, VEGF signaling pathway, calcium signaling pathway, and other hypoxia-related pathways. Five candidate genes that had low methylation (EDNRA, EDNRB2, BMPR1B, BMPRII, and ITGA2) might play key regulatory roles in the adaptation to hypoxia in Tibetan chicken embryos. Our study provides significant explanations for the functions of genes and their epigenetic regulation for hypoxic adaptation in Tibetan chickens. creator: Yawen Zhang creator: Wenyu Gou creator: Jun Ma creator: Hongliang Zhang creator: Ying Zhang creator: Hao Zhang uri: https://doi.org/10.7717/peerj.3891 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Zhang et al. title: voomDDA: discovery of diagnostic biomarkers and classification of RNA-seq data link: https://peerj.com/articles/3890 last-modified: 2017-10-06 description: RNA-Seq is a recent and efficient technique that uses the capabilities of next-generation sequencing technology for characterizing and quantifying transcriptomes. One important task using gene-expression data is to identify a small subset of genes that can be used to build diagnostic classifiers particularly for cancer diseases. Microarray based classifiers are not directly applicable to RNA-Seq data due to its discrete nature. Overdispersion is another problem that requires careful modeling of mean and variance relationship of the RNA-Seq data. In this study, we present voomDDA classifiers: variance modeling at the observational level (voom) extensions of the nearest shrunken centroids (NSC) and the diagonal discriminant classifiers. VoomNSC is one of these classifiers and brings voom and NSC approaches together for the purpose of gene-expression based classification. For this purpose, we propose weighted statistics and put these weighted statistics into the NSC algorithm. The VoomNSC is a sparse classifier that models the mean-variance relationship using the voom method and incorporates voom’s precision weights into the NSC classifier via weighted statistics. A comprehensive simulation study was designed and four real datasets are used for performance assessment. The overall results indicate that voomNSC performs as the sparsest classifier. It also provides the most accurate results together with power-transformed Poisson linear discriminant analysis, rlog transformed support vector machines and random forests algorithms. In addition to prediction purposes, the voomNSC classifier can be used to identify the potential diagnostic biomarkers for a condition of interest. Through this work, statistical learning methods proposed for microarrays can be reused for RNA-Seq data. An interactive web application is freely available at http://www.biosoft.hacettepe.edu.tr/voomDDA/. creator: Gokmen Zararsiz creator: Dincer Goksuluk creator: Bernd Klaus creator: Selcuk Korkmaz creator: Vahap Eldem creator: Erdem Karabulut creator: Ahmet Ozturk uri: https://doi.org/10.7717/peerj.3890 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Zararsiz et al. title: The isolation and identification of pathogenic fungi from Tessaratoma papillosa Drury (Hemiptera: Tessaratomidae) link: https://peerj.com/articles/3888 last-modified: 2017-10-06 description: BackgroundLitchi stink-bug, Tessaratoma papillosa Drury (Hemiptera: Tessaratomidae), is one of the most widespread and destructive pest species on Litchi chinensis Sonn and Dimocarpus longan Lour in Southern China. Inappropriate use of chemical pesticides has resulted in serious environmental problems and food pollution. Generating an improved Integrated Pest Management (IPM) strategy for litchi stink-bug in orchard farming requires development of an effective biological control agent. Entomopathogenic fungi are regarded as a vital ecological factor in the suppression of pest populations under field conditions. With few effective fungi and pathogenic strains available to control litchi stink-bug, exploration of natural resources for promising entomopathogenic fungi is warranted.Methods & ResultsIn this study, two pathogenic fungi were isolated from cadavers of adult T. papillosa. They were identified as Paecilomyces lilacinus and Beauveria bassiana by morphological identification and rDNA-ITS homogeneous analysis. Infection of T. papillosa with B. bassiana and P. lilacinus occurred initially from the antennae, metameres, and inter-segmental membranes. Biological tests showed that the two entomopathogenic fungi induced high mortality in 2nd and 5th instar nymphs of T. papillosa. B. bassiana was highly virulent on 2nd instar nymphs of T. papillosa, with values for cadaver rate, LC50 and LT50 of 88.89%, 1.92 × 107 conidia/mL and 4.34 days respectively.DiscussionThis study provides two valuable entomopathogenic fungi from T. papillosa. This finding suggests that the highly virulent P. lilacinus and B. bassiana play an important role in the biocontrol of T. papillosa in China. These pathogenic fungi had no pollution or residue risk, and could provide an alternative option for IPM of litchi stink-bug. creator: Xiang Meng creator: Junjie Hu creator: Gecheng Ouyang uri: https://doi.org/10.7717/peerj.3888 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Meng et al. title: Anti-apoptotic properties of carbon monoxide in porcine oocyte during in vitro aging link: https://peerj.com/articles/3876 last-modified: 2017-10-06 description: If fertilization of matured oocyte does not occur, unfertilized oocyte undergoes aging, resulting in a time-dependent reduction of the oocyte’s quality. The aging of porcine oocytes can lead to apoptosis. Carbon monoxide (CO), a signal molecule produced by the heme oxygenase (HO), possesses cytoprotective and anti-apoptotic effects that have been described in somatic cells. However, the effects of CO in oocytes have yet to be investigated. By immunocytochemistry method we detected that both isoforms of heme oxygenase (HO-1 and HO-2) are present in the porcine oocytes. Based on the morphological signs of oocyte aging, it was found that the inhibition of both HO isoforms by Zn-protoporphyrin IX (Zn-PP IX) leads to an increase in the number of apoptotic oocytes and decrease in the number of intact oocytes during aging. Contrarily, the presence of CO donors (CORM-2 or CORM-A1) significantly decrease the number of apoptotic oocytes while increasing the number of intact oocytes. We also determined that CO donors significantly decrease the caspase-3 (CAS-3) activity. Our results suggest that HO/CO contributes to the sustaining viability through regulation of apoptosis during in vitro aging of porcine oocytes. creator: David Němeček creator: Markéta Dvořáková creator: Ivona Heroutová creator: Eva Chmelíková creator: Markéta Sedmíková uri: https://doi.org/10.7717/peerj.3876 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Němeček et al. title: Effects of astragalus polysaccharide on the adhesion-related immune response of endothelial cells stimulated with CSFV in vitro link: https://peerj.com/articles/3862 last-modified: 2017-10-06 description: BackgroundAstragalus polysaccharide (APS) has immunomodulatory activities on porcine peripheral blood mononuclear cells. The immunomodulatory effects of APS on porcine endothelial cells (ECs) expose to classical swine fever virus (CSFV) remain unknown.MethodsThe virus was titrated using an indirect immune biotin enzyme standard method to confirm that porcine ECs were susceptible to CSFV infection and to determine the TCID50 of CSFV (C-strain). Porcine ECs were cultured with CSFV in the presence of APS. Relative quantitative PCR was used to assess the mRNA expression of factors that influence EC adhesion and immunity.ResultsThe expression of adhesion factors mRNA increased following stimulation with CSFV; this effect was inhibited by pre-exposing the cells to APS. In addition, the expression of growth factors and some immune factors increased after infection with CSFV; this increase in tissue factor (TF), transforming growth factor (TGF-β), and interleukin-8 (IL-8) could be inhibited by the addition of APS. The immune response mediated by Toll-like receptor 4 (TLR4) in ECs may be unregulated by CSFV as it was also inhibited by pre-treatment with APS.DiscussionThe addition of APS to the culture can obviously regulate the expression of molecules related to the adhesion, growth, and immune response of ECs, as well as the production of cytokines. Therefore, it may have the potential to be an effective component in vaccines against CSFV. creator: Zengyu Zhuge creator: Yanpeng Dong creator: Liuan Li creator: Tianming Jin uri: https://doi.org/10.7717/peerj.3862 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Zhuge et al. title: Enhanced conflict monitoring via a short-duration, video-assisted deep breathing in healthy young adults: an event-related potential approach through the Go/NoGo paradigm link: https://peerj.com/articles/3857 last-modified: 2017-10-06 description: ObjectivesPractitioners of mindfulness are reported to have greater cognitive control especially in conflict monitoring, response inhibition and sustained attention. However, due to the various existing methods in each mindfulness practices and also, the high commitment factor, a barrier still exists for an individual to pick up the practices. Therefore, the effect of short duration deep breathing on the cognitive control is investigated here.MethodsShort duration guided deep breathing videos consisting of 5, 7 and 9 min respectively were created and used on subjects training. The effect on cognitive control was assessed using a Go/NoGo task along with event-related potential (ERP) measurements at Fz, Cz, and Pz.ResultsFrom the study, the significant outcome showed at the follow-up session in which participants engaged for 5 min deep breathing group showed a profound NoGo N2 amplitude increment as compared to the control group, indicating an enhanced conflict monitoring ability. An inverse relationship between the NoGo N2 amplitude and the breathing duration is observed as well at the follow-up session.ConclusionThese results indicated the possibility of performing short duration deep breathing guided by a video to achieve an enhanced conflict monitoring as an alternative to other mindfulness practices and 5 min is found to be the optimum practice duration.SignificantThis study is the first to establish a relationship between deep breathing and conflict monitoring through ERP. The study population of young adults taken from the same environment reduces the variance in ERP results due to age and environment.LimitationA larger sample size would provide a greater statistical power. A longer duration of deep breathing should be investigated to further clarify the relationship between the practice duration and the NoGo N2 amplitude. The result can be split by gender and analyzed separately due to the different brain structure of males and females. creator: Kok Suen Cheng creator: Yun Fah Chang creator: Ray P.S. Han creator: Poh Foong Lee uri: https://doi.org/10.7717/peerj.3857 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Cheng et al. title: Effects of invasion history on physiological responses to immune system activation in invasive Australian cane toads link: https://peerj.com/articles/3856 last-modified: 2017-10-06 description: The cane toad (Rhinella marina) has undergone rapid evolution during its invasion of tropical Australia. Toads from invasion front populations (in Western Australia) have been reported to exhibit a stronger baseline phagocytic immune response than do conspecifics from range core populations (in Queensland). To explore this difference, we injected wild-caught toads from both areas with the experimental antigen lipopolysaccharide (LPS, to mimic bacterial infection) and measured whole-blood phagocytosis. Because the hypothalamic-pituitary-adrenal axis is stimulated by infection (and may influence immune responses), we measured glucocorticoid response through urinary corticosterone levels. Relative to injection of a control (phosphate-buffered saline), LPS injection increased both phagocytosis and the proportion of neutrophils in the blood. However, responses were similar in toads from both populations. This null result may reflect the ubiquity of bacterial risks across the toad’s invaded range; utilization of this immune pathway may not have altered during the process of invasion. LPS injection also induced a reduction in urinary corticosterone levels, perhaps as a result of chronic stress. creator: Daniel Selechnik creator: Andrea J. West creator: Gregory P. Brown creator: Kerry V. Fanson creator: BriAnne Addison creator: Lee A. Rollins creator: Richard Shine uri: https://doi.org/10.7717/peerj.3856 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Selechnik et al. title: Sensory determinants of the autonomous sensory meridian response (ASMR): understanding the triggers link: https://peerj.com/articles/3846 last-modified: 2017-10-06 description: The autonomous sensory meridian response (ASMR) is an atypical sensory phenomenon involving electrostatic-like tingling sensations in response to certain sensory, primarily audio-visual, stimuli. The current study used an online questionnaire, completed by 130 people who self-reported experiencing ASMR. We aimed to extend preliminary investigations into the experience, and establish key multisensory factors contributing to the successful induction of ASMR through online media. Aspects such as timing and trigger load, atmosphere, and characteristics of ASMR content, ideal spatial distance from various types of stimuli, visual characteristics, context and use of ASMR triggers, and audio preferences are explored. Lower-pitched, complex sounds were found to be especially effective triggers, as were slow-paced, detail-focused videos. Conversely, background music inhibited the sensation for many respondents. These results will help in designing media for ASMR induction. creator: Emma L. Barratt creator: Charles Spence creator: Nick J. Davis uri: https://doi.org/10.7717/peerj.3846 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Barratt et al. title: Qualitative study of healthcare providers’ current practice patterns and barriers to successful rehydration for pediatric diarrheal illnesses in Kenya link: https://peerj.com/articles/3829 last-modified: 2017-10-06 description: BackgroundFor children worldwide, diarrhea is the second leading cause of death. These deaths are preventable by fluid resuscitation. Nasogastric tubes (NGs) have been shown to be equivalent to intravenous fluids for rehydration and recommended by the World Health Organization (WHO) for use in severe dehydration. Despite this, NGs are rarely used for rehydration in Kenya. Our objective was to evaluate clinicians’ adherence to rehydration guidelines and to identify barriers to the use of NGs for resuscitating dehydrated children.MethodsA case-based structured survey was administered to pediatric care providers in western Kenya to determine their choices for alternative rehydration therapies when oral rehydration and intravenous fluids fail. Providers then participated in a qualitative, semi-structured interview to identify barriers to using nasogastric tubes for rehydration. Analysis included manual, progressive coding of interview transcripts to identify emerging central themes.ResultsOf 44 participants, only four (9%) followed WHO guidelines that recommend quickly switching to NG for rehydration in their case responses. Participants identified that placing intravenous lines in dehydrated children is a challenge. However, when discussing NG use, many believed NGs are not effective for rehydration. Other participants’ concerns surrounded knowledge and training regarding guidelines as well as not having NGs available.DiscussionHealthcare providers in western Kenya do not report using NGs for rehydration in accordance with WHO guidelines for diarrheal illness with severe dehydration. Barriers to the use of NG tubes were lack of knowledge and availability. Education and implementation of guidelines using NG tubes for rehydration may improve outcomes of children suffering from diarrheal illness with severe dehydration. creator: Darlene R. House creator: Philip Cheptinga creator: Daniel E. Rusyniak creator: Rachel C. Vreeman uri: https://doi.org/10.7717/peerj.3829 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 House et al. title: Combined moderate and high intensity exercise with dietary restriction improves cardiac autonomic function associated with a reduction in central and systemic arterial stiffness in obese adults: a clinical trial link: https://peerj.com/articles/3900 last-modified: 2017-10-05 description: ObjectiveThe present study aimed to assess the effects of exercise with dietary restriction on cardiac autonomic activity, arterial stiffness, and cardiovascular biomarkers in obese individuals.MethodsSeventeen obese adults completed an 8-week exercise and dietary program. Anthropometry, body composition, and multiple biochemical markers were measured. We used carotid-femoral pulse wave velocity (cfPWV), brachial-ankle pulse wave velocity (baPWV), central blood pressure, and augmentation index (AIx) to assess arterial stiffness. To determine cardiac autonomic activity, heart rate variability (HRV) was analyzed by standard deviation of normal-to-normal intervals (SDNN), square root of the mean squared differences of successive normal-to-normal intervals (RMSSD), total power (TF), low-frequency power in normalized units (LFnu), high-frequency power in normalized units (HFnu), and low-frequency power/high-frequency power (LF/HF).ResultsFollowing the exercise and diet intervention, obese subjects had significant reductions in body weight, body mass index, body fat percentage, brachial systolic blood pressure, and resting heart rate, and they had shown improvements in blood chemistry markers such as lipid profiles, insulin, and high-sensitivity C-reactive protein. There was a significant reduction in both cfPWV and baPWV following the intervention when compared to baseline levels. Moreover, the AIx and aortic systolic blood pressure were significantly reduced after the intervention. The diet and exercise intervention significantly increased cardiac autonomic modulation (determined by improved SDNN, RMSSD, TP LF, HF, and LF/HF), which was partly due to changes in heart rate, insulin resistance, and the inflammatory pattern. Furthermore, we observed a correlation between enhanced cardiac autonomic modulation (LF/HF) and decreased arterial stiffness, as measured by central cfPWV and systemic baPWV.DiscussionAn 8-week combined intervention of diet and exercise is effective in improving cardiac autonomic function in obese adults, with an associated decrease in central and systemic arterial stiffness. creator: Min Hu creator: Shen Wang creator: Dan Wang creator: Qinhao Lai creator: Xiaoying Chen creator: Shiwei Duan creator: Mengke Zhao creator: Junhao Huang uri: https://doi.org/10.7717/peerj.3900 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Hu et al. title: Mechanisms of action and in vivo antibacterial efficacy assessment of five novel hybrid peptides derived from Indolicidin and Ranalexin against Streptococcus pneumoniae link: https://peerj.com/articles/3887 last-modified: 2017-10-05 description: BackgroundAntimicrobial peptides (AMPs) are of great potential as novel antibiotics for the treatment of broad spectrum of pathogenic microorganisms including resistant bacteria. In this study, the mechanisms of action and the therapeutic efficacy of the hybrid peptides were examined.MethodsTEM, SEM and ATP efflux assay were used to evaluate the effect of hybrid peptides on the integrity of the pneumococcal cell wall/membrane. DNA retardation assay was assessed to measure the impact of hybrid peptides on the migration of genomic DNA through the agarose gel. In vitro synergistic effect was checked using the chequerboard assay. ICR male mice were used to evaluate the in vivo toxicity and antibacterial activity of the hybrid peptides in a standalone form and in combination with ceftriaxone.ResultsThe results obtained from TEM and SEM indicated that the hybrid peptides caused significant morphological alterations in Streptococcus pneumoniae and disrupting the integrity of the cell wall/membrane. The rapid release of ATP from pneumococcal cells after one hour of incubation proposing that the antibacterial action for the hybrid peptides is based on membrane permeabilization and damage. The DNA retardation assay revealed that at 62.5 µg/ml all the hybrid peptides were capable of binding and preventing the pneumococcal genomic DNA from migrating through the agarose gel. In vitro synergy was observed when pneumococcal cells treated with combinations of hybrid peptides with each other and with conventional drugs erythromycin and ceftriaxone. The in vivo therapeutic efficacy results revealed that the hybrid peptide RN7-IN8 at 20 mg/kg could improve the survival rate of pneumococcal bacteremia infected mice, as 50% of the infected mice survived up to seven days post-infection. In vivo antibacterial efficacy of the hybrid peptide RN7-IN8 was signficantly improved when combined with the standard antibiotic ceftriaxone at (20 mg/kg + 20 mg/kg) as 100% of the infected mice survived up to seven days post-infection.DiscussionOur results suggest that attacking and breaching the cell wall/membrane is most probably the principal mechanism for the hybrid peptides. In addition, the hybrid peptides could possess another mechanism of action by inhibiting intracellular functions such as DNA synthesis. AMPs could play a great role in combating antibiotic resistance as they can reduce the therapeutic concentrations of standard drugs. creator: Hassan Mahmood Jindal creator: Keivan Zandi creator: Kien Chai Ong creator: Rukumani Devi Velayuthan creator: Sara Maisha Rasid creator: Chandramathi Samudi Raju creator: Shamala Devi Sekaran uri: https://doi.org/10.7717/peerj.3887 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Jindal et al. title: Integration of lncRNA–miRNA–mRNA reveals novel insights into oviposition regulation in honey bees link: https://peerj.com/articles/3881 last-modified: 2017-10-05 description: BackgroundThe honey bee (Apis mellifera) is a highly diverse species commonly used for honey production and pollination services. The oviposition of the honey bee queen affects the development and overall performance of the colony. To investigate the ovary activation and oviposition processes on a molecular level, a genome-wide analysis of lncRNAs, miRNAs and mRNA expression in the ovaries of the queens was performed to screen for differentially expressed coding and noncoding RNAs. Further analysis identified relevant candidate genes or RNAs.ResultsThe analysis of the RNA profiles in different oviposition phase of the queens revealed that 740 lncRNAs, 81 miRNAs and 5,481 mRNAs were differently expressed during the ovary activation; 88 lncRNAs, 13 miRNAs and 338 mRNAs were differently expressed during the oviposition inhibition process; and finally, 100 lncRNAs, four miRNAs and 497 mRNAs were differently expressed during the oviposition recovery process. In addition, functional annotation of differentially expressed RNAs revealed several pathways that are closely related to oviposition, including hippo, MAPK, notch, Wnt, mTOR, TGF-beta and FoxO signaling pathways. Furthermore, in the QTL region for ovary size, 73 differentially expressed genes and 14 differentially expressed lncRNAs were located, which are considered as candidate genes affecting ovary size and oviposition. Moreover, a core set of genes served as bridges among different miRNAs were identified through the integrated analysis of lncRNA-miRNA-mRNA network.ConclusionThe observed dramatic expression changes of coding and noncoding RNAs suggest that they may play a critical role in honey bee queens’ oviposition. The identified candidate genes for oviposition activation and regulation could serve as a resource for further studies of genetic markers of oviposition in honey bees. creator: Xiao Chen creator: Ce Ma creator: Chao Chen creator: Qian Lu creator: Wei Shi creator: Zhiguang Liu creator: Huihua Wang creator: Haikun Guo uri: https://doi.org/10.7717/peerj.3881 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Chen et al. title: A randomized control trial feasibility evaluation of an mHealth intervention for wheelchair skill training among middle-aged and older adults link: https://peerj.com/articles/3879 last-modified: 2017-10-05 description: BackgroundProviding mobility skills training to manual wheelchair (MWC) users can have a positive impact on community participation, confidence and quality of life. Often such training is restricted or not provided at all because of the expense of, and limited access to, occupational and physical therapists before and after discharge. This is particularly true among middle-aged and older adults, who often have limited access to rehabilitation services and require more time to learn motor skills. A monitored MWC skills training home program, delivered using a computer tablet (mHealth), was developed as an alternative approach to service delivery. The purpose of this study was to evaluate the feasibility of implementing this mHealth MWC skills training program among middle-aged and older adults.MethodsA 2 × 2 factorial design randomized controlled trial (RCT) was used to compare the mHealth intervention and control groups, with additional wheeling time as a second factor. Community-dwelling MWC users aged 55 and older, who had used their MWC for less than two years and propelled with two hands, were recruited. Feasibility outcomes related to process, resources, management and treatment criteria were collected.ResultsEighteen participants were recruited, with a retention rate of 94%. Mean (±SD) duration for the first and second in-person training sessions were 90.1 ± 20.5 and 62.1 ± 5.5 min, respectively. In the treatment group, 78% achieved the minimum amount of home training (i.e., 300 min) over four weeks and 56% achieved the preferred training threshold (i.e., 600 min). Trainers reported only seven minor protocol deviations. No tablets were lost or damaged and there was one incident of tablet malfunction. No injuries or adverse incidents were reported during data collection or training activities. Participants indicated 98% agreement on the post-treatment benefit questionnaire.DiscussionOverall, the study protocol enabled implementation of the intervention in a safe, efficient and acceptable manner. Participant recruitment proved to be challenging, particularly gaining access to individuals who might benefit. Resource issue demands were acceptable for administration of the intervention; data collection was more time-consuming than anticipated but could be reduced with minor revisions. Participant retention and home program treatment adherence was high; both participant and trainer burden was acceptable. Treatment group participants reported a positive experience and clinical benefits from training program. The findings suggest a full-scale RCT evaluating the clinical impact of the Enhancing Participation In the Community by improving Wheelchair Skills (EPIC Wheels) intervention is warranted, provided the recruitment issues are addressed through collaborative partnerships and active recruitment strategies. creator: Edward M. Giesbrecht creator: William C. Miller uri: https://doi.org/10.7717/peerj.3879 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Giesbrecht and Miller title: Relationship between hemoglobin glycation index and extent of coronary heart disease in individuals with type 2 diabetes mellitus: a cross-sectional study link: https://peerj.com/articles/3875 last-modified: 2017-10-05 description: BackgroundIndividuals with type 2 diabetes (T2D) are at an increased risk of coronary heart disease (CHD). Diabetic complications have recently been associated with a measure of glucose metabolism known as the hemoglobin glycation index (HGI). Currently there is insufficient information regarding a potential link between HGI and cardiovascular disease. This study aimed to investigate the relationship between HGI and extent of CHD in individuals with T2D.MethodsThis cross-sectional study screened individuals visiting the endocrinology clinic between June 2012 and May 2016 for eligibility. Enrollment criteria included individuals above 21 years of age with T2D diagnosed in the preceding ten years. Candidates with hemoglobin disorders, pregnancy, and existing coronary artery disease were excluded. Fasting plasma glucose (FPG) and glycated hemoglobin A1c (HbA1c) were sampled three months prior to angiography. The regression equation of predicted HbA1c = 0.008 × FPG + 6.28 described the linear relationship between these variables. HGI was calculated as the difference between the measured HbA1c and predicted HbA1c. Participants were classified into two groups according to the presence of supranormal (≥0) or subnormal HGI (<0).ResultsAmong 423 participants, people with supranormal HGI harbored an increased prevalence of multiple vessel disease relative to those with subnormal HGI (Odds ratio (OR): 3.9, 95% CI [2.64–5.98], P < 0.001). Moreover, individuals with supranormal HGI more frequently demonstrated lesions involving the left anterior descending artery (OR: 3.0, 95% CI [1.97–4.66], P < 0.001). The intergroup difference in mean HbA1c was statistically nonsignificant (7.5 ± 1.0% versus 7.4 ± 1.1%, P = 0.80).DiscussionThis study demonstrated that HGI correlated with the extent of CHD in individuals with T2D. People with supranormal HGI harbored a higher prevalence of extensive cardiovascular disease compared to those with subnormal HGI. The relationship between HGI and extent of CHD enables cardiovascular risk stratification in at risk individuals. Overall, HGI provides useful information concerning cardiovascular risk in clinical practice. creator: Po Chung Cheng creator: Shang Ren Hsu creator: Yun Chung Cheng creator: Yu Hsiu Liu uri: https://doi.org/10.7717/peerj.3875 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Cheng et al. title: Clone wars: asexual reproduction dominates in the invasive range of Tubastraea spp. (Anthozoa: Scleractinia) in the South-Atlantic Ocean link: https://peerj.com/articles/3873 last-modified: 2017-10-05 description: Although the invasive azooxanthellate corals Tubastraea coccinea and T. tagusensis are spreading quickly and outcompeting native species in the Atlantic Ocean, there is little information regarding the genetic structure and path of introduction for these species. Here we present the first data on genetic diversity and clonal structure from these two species using a new set of microsatellite markers. High proportions of clones were observed, indicating that asexual reproduction has a major role in the local population dynamics and, therefore, represents one of the main reasons for the invasion success. Although no significant population structure was found, results suggest the occurrence of multiple invasions for T. coccinea and also that both species are being transported along the coast by vectors such as oil platforms and monobouys, spreading these invasive species. In addition to the description of novel microsatellite markers, this study sheds new light into the invasive process of Tubastraea. creator: Katia Cristina Cruz Capel creator: Robert J. Toonen creator: Caio T.C.C. Rachid creator: Joel C. Creed creator: Marcelo V. Kitahara creator: Zac Forsman creator: Carla Zilberberg uri: https://doi.org/10.7717/peerj.3873 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Capel et al. title: New whaitsioids (Therapsida: Therocephalia) from the Teekloof Formation of South Africa and therocephalian diversity during the end-Guadalupian extinction link: https://peerj.com/articles/3868 last-modified: 2017-10-05 description: Two new species of therocephalian therapsids are described from the upper Permian Teekloof Formation of the Karoo Basin, South Africa. They include two specimens of a whaitsiid, Microwhaitsia mendrezi gen. et sp. nov., and a single, small whaitsioid Ophidostoma tatarinovi gen. et sp. nov., which preserves a combination of primitive and apomorphic features. A phylogenetic analysis of 56 therapsid taxa and 136 craniodental and postcranial characters places the new taxa within the monophyletic sister group of baurioids—Whaitsioidea—with Microwhaitsia as a basal whaitsiid and Ophidostoma as an aberrant whaitsioid just outside the hofmeyriid+whaitsiid subclade. The new records support that whaitsioids were diverse during the early-late Permian (Wuchiapingian) and that the dichotomy between whaitsiid-line and baurioid-line eutherocephalians was established early on. The oldest Gondwanan whaitsiid Microwhaitsia and additional records from the lower strata of the Teekloof Formation suggest that whaitsioids had diversified by the early Wuchiapingian and no later than Pristerognathus Assemblage Zone times. Prior extinction estimates based on species counts are reflected in an analysis of origination/extinction rates, which imply increasing faunal turnover from Guadalupian to Lopingian (late Permian) times. The new records support a growing body of evidence that some key Lopingian synapsid clades originated near or prior to the Guadalupian-Lopingian boundary ca. 260–259 million years ago, but only radiated following the end-Guadalupian extinction of dinocephalians and basal therocephalian predators (long-fuse model). Ongoing collecting in older portions of the Teekloof Formation (e.g., Pristerognathus Assemblage Zone) will shed further light on early eutherocephalians during this murky but critical time in their evolutionary diversification. creator: Adam K. Huttenlocker creator: Roger M.H. Smith uri: https://doi.org/10.7717/peerj.3868 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Huttenlocker and Smith title: The Plasmodium berghei RC strain is highly diverged and harbors putatively novel drug resistance variants link: https://peerj.com/articles/3766 last-modified: 2017-10-05 description: BackgroundThe current first line drugs for treating uncomplicated malaria are artemisinin (ART) combination therapies. However, Plasmodium falciparum parasites resistant to ART and partner drugs are spreading, which threatens malaria control efforts. Rodent malaria species are useful models for understanding antimalarial resistance, in particular genetic variants responsible for cross resistance to different compounds.MethodsThe Plasmodium berghei RC strain (PbRC) is described as resistant to different antimalarials, including chloroquine (CQ) and ART. In an attempt to identify the genetic basis for the antimalarial resistance trait in PbRC, its genome was sequenced and compared with five other previously sequenced P. berghei strains.ResultsWe found that PbRC is eight-fold less sensitive to the ART derivative artesunate than the reference strain PbANKA. The genome of PbRC is markedly different from other strains, and 6,974 single nucleotide variants private to PbRC were identified. Among these PbRC private variants, non-synonymous changes were identified in genes known to modulate antimalarial sensitivity in rodent malaria species, including notably the ubiquitin carboxyl-terminal hydrolase 1 gene. However, no variants were found in some genes with strong evidence of association with ART resistance in P. falciparum such as K13 propeller protein.DiscussionThe variants identified in PbRC provide insight into P. berghei genome diversity and genetic factors that could modulate CQ and ART resistance in Plasmodium spp. creator: Warangkhana Songsungthong creator: Supasak Kulawonganunchai creator: Alisa Wilantho creator: Sissades Tongsima creator: Pongpisid Koonyosying creator: Chairat Uthaipibull creator: Sumalee Kamchonwongpaisan creator: Philip J. Shaw uri: https://doi.org/10.7717/peerj.3766 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Songsungthong et al. title: Assessing the living and dead proportions of cold-water coral colonies: implications for deep-water Marine Protected Area monitoring in a changing ocean link: https://peerj.com/articles/3705 last-modified: 2017-10-05 description: Coral growth patterns result from an interplay of coral biology and environmental conditions. In this study colony size and proportion of live and dead skeletons in the cold-water coral (CWC) Lophelia pertusa (Linnaeus, 1758) were measured using video footage from Remotely Operated Vehicle (ROV) transects conducted at the inshore Mingulay Reef Complex (MRC) and at the offshore PISCES site (Rockall Bank) in the NE Atlantic. The main goal of this paper was to explore the development of a simple method to quantify coral growth and its potential application as an assessment tool of the health of these remote habitats. Eighteen colonies were selected and whole colony and dead/living layer size were measured. Live to dead layer ratios for each colony were then determined and analysed. The age of each colony was estimated using previously published data. Our paper shows that: (1) two distinct morphotypes can be described: at the MRC, colonies displayed a ‘cauliflower-shaped’ morphotype whereas at the PISCES site, colonies presented a more flattened ‘bush-shaped’ morphotype; (2) living layer size was positively correlated with whole colony size; (3) live to dead layer ratio was negatively correlated to whole colony size; (4) live to dead layer ratio never exceeded 0.27. These results suggest that as a colony develops and its growth rate slows down, the proportion of living polyps in the colony decreases. Furthermore, at least 73% of L. pertusa colonies are composed of exposed dead coral skeleton, vulnerable to ocean acidification and the associated shallowing of the aragonite saturation horizon, with significant implications for future deep-sea reef framework integrity. The clear visual contrast between white/pale living and grey/dark dead portions of the colonies also gives a new way by which they can be visually monitored over time. The increased use of marine autonomous survey vehicles offers an important new platform from which such a surveying technique could be applied to monitor deep-water marine protected areas in the future. creator: Johanne Vad creator: Covadonga Orejas creator: Juan Moreno-Navas creator: Helen S. Findlay creator: J. Murray Roberts uri: https://doi.org/10.7717/peerj.3705 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Vad et al. title: Impact of land reclamation and agricultural water regime on the distribution and conservation status of the endangered Dryophytes suweonensis link: https://peerj.com/articles/3872 last-modified: 2017-10-04 description: Knowledge about the distribution and habitat preferences of a species is critical for its conservation. The Suweon Treefrog (Dryophytes suweonensis) is an endangered species endemic to the Republic of Korea. We conducted surveys from 2014 to 2016 at 890 potentially suitable sites across the entire range of the species in South Korea. We then assessed whether D. suweonensis was found in the current and ancestral predicted ranges, reclaimed and protected areas, and how the presence of agricultural floodwater affected its occurrence. Our results describe a 120 km increase in the southernmost known distribution of the species, and the absence of the species at lower latitudes. We then demonstrate a putative constriction on the species ancestral range due to urban encroachment, and provide evidence for a significant increase in its coastal range due to the colonisation of reclaimed land by the species. In addition, we demonstrate that D. suweonensis is present in rice fields that are flooded with water originating from rivers as opposed to being present in rice fields that are irrigated from underground water. Finally, the non-overlap of protected areas and the occurrence of the species shows that only the edge of a single site where D. suweonensis occurs is legally protected. Based on our results and the literature, we suggest the design of a site fitting all the ecological requirements of the species, and suggest the use of such sites to prevent further erosion in the range of D. suweonensis. creator: Amaël Borzée creator: Kyungmin Kim creator: Kyongman Heo creator: Piotr G. Jablonski creator: Yikweon Jang uri: https://doi.org/10.7717/peerj.3872 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Borzée et al. title: Accuracy of microbial community diversity estimated by closed- and open-reference OTUs link: https://peerj.com/articles/3889 last-modified: 2017-10-04 description: Next-generation sequencing of 16S ribosomal RNA is widely used to survey microbial communities. Sequences are typically assigned to Operational Taxonomic Units (OTUs). Closed- and open-reference OTU assignment matches reads to a reference database at 97% identity (closed), then clusters unmatched reads using a de novo method (open). Implementations of these methods in the QIIME package were tested on several mock community datasets with 20 strains using different sequencing technologies and primers. Richness (number of reported OTUs) was often greatly exaggerated, with hundreds or thousands of OTUs generated on Illumina datasets. Between-sample diversity was also found to be highly exaggerated in many cases, with weighted Jaccard distances between identical mock samples often close to one, indicating very low similarity. Non-overlapping hyper-variable regions in 70% of species were assigned to different OTUs. On mock communities with Illumina V4 reads, 56% to 88% of predicted genus names were false positives. Biological inferences obtained using these methods are therefore not reliable. creator: Robert C. Edgar uri: https://doi.org/10.7717/peerj.3889 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Edgar title: Exceptional soft tissues preservation in a mummified frog-eating Eocene salamander link: https://peerj.com/articles/3861 last-modified: 2017-10-03 description: Fossils are almost always represented by hard tissues but we present here the exceptional case of a three-dimensionally preserved specimen that was ‘mummified’ (likely between 40 and 34 million years ago) in a terrestrial karstic environment. This fossil is the incomplete body of a salamander, Phosphotriton sigei, whose skeleton and external morphology are well preserved, as revealed by phase-contrast synchrotron X-ray microtomography. In addition, internal structures composed of soft tissues preserved in three dimensions are now identified: a lung, the spinal cord, a lumbosacral plexus, the digestive tract, muscles and urogenital organs that may be cloacal glands. These are among the oldest known cases of three-dimensional preservation of these organs in vertebrates and shed light on the ecology of this salamander. Indeed, the digestive tract contains remains of a frog, which represents the only known case of an extinct salamander that fed on a frog, an extremely rare type of predation in extant salamanders. These new data improve our scarce knowledge on soft tissue anatomy of early urodeles and should prove useful for future biologists and palaeontologists working on urodele evolutionary biology. We also suggest that the presence of bat guano and carcasses represented a close source of phosphorus, favouring preservation of soft tissues. Bone microanatomy indicates that P. sigei was likely amphibious or terrestrial, and was probably not neotenic. creator: Jérémy Tissier creator: Jean-Claude Rage creator: Michel Laurin uri: https://doi.org/10.7717/peerj.3861 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Tissier et al. title: Alpha-arylphorin is a mitogen in the Heliothis virescens midgut cell secretome upon Cry1Ac intoxication link: https://peerj.com/articles/3886 last-modified: 2017-10-03 description: Insecticidal crystal (Cry) proteins produced by the bacterium Bacillus thuringiensis (Bt) target cells in the midgut epithelium of susceptible larvae. While the mode of action of Cry toxins has been extensively investigated, the midgut response to Cry intoxication and its regulation are not well characterized. In this work, we describe the secreted proteome (secretome) of primary mature midgut cell cultures from Heliothis virescens larvae after exposure to Cry1Ac toxin compared to control buffer treatment. The Cry1Ac-induced secretome caused higher proliferation and differentiation and an overall reduction in total cell mortality over time in primary H. virescens midgut stem cell cultures when compared to treatment with control buffer secretome. Differential proteomics identified four proteins with significant differences in abundance comparing Cry1Ac-treated and control secretomes. The most significant difference detected in the Cry1Ac secretome was an arylphorin subunit alpha protein not detected in the control secretome. Feeding of purified alpha-arylphorin to H. virescens larvae resulted in midgut hyperplasia and significantly reduced susceptibility to Cry1Ac toxin compared to controls. These data identify alpha-arylphorin as a protein with a new putative role in the midgut regeneration process in response to Cry1Ac intoxication and possibly pathogen/abiotic stress, identifying alpha-arylphorin as a potential gene to target with insecticidal gene silencing for pest control. creator: Anais Castagnola creator: Jerreme Jackson creator: Omaththage P. Perera creator: Cris Oppert creator: Shigetoshi Eda creator: Juan Luis Jurat-Fuentes uri: https://doi.org/10.7717/peerj.3886 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Castagnola et al. title: Perch, Perca fluviatilis show a directional preference for, but do not increase attacks toward, prey in response to water-borne cortisol link: https://peerj.com/articles/3883 last-modified: 2017-10-03 description: In freshwater environments, chemosensory cues play an important role in predator-prey interactions. Prey use a variety of chemosensory cues to detect and avoid predators. However, whether predators use the chemical cues released by disturbed or stressed prey has received less attention. Here we tested the hypothesis that the disturbance cue cortisol, in conjunction with visual cues of prey, elevates predatory behavior. We presented predators (perch, Perca fluviatilis) with three chemosensory choice tests and recorded their location, orientation, and aggressive behavior. We compared the responses of predators when provided with (i) visual cues of prey only (two adjacent tanks containing sticklebacks); (ii) visual and natural chemical cues of prey vs. visual cues only; and (iii) visual cues of prey with cortisol vs. visual cues only. Perch spent a significantly higher proportion of time in proximity to prey, and orientated toward prey more, when presented with a cortisol stimulus plus visual cues, relative to presentations of visual and natural chemical cues of prey, or visual cues of prey only. There was a trend that perch directed a higher proportion of predatory behaviors (number of lunges) toward sticklebacks when presented with a cortisol stimulus plus visual cues, relative to the other chemosensory conditions. But they did not show a significant increase in total predatory behavior in response to cortisol. Therefore, it is not clear whether water-borne cortisol, in conjunction with visual cues of prey, affects predatory behavior. Our results provide evidence that cortisol could be a source of public information about prey state and/or disturbance, but further work is required to confirm this. creator: Lindsay J. Henderson creator: Mary R. Ryan creator: Hannah M. Rowland uri: https://doi.org/10.7717/peerj.3883 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Henderson et al. title: Segmentation and classification of colon glands with deep convolutional neural networks and total variation regularization link: https://peerj.com/articles/3874 last-modified: 2017-10-03 description: Segmentation of histopathology sections is a necessary preprocessing step for digital pathology. Due to the large variability of biological tissue, machine learning techniques have shown superior performance over conventional image processing methods. Here we present our deep neural network-based approach for segmentation and classification of glands in tissue of benign and malignant colorectal cancer, which was developed to participate in the GlaS@MICCAI2015 colon gland segmentation challenge. We use two distinct deep convolutional neural networks (CNN) for pixel-wise classification of Hematoxylin-Eosin stained images. While the first classifier separates glands from background, the second classifier identifies gland-separating structures. In a subsequent step, a figure-ground segmentation based on weighted total variation produces the final segmentation result by regularizing the CNN predictions. We present both quantitative and qualitative segmentation results on the recently released and publicly available Warwick-QU colon adenocarcinoma dataset associated with the GlaS@MICCAI2015 challenge and compare our approach to the simultaneously developed other approaches that participated in the same challenge. On two test sets, we demonstrate our segmentation performance and show that we achieve a tissue classification accuracy of 98% and 95%, making use of the inherent capability of our system to distinguish between benign and malignant tissue. Our results show that deep learning approaches can yield highly accurate and reproducible results for biomedical image analysis, with the potential to significantly improve the quality and speed of medical diagnoses. creator: Philipp Kainz creator: Michael Pfeiffer creator: Martin Urschler uri: https://doi.org/10.7717/peerj.3874 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Kainz et al. title: Development and validation of near-infrared spectroscopy for the prediction of forage quality parameters in Lolium multiflorum link: https://peerj.com/articles/3867 last-modified: 2017-10-03 description: Italian ryegrass (Lolium multiflorum) is an important cool-season, annual forage crop for the grassland rotation system in Southern China. The primary aim of breeding programs is always to seek to improve forage quality in the animal productivity system; however, it is time- and labor-consuming when analyzed excessive large number of samples. The main objectives of this study were to construct near-infrared reflectance spectroscopy (NIRS) models to predict the forage chemistry quality of Italian ryegrass including the concentrations of crude protein (CP), acid detergent fiber (ADF), neutral detergent fiber (NDF), and water soluble carbohydrate (WSC). The results showed that a broader range of CP, NDF, ADF and WSC contents (%DM) were obtained (4.45–30.60, 21.29–60.47, 11.66–36.17 and 3.95–51.52, respectively) from the samples selected for developing NIRS models. In addition, the critical wavelengths identified in this study to construct optimal NIRS models were located in 4,247–6,102 and 4,247–5,450 cm-1 for CP and NDF content, and both wavelengths 5,446–6,102 and 4,247–4,602 cm-1 could for ADF and WSC. Finally, the optimal models were developed based on the laboratory data and the spectral information by partial least squares (PLS) regression, with relatively high coefficients of determination (R2CV, CP = 0.99, NDF = 0.94, ADF = 0.92, WSC = 0.88), ratio of prediction to devitation (RPD, CP = 8.58, NDF = 4.25, ADF = 3.64, WSC = 3.10). The further statistics of prediction errors relative to laboratory (PRL) and the range error ratio (RER) give excellent assessments of the models with the PRL ratios lower than 2 and the RER values greater than 10. The NIRS models were validated using a completely independent set of samples and have coefficients of determination (R2V, CP = 0.99, NDF = 0.91, ADF = 0.95, WSC = 0.91) and ratio of prediction to deviation (RPD, CP = 9.37, NDF = 3.44, ADF = 4.40, WSC = 3.39). The result suggested that routine screening for forage quality parameters with large numbers of samples is available with the NIRS model in Italian ryegrass breeding programs, as well as facilitating graziers to monitor the forage development stage for improving grazing efficiency. creator: Zhongfu Yang creator: Gang Nie creator: Ling Pan creator: Yan Zhang creator: Linkai Huang creator: Xiao Ma creator: Xinquan Zhang uri: https://doi.org/10.7717/peerj.3867 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Yang et al. title: Assessment on the coupling effects of drip irrigation and organic fertilization based on entropy weight coefficient model link: https://peerj.com/articles/3855 last-modified: 2017-10-03 description: Water and fertilizer are two important factors influencing crop growth, development and yield formation. To investigate their combined effects on the soil-plant system, and to find out the optimal water and organic fertilizer coupling strategy for tomato (Solanum lycopersicum L), an experiment was carried out from May to October in 2016 in the south of China. The experiment consisted of three drip irrigation quotas (150, 180, 210 m3/ha) and three organic fertilizer application amounts (2,800, 3,600, 4,400 kg/ha). A water-fertilizer treatment (abbreviated as CK) that is in line with local practice was used for comparison. The tomato marketable yield, sugar/acid ratio (SAR) and irrigation water use efficiency (IWUE), as well as the soil salinity and available nutrient concentrations were measured. The results showed that the marketable yield was highly significantly (p < 0.01) affected by irrigation or fertilization. The SAR of tomato were significantly (p < 0.05) affected by irrigation or/and fertilization. The fertilization had an highly significant (p < 0.01) effect on the concentrations of soil nutrients (N, P, K), while the coupling effect of irrigation and fertilization was not pronounced. According to the multi-index analysis and the computed result by the entropy weight coefficient model, a 180 m3/ha irrigation quota in combination with 4,400 kg/ha organic fertilizer application amount was the optimal water-fertilizer coupling strategy which owned the most satisfactory comprehensive benefits. The marketable yield, SAR and IWUE under this optimal strategy were 122.4 t/ha, 9.2, 32.4 kg/m3, respectively, and by 28.0%, 29.6% and 28.1% higher compared to that under CK. creator: Fenglin Zhong creator: Maomao Hou creator: Bizhu He creator: Iouzen Chen uri: https://doi.org/10.7717/peerj.3855 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Zhong et al. title: A preliminary survey of zoantharian endosymbionts shows high genetic variation over small geographic scales on Okinawa-jima Island, Japan link: https://peerj.com/articles/3740 last-modified: 2017-10-03 description: Symbiotic dinoflagellates (genus Symbiodinium) shape the responses of their host reef organisms to environmental variability and climate change. To date, the biogeography of Symbiodinium has been investigated primarily through phylogenetic analyses of the ribosomal internal transcribed spacer 2 region. Although the marker can approximate species-level diversity, recent work has demonstrated that faster-evolving genes can resolve otherwise hidden species and population lineages, and that this diversity is often distributed over much finer geographical and environmental scales than previously recognized. Here, we use the noncoding region of the chloroplast psbA gene (psbAncr) to examine genetic diversity among clade C Symbiodinium associating with the common reef zoantharian Palythoa tuberculosa on Okinawa-jima Island, Japan. We identify four closely related Symbiodinium psbAncr lineages including one common generalist and two potential specialists that appear to be associated with particular microhabitats. The sea surface temperature differences that distinguish these habitats are smaller than those usually investigated, suggesting that future biogeographic surveys of Symbiodinium should incorporate fine scale environmental information as well as fine scale molecular data to accurately determine species diversity and their distributions. creator: Hatsuko Noda creator: John Everett Parkinson creator: Sung-Yin Yang creator: James Davis Reimer uri: https://doi.org/10.7717/peerj.3740 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Noda et al. title: Framework for community functioning: synthesis of stress gradient and resource partitioning concepts link: https://peerj.com/articles/3885 last-modified: 2017-10-02 description: To understand how communities function and generate abundance, I develop a framework integrating elements from the stress gradient and resource partitioning concepts. The framework suggests that guild abundance depends on environmental and spatial factors but also on inter-guild interactions (competitor or facilitator richness), which can alter the fundamental niche of constituent species in negative (competition) or positive direction (facilitation). Consequently, the environmental and spatial mechanisms driving guild abundance would differ across guilds and interaction modes. Using continental data on stream diatoms and physico-chemistry, the roles of these mechanisms were tested under three interaction modes—shared preference, distinct preference, and facilitative, whereby pairs of guilds exhibited, respectively, a dominance-tolerance tradeoff along a eutrophication gradient, specialization along a pH gradient, or a donor-recipient relationship along a nitrogen gradient. Representative of the shared preference mode were the motile (dominant) and low profile (tolerant) guilds, of the distinct preference mode—the acidophilous and alkaliphilous (low profile) guilds, and of the facilitative mode—nitrogen fixers (donors) and motile species (recipients). In each mode, the influences of environment, space (latitude and longitude), and competitor or facilitator richness on guild density were assessed by variance partitioning. Pure environment constrained most strongly the density of the dominant, the acidophilous, and the recipient guild in the shared preference, distinct preference, and facilitative mode, respectively, while spatial effects were important only for the low profile guild. Higher competitor richness was associated with lower density of the tolerant guild in the shared preference mode, both guilds in the distinct preference mode, and the donor guild in the facilitative mode. Conversely, recipient density in the facilitative mode increased with donor richness in stressful nitrogen-poor environments. Thus, diatom guild abundance patterns were determined primarily by biotic and/or environmental impacts and, with the exception of the low profile guild, were insensitive to spatial effects. This framework identifies major sources of variability in diatom guild abundance with implications for the understanding of biodiversity-ecosystem functioning. creator: Sophia I. Passy uri: https://doi.org/10.7717/peerj.3885 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Passy title: Elevated serum osteoprotegerin may predict peripheral arterial disease after kidney transplantation: a single-center prospective cross-sectional study in Taiwan link: https://peerj.com/articles/3847 last-modified: 2017-10-02 description: BackgroundOsteoprotegerin (OPG) is a potential biomarker for severity and complications of cardiovascular diseases. Peripheral arterial disease (PAD) is associated with an increased risk of death in kidney transplantation (KT) patients. This prospective cross-sectional study evaluated the relationship between serum OPG and PAD in KT patients.MethodsSeventy-four KT patients were enrolled for this PAD study. Fasting blood samples were obtained to measure serum OPG levels by using enzyme-linked immunosorbent assay kits. The ankle-brachial index (ABI) of less than 0.9 was applied for PAD diagnosis.ResultsThirteen patients (17.6%) were diagnosed with PAD. Diabetes (P = 0.025), smoking (P = 0.010), and increased OPG levels (P = 0.001) were significantly more frequent in the PAD group. Multivariate logistic regression analysis showed that serum OPG (odds ratio [OR], 1.336; 95% CI [1.108–1.611]; P = 0.002) and diabetes (OR, 7.120; 95% CI [1.080–46.940]; P = 0.041) were independent predictors of PAD in KT patients. The area under the receiver operating characteristic (ROC) curve determined that the probability of a serum OPG level of 7.117 pg/L in predicting PAD in KT patients was 0.799 (95% CI [0.690–0.884]; P < 0.001).DiscussionExploration of reliable biomarkers for early identification of vascular risk is crucial for KT patients. Elevated serum OPG levels may predict PAD in KT patients with cutoff value of 7.117 pg/L. creator: Yen-Cheng Chen creator: Bang-Gee Hsu creator: Ching-Chun Ho creator: Chung-Jen Lee creator: Ming-Che Lee uri: https://doi.org/10.7717/peerj.3847 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Chen et al. title: Diverse responses of Symbiodinium types to menthol and DCMU treatment link: https://peerj.com/articles/3843 last-modified: 2017-10-02 description: To understand the mechanism of photosynthetic inhibition and generation of reactive oxygen species (ROS) in Symbiodinium types under stress, chemicals such as dichlorophenyl dimethylurea (DCMU) are widely used. Moreover, DCMU and recently menthol were used to generate aposymbiotic cnidarian hosts. While the effects of DCMU on Symbiodinium cells have been extensively studied, no studies have shown the mechanism behind menthol-induced coral bleaching. Moreover, no study has compared the effects of DCMU and menthol treatments on photosystem II (PSII) activity and generation of ROS in different Symbiodinium types. In this study, we utilized five freshly isolated Symbiodinium types (S. minutum (B1), S. goreaui (C1), C3, C15, and S. trenchii (D1a)) to compare the effects of DCMU and menthol treatments. Symbiodinium cells were exposed to DCMU and menthol at different concentrations for 4 h. Results showed that values of the 50% inhibitory concentration (IC50) for PSII inhibition were 0.72∼1.96 mM for menthol-treated cells compared to 29∼74 pM for DCMU-treated cells. Diverse responses of Symbiodinium types were displayed in terms of PSII tolerance to menthol (S. minutum > S. trenchii = C15 > C3 = S. goreaui), and also in the response curves. In contrast, responses were not so diverse when the different types were treated with DCMU. Three of five menthol-treated Symbiodinium types showed instant and significant ROS generation when PSII activity was inhibited, compared to no ROS being generated in DCMU-treated Symbiodinium types. Both results indicated that menthol inhibited Symbiodinium PSII activity through Symbiodinium type-dependent mechanisms, which were also distinct from those with DCMU treatment. This study further confirmed that photosynthetic functions Symbiodinium have diverse responses to stress even within the same clade. creator: Jih-Terng Wang creator: Shashank Keshavmurthy creator: Tzu-Ying Chu creator: Chaolun Allen Chen uri: https://doi.org/10.7717/peerj.3843 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Wang et al. title: Harnessing mtDNA variation to resolve ambiguity in ‘Redfish’ sold in Europe link: https://peerj.com/articles/3746 last-modified: 2017-10-02 description: Morphology-based identification of North Atlantic Sebastes has long been controversial and misidentification may produce misleading data, with cascading consequences that negatively affect fisheries management and seafood labelling. North Atlantic Sebastes comprises of four species, commonly known as ‘redfish’, but little is known about the number, identity and labelling accuracy of redfish species sold across Europe. We used a molecular approach to identify redfish species from ‘blind’ specimens to evaluate the performance of the Barcode of Life (BOLD) and Genbank databases, as well as carrying out a market product accuracy survey from retailers across Europe. The conventional BOLD approach proved ambiguous, and phylogenetic analysis based on mtDNA control region sequences provided a higher resolution for species identification. By sampling market products from four countries, we found the presence of two species of redfish (S. norvegicus and S. mentella) and one unidentified Pacific rockfish marketed in Europe. Furthermore, public databases revealed the existence of inaccurate reference sequences, likely stemming from species misidentification from previous studies, which currently hinders the efficacy of DNA methods for the identification of Sebastes market samples. creator: Peter Shum creator: Lauren Moore creator: Christophe Pampoulie creator: Cristina Di Muri creator: Sara Vandamme creator: Stefano Mariani uri: https://doi.org/10.7717/peerj.3746 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Shum et al. title: Comparative study of Cd uptake and tolerance of two Italian ryegrass (Lolium multiflorum) cultivars link: https://peerj.com/articles/3621 last-modified: 2017-10-02 description: Cadmium (Cd) is one of the most toxic heavy metals and is difficult to be removed from contaminated soil and water. Italian ryegrass (Lolium multiflorum), as an energy crop, exhibits a valuable potential to develop Cd polluted sites due to its use as a biofuel rather than as food and forage. Previously, via a screening for Cd-tolerant ryegrass, the two most extreme cultivars (IdyII and Harukaze) with high and low Cd tolerance during seed germination, respectively, were selected. However, the underlying mechanism for Cd tolerance was not well investigated. In this study, we comparatively investigated the growth, physiological responses, and Cd uptake and translocation of IdyII and Harukaze when the seedlings were exposed to a Cd (0–100 μM) solution for 12 days. As expected, excess Cd inhibited seedling growth and was accompanied by an accumulation of malondialdehyde (MDA) and reduced photosynthetic pigments in both cultivars. The effects of Cd on the uptake and translocation of other nutrient elements (Zn, Fe, Mn and Mg) were dependent on Cd concentrations, cultivars, plant tissues and elements. Compared with Harukaze, IdyII exhibited better performance with less MDA and higher pigment content. Furthermore, IdyII was less efficient in Cd uptake and translocation compared to Harukaze, which might be explained by the higher non-protein thiols content in its roots. Taken together, our data indicate that IdyII is more tolerant than Harukaze, which partially resulted from the differences in Cd uptake and translocation. creator: Zhigang Fang creator: Laiqing Lou creator: Zhenglan Tai creator: Yufeng Wang creator: Lei Yang creator: Zhubing Hu creator: Qingsheng Cai uri: https://doi.org/10.7717/peerj.3621 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Fang et al.