title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2016-06 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Protogyny in a tropical damselfish: females queue for future benefit link: https://peerj.com/articles/2198 last-modified: 2016-06-30 description: Membership of the group is a balance between the benefits associated with group living and the cost of socially constrained growth and breeding opportunities, but the costs and benefits are seldom examined. The goal of the present study was to explore the trade-offs associated with group living for a sex-changing, potentially protogynous coral reef fish, the Ambon damselfish, Pomacentrus amboinensis. Extensive sampling showed that the species exhibits resource defence polygyny, where dominant males guard a nest site that is visited by females. P. amboinensis have a longevity of about 6.5 years on the northern Great Barrier Reef. While the species can change sex consistent with being a protogynous hermaphrodite, it is unclear the extent to which the species uses this capability. Social groups are comprised of one reproductive male, 1–7 females and a number of juveniles. Females live in a linear dominance hierarchy, with the male being more aggressive to the beta-female than the alpha-female, who exhibits lower levels of ovarian cortisol. Surveys and a tagging study indicated that groups were stable for at least three months. A passive integrated transponder tag study showed that males spawn with females from their own group, but also females from neighbouring groups. In situ behavioural observations found that alpha-females have priority of access to the nest site that the male guarded, and access to higher quality foraging areas. Male removal studies suggest that the alpha-females can change sex to take over from the male when the position becomes available. Examination of otolith microstructure showed that those individuals which change sex to males have different embryonic characteristics at hatching, suggesting that success may involve a component that is parentally endowed. The relative importance of parental effects and social organisation in affecting the importance of female queuing is yet to be studied, but will likely depend on the strength of social control by the dominant members of the group. creator: Mark I. McCormick uri: https://doi.org/10.7717/peerj.2198 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 McCormick title: An exploration of the influence of diagonal dissociation and moderate changes in speed on locomotor parameters in trotting horses link: https://peerj.com/articles/2190 last-modified: 2016-06-30 description: Background. Although the trot is described as a diagonal gait, contacts of the diagonal pairs of hooves are not usually perfectly synchronized. Although subtle, the timing dissociation between contacts of each diagonal pair could have consequences on gait dynamics and provide insight into the functional strategies employed. This study explores the mechanical effects of different diagonal dissociation patterns when speed was matched between individuals and how these effects link to moderate, natural changes in trotting speed. We anticipate that hind-first diagonal dissociation at contact increases with speed, diagonal dissociation at contact can reduce collision-based energy losses and predominant dissociation patterns will be evident within individuals.Methods. The study was performed in two parts: in the first 17 horses performed speed-matched trotting trials and in the second, five horses each performed 10 trotting trials that represented a range of individually preferred speeds. Standard motion capture provided kinematic data that were synchronized with ground reaction force (GRF) data from a series of force plates. The data were analyzed further to determine temporal, speed, GRF, postural, mass distribution, moment, and collision dynamics parameters.Results. Fore-first, synchronous, and hind-first dissociations were found in horses trotting at (3.3 m/s ± 10%). In these speed-matched trials, mean centre of pressure (COP) cranio-caudal location differed significantly between the three dissociation categories. The COP moved systematically and significantly (P = .001) from being more caudally located in hind-first dissociation (mean location = 0.41 ± 0.04) through synchronous (0.36 ± 0.02) to a more cranial location in fore-first dissociation (0.32 ± 0.02). Dissociation patterns were found to influence function, posture, and balance parameters. Over a moderate speed range, peak vertical forelimb GRF had a strong relationship with dissociation time (R = .594; P < .01) and speed (R = .789; P < .01), but peak vertical hindlimb GRF did not have a significant relationship with dissociation time (R = .085; P > 0.05) or speed (R = .223; P = .023).Discussion. The results indicate that at moderate speeds individual horses use dissociation patterns that allow them to maintain trunk pitch stability through management of the cranio-caudal location of the COP. During the hoof-ground collisions, reduced mechanical energy losses were found in hind-first dissociations compared to fully synchronous contacts. As speed increased, only forelimb vertical peak force increased so dissociations tended towards hind-first, which shifted the net COP caudally and balanced trunk pitching moments. creator: Sarah Jane Hobbs creator: John E.A. Bertram creator: Hilary M. Clayton uri: https://doi.org/10.7717/peerj.2190 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Hobbs et al. title: Cost-benefit trade-offs of bird activity in apple orchards link: https://peerj.com/articles/2179 last-modified: 2016-06-30 description: Birds active in apple orchards in south–eastern Australia can contribute positively (e.g., control crop pests) or negatively (e.g., crop damage) to crop yields. Our study is the first to identify net outcomes of these activities, using six apple orchards, varying in management intensity, in south–eastern Australia as a study system. We also conducted a predation experiment using real and artificial codling moth (Cydia pomonella) larvae (a major pest in apple crops). We found that: (1) excluding birds from branches of apple trees resulted in an average of 12.8% more apples damaged by insects; (2) bird damage to apples was low (1.9% of apples); and (3) when trading off the potential benefits (biological control) with costs (bird damage to apples), birds provided an overall net benefit to orchard growers. We found that predation of real codling moth larvae was higher than for plasticine larvae, suggesting that plasticine prey models are not useful for inferring actual predation levels. Our study shows how complex ecological interactions between birds and invertebrates affect crop yield in apples, and provides practical strategies for improving the sustainability of orchard systems. creator: Rebecca K. Peisley creator: Manu E. Saunders creator: Gary W. Luck uri: https://doi.org/10.7717/peerj.2179 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Peisley et al. title: Pteridine levels and head weights are correlated with age and colony task in the honey bee, Apis mellifera link: https://peerj.com/articles/2155 last-modified: 2016-06-30 description: Background. The age of an insect strongly influences many aspects of behavior and reproduction. The interaction of age and behavior is epitomized in the temporal polyethism of honey bees in which young adult bees perform nurse and maintenance duties within the colony, while older bees forage for nectar and pollen. Task transition is dynamic and driven by colony needs. However, an abundance of precocious foragers or overage nurses may have detrimental effects on the colony. Additionally, honey bee age affects insecticide sensitivity. Therefore, determining the age of a set of individual honey bees would be an important measurement of colony health. Pteridines are purine-based pigment molecules found in many insect body parts. Pteridine levels correlate well with age, and wild caught insects may be accurately aged by measuring pteridine levels. The relationship between pteridines and age varies with a number of internal and external factors among many species. Thus far, no studies have investigated the relationship of pteridines with age in honey bees.Methods. We established single-cohort colonies to obtain age-matched nurse and forager bees. Bees of known ages were also sampled from colonies with normal demographics. Nurses and foragers were collected every 3–5 days for up to 42 days. Heads were removed and weighed before pteridines were purified and analyzed using previously established fluorometric methods.Results. Our analysis showed that pteridine levels significantly increased with age in a linear manner in both single cohort colonies and colonies with normal demography. Pteridine levels were higher in foragers than nurses of the same age in bees from single cohort colonies. Head weight significantly increased with age until approximately 28-days of age and then declined for both nurse and forager bees in single cohort colonies. A similar pattern of head weight in bees from colonies with normal demography was observed but head weight was highest in 8-day old nurse bees and there was no relationship of head weight with age of foragers.Discussion. Although the relationship between pteridine levels and age was significant, variation in the data yielded a +4-day range in age estimation. This allows an unambiguous method to determine whether a bee may be a young nurse or old forager in colonies with altered demographics as in the case of single cohort colonies. Pteridine levels in bees do not correlate with age as well as in other insects. However, most studies used insects reared under tightly controlled laboratory conditions, while we used free-living bees. The dynamics of head weight change with age is likely to be due to growth and atrophy of the hypopharyngeal glands. Taken together, these methods represent a useful tool for assessing the age of an insect. Future studies utilizing these methods will provide a more holistic view of colony health. creator: Frank D. Rinkevich creator: Joseph W. Margotta creator: Jean M. Pittman creator: James A. Ottea creator: Kristen B. Healy uri: https://doi.org/10.7717/peerj.2155 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Rinkevich et al. title: Sub-chronic testosterone treatment increases the levels of epithelial sodium channel (ENaC)-α, β and γ in the kidney of orchidectomized adult male Sprague–Dawley rats link: https://peerj.com/articles/2145 last-modified: 2016-06-30 description: Testosterone has been reported to cause blood pressure to increase. However mechanisms that underlie the effect of this hormone on this physiological parameter are currently not well understood. The aims of this study were to investigate effects of testosterone on expression of α, β and γ-epithelial sodium channel (ENaC) proteins and messenger RNAs (mRNAs) in kidneys, the channel known to be involved in Na+ reabsorption, which subsequently can affect the blood pressure.Methods. Adult male Sprague–Dawley (SD) rats were orchidectomized fourteen days prior to receiving seven days treatment with testosterone propionate (125 µg/kg/day or 250 µg/kg/day) with or without flutamide (androgen receptor blocker) or finasteride (5α-reductase inhibitor). Following sacrifice, the kidneys were removed and were subjected for α, β and γ-ENaC protein and mRNA expression analyses by Western blotting and Real-time PCR (qPCR) respectively. The distribution of α, β and γ-ENaC proteins in kidneys were observed by immunofluorescence.Results. The α, β and γ-ENaC proteins and mRNA levels in kidneys were enhanced in rats which received testosterone-only treatment. In these rats, α, β and γ-ENaC proteins were distributed in the distal tubules and collecting ducts of the nephrons. Co-treatment with flutamide or finasteride resulted in the levels of α, β and γ-ENaC proteins and mRNAs in kidneys to decrease. In conclusions, increases in α, β and γ-ENaC protein and mRNA levels in kidneys mainly in the distal tubules and collecting ducts under testosterone influence might lead to enhance Na+ reabsorption which subsequently might cause an increase in blood pressure. creator: Su Yi Loh creator: Nelli Giribabu creator: Naguib Salleh uri: https://doi.org/10.7717/peerj.2145 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Loh et al. title: A new method for ecoacoustics? Toward the extraction and evaluation of ecologically-meaningful soundscape components using sparse coding methods link: https://peerj.com/articles/2108 last-modified: 2016-06-30 description: Passive acoustic monitoring is emerging as a promising non-invasive proxy for ecological complexity with potential as a tool for remote assessment and monitoring (Sueur & Farina, 2015). Rather than attempting to recognise species-specific calls, either manually or automatically, there is a growing interest in evaluating the global acoustic environment. Positioned within the conceptual framework of ecoacoustics, a growing number of indices have been proposed which aim to capture community-level dynamics by (e.g., Pieretti, Farina & Morri, 2011; Farina, 2014; Sueur et al., 2008b) by providing statistical summaries of the frequency or time domain signal. Although promising, the ecological relevance and efficacy as a monitoring tool of these indices is still unclear. In this paper we suggest that by virtue of operating in the time or frequency domain, existing indices are limited in their ability to access key structural information in the spectro-temporal domain. Alternative methods in which time-frequency dynamics are preserved are considered. Sparse-coding and source separation algorithms (specifically, shift-invariant probabilistic latent component analysis in 2D) are proposed as a means to access and summarise time-frequency dynamics which may be more ecologically-meaningful. creator: Alice Eldridge creator: Michael Casey creator: Paola Moscoso creator: Mika Peck uri: https://doi.org/10.7717/peerj.2108 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Eldridge et al. title: Emergent properties of a computational model of tumour growth link: https://peerj.com/articles/2176 last-modified: 2016-06-29 description: While there have been enormous advances in our understanding of the genetic drivers and molecular pathways involved in cancer in recent decades, there also remain key areas of dispute with respect to fundamental theories of cancer. The accumulation of vast new datasets from genomics and other fields, in addition to detailed descriptions of molecular pathways, cloud the issues and lead to ever greater complexity. One strategy in dealing with such complexity is to develop models to replicate salient features of the system and therefore to generate hypotheses which reflect on the real system. A simple tumour growth model is outlined which displays emergent behaviours that correspond to a number of clinically relevant phenomena including tumour growth, intra-tumour heterogeneity, growth arrest and accelerated repopulation following cytotoxic insult. Analysis of model data suggests that the processes of cell competition and apoptosis are key drivers of these emergent behaviours. Questions are raised as to the role of cell competition and cell death in physical cancer growth and the relevance that these have to cancer research in general is discussed. creator: Pan Pantziarka uri: https://doi.org/10.7717/peerj.2176 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Pantziarka title: The chemomodulatory effects of glufosfamide on docetaxel cytotoxicity in prostate cancer cells link: https://peerj.com/articles/2168 last-modified: 2016-06-29 description: Background. Glufosfamide (GLU) is a glucose conjugate of ifosfamide in which isophosphoramide mustard is glycosidically linked to the β-D-glucose molecule. Based on GLU structure, it is considered a targeted chemotherapy with fewer side effects. The main objective of the current study is to assess the cytotoxic potential of GLU for the first time in prostate cancer (PC) cells representing different stages of the tumor. Furthermore, this study examined the potential synergistic activity of GLU in combination with docetaxel (DOC).Methods. Two different cell lines were used, LNCaP and PC-3. Concentration-response curves were assessed. The tested groups per cell line were, control, GLU, DOC and combination. Treatment duration was 72 h. Cytotoxicity was assessed using sulforhodamine B (SRB) assay and half maximal inhibitory concentration (IC50) was calculated. Synergy analyses were performed using Calcusyn®software. Subsequent mechanistic studies included β-glucosidase activity assay, glucose uptake and apoptosis studies, namely annexin V-FITC assay and the protein expression of mitochondrial pathway signals including Bcl-2, Bax, Caspase 9 and 3 were assessed. Data are presented as mean ± SD; comparisons were carried out using one way analysis of variance (ANOVA) followed by Tukey-Kramer’s test for post hoc analysis.Results. GLU induced cytotoxicity in both cell lines in a concentration-dependent manner. The IC50 in PC-3 cells was significantly lower by 19% when compared to that of LNCaP cells. The IC50 of combining both drugs showed comparable effect to DOC in PC-3 but was tremendously lowered by 49% compared to the same group in LNCaP cell line. β-glucosidase activity was higher in LNCaP by about 67% compared to that determined in PC-3 cells while the glucose uptake in PC-3 cells was almost 2 folds that found in LNCaP cells. These results were directly correlated to the efficacy of GLU in each cell line. Treatment of PC cells with GLU as single agent or in combination with DOC induced significantly higher apoptosis as evidenced by Annexin V-staining. Apoptosis was significantly increased in combination group by 4.9 folds and by 2.1 Folds when compared to control in LNCaP cells and PC-3 cells; respectively. Similarly, the expression of Bcl-2 was significantly decreased while Bax, caspase 9 and 3 were significantly increased in the combined treatment groups compared to the control.Conclusion. GLU has a synergistic effect in combination with DOC as it increases the cell kill which can be attributed at least partially to apoptosis in both the tested cell lines and it is suggested as a new combination regimen to be considered in the treatment of the prostate cancer. Further experiments and clinical investigations are needed for assessment of that regimen. creator: Reem T. Attia creator: Mai F. Tolba creator: Ruchit Trivedi creator: Mariane G. Tadros creator: Hossam M.M. Arafa creator: Ashraf B. Abdel-Naim uri: https://doi.org/10.7717/peerj.2168 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Attia et al. title: Virus wars: using one virus to block the spread of another link: https://peerj.com/articles/2166 last-modified: 2016-06-29 description: The failure of traditional interventions to block and cure HIV infections has led to novel proposals that involve treating infections with therapeutic viruses–infectious viruses that specifically inhibit HIV propagation in the host. Early efforts in evaluating these proposals have been limited chiefly to mathematical models of dynamics, for lack of suitable empirical systems. Here we propose, develop and analyze an empirical system of a therapeutic virus that protects a host cell population against a lethal virus. The empirical system uses E. coli bacteria as the host cell population, an RNA phage as the lethal virus and a filamentous phage as the therapeutic virus. Basic dynamic properties are established for each virus alone and then together. Observed dynamics broadly agree with those predicted by a computer simulation model, although some differences are noted. Two cases of dynamics are contrasted, differing in whether the therapeutic virus is introduced before the lethal virus or after the lethal virus. The therapeutic virus increases in both cases but by different mechanisms. With the therapeutic virus introduced first, it spreads infectiously without any appreciable change in host dynamics. With the therapeutic virus introduced second, host abundance is depressed at the time therapy is applied; following an initial period of therapeutic virus spread by infection, the subsequent rise of protection is through reproduction by hosts already protected. This latter outcome is due to inheritance of the therapeutic virus state when the protected cell divides. Overall, the work establishes the feasibility and robustness to details of a viral interference using a therapeutic virus. creator: Matthew L. Paff creator: Scott L. Nuismer creator: Andrew Ellington creator: Ian J. Molineux creator: James J. Bull uri: https://doi.org/10.7717/peerj.2166 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Paff et al. title: The crouching of the shrew: Mechanical consequences of limb posture in small mammals link: https://peerj.com/articles/2131 last-modified: 2016-06-29 description: An important trend in the early evolution of mammals was the shift from a sprawling stance, whereby the legs are held in a more abducted position, to a parasagittal one, in which the legs extend more downward. After that transition, many mammals shifted from a crouching stance to a more upright one. It is hypothesized that one consequence of these transitions was a decrease in the total mechanical power required for locomotion, because side-to-side accelerations of the body have become smaller, and thus less costly with changes in limb orientation. To test this hypothesis we compared the kinetics of locomotion in two mammals of body size close to those of early mammals (< 40 g), both with parasagittally oriented limbs: a crouching shrew (Blarina brevicauda; 5 animals, 17 trials) and a more upright vole (Microtus pennsylvanicus; 4 animals, 22 trials). As predicted, voles used less mechanical power per unit body mass to perform steady locomotion than shrews did (P = 0.03). However, while lateral forces were indeed smaller in voles (15.6 ± 2.0% body weight) than in shrews (26.4 ± 10.9%; P = 0.046), the power used to move the body from side-to-side was negligible, making up less than 5% of total power in both shrews and voles. The most power consumed for both species was that used to accelerate the body in the direction of travel, and this was much larger for shrews than for voles (P = 0.01). We conclude that side-to-side accelerations are negligible for small mammals–whether crouching or more upright–compared to their sprawling ancestors, and that a more upright posture further decreases the cost of locomotion compared to crouching by helping to maintain the body’s momentum in the direction of travel. creator: Daniel K. Riskin creator: Corinne J. Kendall creator: John W. Hermanson uri: https://doi.org/10.7717/peerj.2131 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Riskin et al. title: A novel baculovirus-derived promoter with high activity in the baculovirus expression system link: https://peerj.com/articles/2183 last-modified: 2016-06-28 description: The baculovirus expression vector system (BEVS) has been widely used to produce a large number of recombinant proteins, and is becoming one of the most powerful, robust, and cost-effective systems for the production of eukaryotic proteins. Nevertheless, as in any other protein expression system, it is important to improve the production capabilities of this vector. The orf46 viral gene was identified among the most highly abundant sequences in the transcriptome of Spodoptera exigua larvae infected with its native baculovirus, the S. exigua multiple nucleopolyhedrovirus (SeMNPV). Different sequences upstream of the orf46 gene were cloned, and their promoter activities were tested by the expression of the GFP reporter gene using the Autographa californica nucleopolyhedrovirus (AcMNPV) vector system in different insect cell lines (Sf21, Se301, and Hi5) and in larvae from S. exigua and Trichoplusia ni. The strongest promoter activity was defined by a 120 nt sequence upstream of the ATG start codon for the orf46 gene. On average, GFP expression under this new promoter was more than two fold higher than the expression obtained with the standard polyhedrin (polh) promoter. Additionally, the orf46 promoter was also tested in combination with the polh promoter, revealing an additive effect over the polh promoter activity. In conclusion, this new characterized promoter represents an excellent alternative to the most commonly used baculovirus promoters for the efficient expression of recombinant proteins using the BEVS. creator: María Martínez-Solís creator: Silvia Gómez-Sebastián creator: José M. Escribano creator: Agata K. Jakubowska creator: Salvador Herrero uri: https://doi.org/10.7717/peerj.2183 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Martínez-Solís et al. title: Reciproc vs. hand instrumentation in dental practice: a study in routine care link: https://peerj.com/articles/2182 last-modified: 2016-06-28 description: Background. Little is known about the clinical impact of new root canal preparation systems in general dental practice under routine care conditions. Therefore, we compared hand instrumentation (H) with Reciproc (R) (VDW, Munich, Germany) preparation. The outcomes were endodontic related pain and oral health related quality of life (OHRQoL), evaluation of the procedures by the patients and the strain felt by the dentists during root canal therapy.Methods. Six dentists participated in the trial as practitioner–investigators. In the first phase of the trial they prepared root canals with H and in the second phase with R. The patients documented their pain felt with a visual analogue scale (VAS 100) and OHRQoL with the German short version of the oral health impact profile (OHIP-G-14) before treatment and before the completion of therapy and answered questions about how they experienced the treatment. The dentists documented their physical strain during treatment.Results. A total of 137 patients were included in the evaluation. 66 patients were treated with H, 71 with R. Pain reduction was 32.6 (SD 32.9) VAS (H) vs. 29.4 (SD 26.9) VAS (R) (p = 0.550), and the improvement of the OHIP-14 score was 5.5 (SD 9.2) (H) vs. 6.7 (SD 7.4) (R) (p = 0.383). There were no statistical differences in both groups. Significantly fewer patients felt stressed by the duration of treatment with R as with H (p = 0.018). Significantly more dentists reported that their general physical strain and the strain on their fingers were less severe with R than with H (p = 0.013 and p < 0.001).Discussion. H as well as R effectively reduced endodontic related pain and OHRQoL without statistical differences. R has advantages in terms of how patients experience the treatment and regarding the physical strain felt by the dentists. creator: Andreas Bartols creator: Claudius A. Reutter creator: Bernt-Peter Robra creator: Winfried Walther uri: https://doi.org/10.7717/peerj.2182 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Bartols et al. title: Collecting reliable clades using the Greedy Strict Consensus Merger link: https://peerj.com/articles/2172 last-modified: 2016-06-28 description: Supertree methods combine a set of phylogenetic trees into a single supertree. Similar to supermatrix methods, these methods provide a way to reconstruct larger parts of the Tree of Life, potentially evading the computational complexity of phylogenetic inference methods such as maximum likelihood. The supertree problem can be formalized in different ways, to cope with contradictory information in the input. Many supertree methods have been developed. Some of them solve NP-hard optimization problems like the well-known Matrix Representation with Parsimony, while others have polynomial worst-case running time but work in a greedy fashion (FlipCut). Both can profit from a set of clades that are already known to be part of the supertree. The Superfine approach shows how the Greedy Strict Consensus Merger (GSCM) can be used as preprocessing to find these clades. We introduce different scoring functions for the GSCM, a randomization, as well as a combination thereof to improve the GSCM to find more clades. This helps, in turn, to improve the resolution of the GSCM supertree. We find this modifications to increase the number of true positive clades by 18% compared to the currently used Overlap scoring. creator: Markus Fleischauer creator: Sebastian Böcker uri: https://doi.org/10.7717/peerj.2172 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Fleischauer and Böcker title: Shapes of leaves with parallel venation. Modelling of the Epipactis sp. (Orchidaceae) leaves with the help of a system of coupled elastic beams link: https://peerj.com/articles/2165 last-modified: 2016-06-28 description: Static properties of leaves with parallel venation, with particular emphasis on the genus EpipactisZinn, 1757 (Orchidaceae, Neottieae) have been modelled with coupled quasi-parallel elastic “beams.” The non-linear theory of strongly bended beams have been employed. The resulting boundary-value problem has been solved numerically with the help of the finite-difference method. Possible dislocations resulting in additional Dirac-delta like forces have been take into account. Morphological similarity of the model and real leaves has been obtained. In particular, the concentrated forces have been shown to cause undulation in the leaves. creator: Anna Jakubska-Busse creator: Maciej Janowicz creator: Luiza Ochnio creator: Beata Jackowska-Zduniak uri: https://doi.org/10.7717/peerj.2165 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Jakubska-Busse et al. title: Design and validation of a next generation sequencing assay for hereditary BRCA1 and BRCA2 mutation testing link: https://peerj.com/articles/2162 last-modified: 2016-06-28 description: Hereditary breast and ovarian cancer syndrome, caused by a germline pathogenic variant in the BRCA1 or BRCA2 (BRCA1/2) genes, is characterized by an increased risk for breast, ovarian, pancreatic and other cancers. Identification of those who have a BRCA1/2 mutation is important so that they can take advantage of genetic counseling, screening, and potentially life-saving prevention strategies. We describe the design and analytic validation of the Counsyl Inherited Cancer Screen, a next-generation-sequencing-based test to detect pathogenic variation in the BRCA1 and BRCA2 genes. We demonstrate that the test is capable of detecting single-nucleotide variants (SNVs), short insertions and deletions (indels), and copy-number variants (CNVs, also known as large rearrangements) with zero errors over a 114-sample validation set consisting of samples from cell lines and deidentified patient samples, including 36 samples with BRCA1/2pathogenic germline mutations. creator: Hyunseok P. Kang creator: Jared R. Maguire creator: Clement S. Chu creator: Imran S. Haque creator: Henry Lai creator: Rebecca Mar-Heyming creator: Kaylene Ready creator: Valentina S. Vysotskaia creator: Eric A. Evans uri: https://doi.org/10.7717/peerj.2162 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Kang et al. title: Modulation of the behavioral and electrical responses to the repellent DEET elicited by the pre-exposure to the same compound in Blattella germanica link: https://peerj.com/articles/2150 last-modified: 2016-06-28 description: Insects under different stimuli from the environment modify behavioural responses due to changes in the sensitivity of neurons at the peripheral and/or at the central level of the nervous system. This phenomenon is called neuronal plasticity, and sensory adaptation is an example of it. An insect repellent is a chemical that produces oriented movements of the insects away from its source. In this work we studied the modulation of the behavioural and electrical response to the repellent N, N-diethyl-3-methylbenzamide (DEET) in males of the German cockroach B. germanica produced by previous exposure to the same repellent.Methods. We determined repellency using a circular arena, one half of which was treated with DEET. The time spent by insects in each half of the arena was measured, and a repellency coefficient (RC) was calculated. The RCs of pre-exposed and non-pre-exposed insects were compared. To determine a possible role of nitric oxide in the modulation of the response to DEET after pre-exposure, the nitric oxide donor S-nitroso-acetyl-cysteine (SNAC) was applied on cockroaches’ antennae. The electrical activity of the cockroaches’ antennae in response to DEET was recorded using electroantennogram (EAG) technique. The response to DEET was recorded also after a long stimulation with the same repellent, and after topical application of SNAC and dbcGMP (a cGMP analogue) on the antennae.Results. We found that previous exposure of B. germanica males to the repellent DEET produced an increase of the repellency at the behavioural level, measured as RC. A possible role of nitric oxide (NO) in the transduction pathway of this phenomenon is suggested, since treatment of the cockroaches with the NO donor SNAC also produced an increase of the repellency elicited by DEET. On the other hand, the response of the cockroaches’ antennae exposed to DEET was determined electrophysiologically. The electrical activity in response to DEET decreased when the insects’ antennae were stimulated with a long pulse of the repellent. The activity of the antennae was restored after 10 min. Treatment of the antennae either with SNAC or dbGMPc also produced a decrease in the response of the antennae to the repellent.Discussion.The previous exposure to a chemical stimulus can modify the behaviour associated to the same stimulus, increasing or decreasing the behavioural response. In the case of DEET we found that pre-exposure increased DEET repellency in male cockroaches. We also found NO involvement in a similar phenomenon. On the other hand, the test showed that DEET is perceived by insects’ antennae as an odour. A long exposure of the antennae to DEET caused a transient decrease in the response of the antennae to the same compound. The same effect was achieved by treating the antennae with SNAC or dbcGMP, suggesting the involvement of the NO/cGMP system in the transduction pathway of the sensory adaptation phenomenon elicited by an odour in this species. creator: Valeria Sfara creator: Gastón A. Mougabure-Cueto creator: Paola A. González-Audino uri: https://doi.org/10.7717/peerj.2150 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Sfara et al. title: Protein-RNA linkage and posttranslational modifications of feline calicivirus and murine norovirus VPg proteins link: https://peerj.com/articles/2134 last-modified: 2016-06-28 description: Members of the Caliciviridae family of positive sense RNA viruses cause a wide range of diseases in both humans and animals. The detailed characterization of the calicivirus life cycle had been hampered due to the lack of robust cell culture systems and experimental tools for many of the members of the family. However, a number of caliciviruses replicate efficiently in cell culture and have robust reverse genetics systems available, most notably feline calicivirus (FCV) and murine norovirus (MNV). These are therefore widely used as representative members with which to examine the mechanistic details of calicivirus genome translation and replication. The replication of the calicivirus RNA genome occurs via a double-stranded RNA intermediate that is then used as a template for the production of new positive sense viral RNA, which is covalently linked to the virus-encoded protein VPg. The covalent linkage to VPg occurs during genome replication via the nucleotidylylation activity of the viral RNA-dependent RNA polymerase. Using FCV and MNV, we used mass spectrometry-based approach to identify the specific amino acid linked to the 5′ end of the viral nucleic acid. We observed that both VPg proteins are covalently linked to guanosine diphosphate (GDP) moieties via tyrosine positions 24 and 26 for FCV and MNV respectively. These data fit with previous observations indicating that mutations introduced into these specific amino acids are deleterious for viral replication and fail to produce infectious virus. In addition, we also detected serine phosphorylation sites within the FCV VPg protein with positions 80 and 107 found consistently phosphorylated on VPg-linked viral RNA isolated from infected cells. This work provides the first direct experimental characterization of the linkage of infectious calicivirus viral RNA to the VPg protein and highlights that post-translational modifications of VPg may also occur during the viral life cycle. creator: Allan Olspert creator: Myra Hosmillo creator: Yasmin Chaudhry creator: Lauri Peil creator: Erkki Truve creator: Ian Goodfellow uri: https://doi.org/10.7717/peerj.2134 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Olspert et al. title: Complete plastid genome sequence of Primula sinensis (Primulaceae): structure comparison, sequence variation and evidence for accD transfer to nucleus link: https://peerj.com/articles/2101 last-modified: 2016-06-28 description: Species-rich genus Primula L. is a typical plant group with which to understand genetic variance between species in different levels of relationships. Chloroplast genome sequences are used to be the information resource for quantifying this difference and reconstructing evolutionary history. In this study, we reported the complete chloroplast genome sequence of Primula sinensis and compared it with other related species. This genome of chloroplast showed a typical circular quadripartite structure with 150,859 bp in sequence length consisting of 37.2% GC base. Two inverted repeated regions (25,535 bp) were separated by a large single-copy region (82,064 bp) and a small single-copy region (17,725 bp). The genome consists of 112 genes, including 78 protein-coding genes, 30 tRNA genes and four rRNA genes. Among them, seven coding genes, seven tRNA genes and four rRNA genes have two copies due to their locations in the IR regions. The accD and infA genes lacking intact open reading frames (ORF) were identified as pseudogenes. SSR and sequence variation analyses were also performed on the plastome of Primula sinensis, comparing with another available plastome of P. poissonii. The four most variable regions, rpl36–rps8, rps16–trnQ, trnH–psbA and ndhC–trnV, were identified. Phylogenetic relationship estimates using three sub-datasets extracted from a matrix of 57 protein-coding gene sequences showed the identical result that was consistent with previous studies. A transcript found from P. sinensis transcriptome showed a high similarity to plastid accD functional region and was identified as a putative plastid transit peptide at the N-terminal region. The result strongly suggested that plastid accD has been functionally transferred to the nucleus in P. sinensis. creator: Tong-Jian Liu creator: Cai-Yun Zhang creator: Hai-Fei Yan creator: Lu Zhang creator: Xue-Jun Ge creator: Gang Hao uri: https://doi.org/10.7717/peerj.2101 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Liu et al. title: Using homogenization, sonication and thermo-sonication to inactivate fungi link: https://peerj.com/articles/2020 last-modified: 2016-06-28 description: Ultrasound (US), Thermo-sonication (TS) and High Pressure Homogenization (HPH) were studied as tools to inactivate the spores of Penicillium spp. and Mucor spp. inoculated in distilled water. For US, the power ranged from 40% to 100%, pulse from 2 to 10 s, and duration of the treatment from 2 to 10 min. TS was performed combining US (40–80% of power, for 8 min and pulse of 2 s) with a thermal treatment (50, 55 and 60°C at 4, 8 and 12 min). Homogenization was done at 30–150 MPa for 1, 2 and 3 times. Power was the most important factors to determine the antifungal effect of US and TS towards the conidia of Penicillium spp.; on the other hand, in US treatments Mucor spp. was also affected by pulse and time. HPH exerted a significant antifungal effect only if the highest pressures were applied for 2–3 times. creator: Daniela Campaniello creator: Antonio Bevilacqua creator: Milena Sinigaglia creator: Maria Rosaria Corbo uri: https://doi.org/10.7717/peerj.2020 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Campaniello et al. title: Monitoring coastal pollution associated with the largest oil refinery complex of Venezuela link: https://peerj.com/articles/2171 last-modified: 2016-06-23 description: This study evaluated pollution levels in water and sediments of Península de Paraguaná and related these levels with benthic macrofauna along a coastal area where the largest Venezuelan oil refineries have operated over the past 60 years. For this, the concentration of heavy metals, of hydrocarbon compounds and the community structure of the macrobenthos were examined at 20 sites distributed along 40 km of coastline for six consecutive years, which included windy and calm seasons. The spatial variability of organic and inorganic compounds showed considerably high coastal pollution along the study area, across both years and seasons. The southern sites, closest to the refineries, had consistently higher concentrations of heavy metals and organic compounds in water and sediments when compared to those in the north. The benthic community was dominated by polychaetes at all sites, seasons and years, and their abundance and distribution were significantly correlated with physical and chemical characteristics of the sediments. Sites close to the oil refineries were consistently dominated by families known to tolerate xenobiotics, such as Capitellidae and Spionidae. The results from this study highlight the importance of continuing long-term environmental monitoring programs to assess the impact of effluent discharge and spill events from the oil refineries that operate in the western coast of Paraguaná, Venezuela. creator: Aldo Croquer creator: David Bone creator: Carolina Bastidas creator: Ruth Ramos creator: Elia García uri: https://doi.org/10.7717/peerj.2171 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Croquer et al. title: Local avian density influences risk of mortality from window strikes link: https://peerj.com/articles/2170 last-modified: 2016-06-23 description: Up to a billion birds die per year in North America as a result of striking windows. Both transparent and reflective glass panes are a cause for concern, misleading birds by either acting as invisible, impenetrable barriers to desired resources, or reflecting those resources over a large surface area. A high number of window strikes occur during migration, but little is known about the factors of susceptibility, or whether particular avian taxa are more vulnerable than others. We report on a study of window strikes and mist-netting data at the Virginia Zoological Park (Norfolk, Virginia, USA), conducted in the autumn of 2013 and 2014. We focused on three factors likely to contribute to an individual’s predisposition to collide with windows: (i) taxonomic classification, (ii) age, and (iii) migrant vs. resident status. Thrushes, dominated by the partial migrant American Robin (Turdus migratorius), were significantly less likely to strike glass than be sampled in mist nets (χ2 = 9.21, p = 0.002), while wood-warblers (Parulidae) were more likely to strike than expected (χ2 = 13.55, p < 0.001). The proportion of juveniles striking windows (45.4%) was not significantly different (χ2 = 0.05, p = 0.827) than the population of juvenile birds naturally occurring at the zoo (48.8%). Migrants, however, were significantly more susceptible to window strikes than residents (χ2 = 6.35, p = 0.012). Our results suggest that resident birds are able to learn to avoid and thus reduce their likelihood of striking windows; this intrinsic risk factor may help explain the apparent susceptibility of certain taxa to window strikes. creator: Ann M. Sabo creator: Natasha D.G. Hagemeyer creator: Ally S. Lahey creator: Eric L. Walters uri: https://doi.org/10.7717/peerj.2170 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Sabo et al. title: Determinants of acute mortality of Hippodamia convergens (Coleoptera: Coccinellidae) to ultra-low volume permethrin used for mosquito management link: https://peerj.com/articles/2167 last-modified: 2016-06-23 description: There are relatively few experimental studies and risk assessments of the effects on non-target insects from ultra-low volume (ULV) insecticides used for management of adult mosquitoes. Therefore, we evaluated factors that may influence the ability of an insect to intercept the insecticide at the time of application by using Hippodamia convergens (Coleoptera: Coccinellidae) in field bioassay experiments in 2011 and 2015. Treatment factors included different distances, two cage heights (ground-level and 1.5 m above ground) to the point of the application, and covered vs. uncovered cage faces (2015 only). Insecticides used included a water-based formulation (Aqua-Reslin®) and an oil-based formulation (Permanone® 30-30) of permethrin. Cage height was highly significant both years, with much less acute (i.e., short-term exposure) mortality at ground-level compared with 1.5 m. In 2011, acute mortality was less at ground-level (mean = 3.2%, median = 0%) compared to 1.5 m (mean = 85.2%, median = 100%). Cage type also was highly significant, with less mortality in covered cages compared to uncovered cages. Mortality by cage height and cage type was as follows: ground level, covered cage (mean = 2.8%, median = 0.1%); ground level, uncovered cage (mean = 41.9%, median = 9.6%); 1.5 m, covered cage (mean = 6.8%, median = 0%); 1.5 m, uncovered cage (mean = 83.7%, median = 100%). Results suggest that acute mortality to non-target insects may vary considerably based on their height and their ability to directly intercept the insecticide as the aerosol passes through the area being sprayed. creator: Robert K.D. Peterson creator: Collin J. Preftakes creator: Jennifer L. Bodin creator: Christopher R. Brown creator: Alyssa M. Piccolomini creator: Jerome J. Schleier uri: https://doi.org/10.7717/peerj.2167 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Peterson et al. title: Stochasticity in space, persistence in time: genetic heterogeneity in harbour populations of the introduced ascidian Styela plicata link: https://peerj.com/articles/2158 last-modified: 2016-06-23 description: Spatio-temporal changes in genetic structure among populations provide crucial information on the dynamics of secondary spread for introduced marine species. However, temporal components have rarely been taken into consideration when studying the population genetics of non-indigenous species. This study analysed the genetic structure of Styela plicata, a solitary ascidian introduced in harbours and marinas of tropical and temperate waters, across spatial and temporal scales. A fragment of the mitochondrial gene Cytochrome Oxidase subunit I (COI) was sequenced from 395 individuals collected at 9 harbours along the NW Mediterranean coast and adjacent Atlantic waters (> 1,200 km range) at two time points 5 years apart (2009 and 2014). The levels of gene diversity were relatively low for all 9 locations in both years. Analyses of genetic differentiation and distribution of molecular variance revealed strong genetic structure, with significant differences among many populations, but no significant differences among years. A weak and marginally significant correlation between geographic distance and gene differentiation was found. Our results revealed spatial structure and temporal genetic homogeneity in S. plicata, suggesting a limited role of recurrent, vessel-mediated transport of organisms among small to medium-size harbours. Our study area is representative of many highly urbanized coasts with dense harbours. In these environments, the episodic chance arrival of colonisers appears to determine the genetic structure of harbour populations and the genetic composition of these early colonising individuals persists in the respective harbours, at least over moderate time frames (five years) that encompass ca. 20 generations of S. plicata. creator: Mari-Carmen Pineda creator: Beatriz Lorente creator: Susanna López-Legentil creator: Creu Palacín creator: Xavier Turon uri: https://doi.org/10.7717/peerj.2158 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Pineda et al. title: Five new species and one new genus of recent miliolid foraminifera from Raja Ampat (West Papua, Indonesia) link: https://peerj.com/articles/2157 last-modified: 2016-06-23 description: Raja Ampat is an archipelago of about 1,500 small islands located northwest off the Bird’s Head Peninsula of Indonesia’s West Papua province. It is part of the Coral Triangle, a region recognized as the “epicenter” of tropical marine biodiversity. In the course of a large-scale survey on shallow benthic foraminifera we have discovered one new genus and five new species of recent miliolid benthic foraminifera from the highly diverse reefal and nearshore environments. The new fischerinid genus Dentoplanispirinella is characterized by its planispiral coiling and by the presence of a simple tooth, that differentiate it from Planispirinella Wiesner. It is represented in our sample material by the new species Dentoplanispirinella occulta. The other four species described herein are Miliolinella moia, Miliolinella undina, Triloculina kawea and Siphonaperta hallocki. All new species are comparatively rare and occur sporadically in the sample material. Detailed morphological descriptions, scanning electron microscopy pictures of complete and dissected specimens as well as micro-computed tomography images are provided. creator: Meena Förderer creator: Martin R. Langer uri: https://doi.org/10.7717/peerj.2157 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Förderer and Langer title: Does our legal minimum drinking age modulate risk of first heavy drinking episode soon after drinking onset? Epidemiological evidence for the United States, 2006–2014 link: https://peerj.com/articles/2153 last-modified: 2016-06-23 description: Background. State-level ‘age 21’ drinking laws conform generally with the United States National Minimum Drinking Age Act of 1984 (US), and are thought to protect young people from adverse drinking experiences such as heavy episodic drinking (HED, sometimes called ‘binge drinking’). We shed light on this hypothesis while estimating the age-specific risk of transitioning from 1st full drink to 1st HED among 12-to-23-year-old newly incident drinkers, with challenge to a “gender gap” hypothesis and male excess described in HED prevalence reports.Methods. The study population consisted of non-institutionalized civilians in the United States, with nine independently drawn nationally representative samples of more than 40,000 12-to-23-year-olds (2006–2014). Standardized audio computer-assisted self-interviews identified 43,000 newly incident drinkers (all with 1st HED evaluated within 12 months of drinking onset). Estimated age-specific HED risk soon after first full drink is evaluated for males and females.Results. Among 12-to-23-year-old newly incident drinkers, an estimated 20–30% of females and 35–45% of males experienced their 1st HED within 12 months after drinking onset. Before mid-adolescence, there is no male excess in such HED risk. Those who postponed drinking to age 21 are not spared (27% for ‘postponer’ females; 95% CI [24–30]; 42% for ‘postponer’ males; 95% CI [38–45]). An estimated 10–18% females and 10–28% males experienced their 1st HED in the same month of their 1st drink; peak HED risk estimates are 18% for ‘postponer’ females (95% CI [15–21]) and 28% for ‘postponer’ males (95% CI [24–31]).Conclusions. In the US, one in three young new drinkers transition into HED within 12 months after first drink. Those who postpone the 1st full drink until age 21 are not protected. Furthermore, ‘postponers’ have substantial risk for very rapid transition to HED. A male excess in this transition to HED is not observed until after age 14. creator: Hui G. Cheng creator: James C. Anthony uri: https://doi.org/10.7717/peerj.2153 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Cheng and Anthony title: Biodiversity management of organic orchard enhances both ecological and economic profitability link: https://peerj.com/articles/2137 last-modified: 2016-06-23 description: Organic farming has been regarded as an alternative solution for both agricultural sustainability and human health maintenance. Few researches have concentrated on the differences of biodiversity and eco-economic benefits between organic and conventional orchards. Organic management (OM) of orchards mainly includes taking advantage of natural enemies and beneficial weeds as well as soil organisms and controlling harmful pests. Here we conducted a three-year experiment on the effects of managing biodiversity in an organic apple orchard, using cattle manure to enrich soil biota, propagating native plant to suppress weeds and applying ecological pest management to control pests. The effect was assessed against the conventional management (CM) model. We found that OM enhanced soil organic carbon, total nitrogen, microbial biomass carbon and nitrogen. The 16S rDNA high-throughput sequencing results indicated that the dominant bacterial phyla of the top soil were Proteobacteria and Actinobacteria, and OM had richer bacteria diversity with a 7% higher Shannon’s index than the CM. In particular, the relative abundance of rhizobium in the OM was higher than that of the CM. For OM, Duchesnea indica was an ideal ground-cover plant to control weeds through winning the niche competition and thus decreased weeds’ Simpson, Shannon–Wiener and Pielou index by 38.2%, 53.8% and 16.9% separately. The phototactic pests’ weight and scarab beetle’s population were effectively decreased by 35% and 86% respectively through long time control and prevention. OM had an average of 20 times more earthworms than CM, and the maximum density had reached 369 m−2 (0–20 cm soil). The dominant earthworm species of the OM were detritivores which preferring soil with high organic matter content. Due to no synthetic chemicals being used, the OM produced much safer apple fruits which were sold at high prices. Economically, up to a 103% increase of output–input ratio had been achieved in the OM. Our study clearly demonstrated that biodiversity management without chemical pollution increased the biodiversity of beneficial organisms, reduced antagonists of the fruit tree, and enhanced economic benefits of the apple orchard. creator: Jie Meng creator: Lijun Li creator: Haitao Liu creator: Yong Li creator: Caihong Li creator: Guanglei Wu creator: Xiaofan Yu creator: Liyue Guo creator: Da Cheng creator: Mahmud A. Muminov creator: Xiaotian Liang creator: Gaoming Jiang uri: https://doi.org/10.7717/peerj.2137 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Meng et al. title: Adaptive changes in chlorophyll content and photosynthetic features to low light in Physocarpus amurensis Maxim and Physocarpus opulifolius “Diabolo” link: https://peerj.com/articles/2125 last-modified: 2016-06-23 description: The present study aims to investigate the differences in leaf pigment content and the photosynthetic characteristics under natural and low light intensities between the Chinese native Physocarpus amurensis Maxim and the imported Physocarpus opulifolius “Diabolo” from North America. We aim to discuss the responses and the adaptive mechanism of these two cultivars of Physocarpus to a low light environment. The results show that the specific leaf area (SLA) and the chlorophyll content were significantly increased in the leaves of both Physocarpus cultivars in response to a low light intensity, and the SLA and chlorophyll content were higher in the leaves of low light-treated P. opulifolius “Diabolo” compared with the leaves of low light-treated P. amurensis Maxim. Moreover, the content of anthocyanin was markedly reduced in the leaves of P. opulifolius “Diabolo” under low light intensity, which allowed for a greater capacity of photon capture under the low light condition. Under natural light, the photosynthetic carbon assimilation capacity was greater in the leaves of P. amurensis Maxim compared with the leaves of P. opulifolius “Diabolo” that were rich with anthocyanin. However, in response to low light, AQY, Pmax, LCP and LSP decreased to a lesser extent in the leaves of P. opulifolius “Diabolo” compared with the leaves of P. amurensis Maxim. These results suggest that P. opulifolius “Diabolo” exhibits a greater ability in adaption to low light, and it is probably related to the relatively higher chlorophyll content and the smaller SLA in the leaves of P. opulifolius “Diabolo.” In addition, the low light intensity resulted in a reduced photochemical activity of photosystem (PS) II in the leaves of both Physocarpus, as evidenced by increased values of the relative variable fluorescence at point J and point I on the OJIP curve. This result suggests that the electron acceptor in PS II was the major responsive site to the low light stress in the leaves of both Physocarpus cultivars, and that the low light intensity significantly inhibited electron transfer on the acceptor side of PS II and reduced the activity of the oxygen-evolving complex (OEC) in the leaves of both Physocarpus cultivars. The PS II function in P. opulifolius “Diabolo” was higher than that in P. amurensis Maxim in response to low light. Under low light, the composition of photosynthetic pigments was altered in the leaves of P. opulifolius “Diabolo” in order to maintain a relatively high activity of primary photochemical reactions, and this is the basis of the greater photosynthetic carbon assimilation capacity and one of the main reasons for the better shade-tolerance in P. opulifolius “Diabolo.” creator: Huihui Zhang creator: Haixiu Zhong creator: JIfeng Wang creator: Xin Sui creator: Nan Xu uri: https://doi.org/10.7717/peerj.2125 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Zhang et al. title: Genetic markers of inflammation may not contribute to metabolic traits in Mexican children link: https://peerj.com/articles/2090 last-modified: 2016-06-23 description: Background: Low-grade chronic inflammation is a common feature of obesity and its cardio-metabolic complications. However, little is known about a possible causal role of inflammation in metabolic disorders. Mexico is among the countries with the highest obesity rates in the world and the admixed Mexican population is a relevant sample due to high levels of genetic diversity.Methods: Here, we studied 1,462 Mexican children recruited from Mexico City. Six genetic variants in five inflammation-related genes were genotyped: rs1137101 (leptin receptor (LEPR)), rs7305618 (hepatocyte nuclear factor 1 alpha (HNF1A)), rs1800629 (tumor necrosis factor alpha (TNFA)), rs1800896, rs1800871 (interleukin-10 (IL-10)), rs1862513 (resistin (RETN)). Ten continuous and eight binary traits were assessed. Linear and logistic regression models were used adjusting for age, sex, and recruitment centre.Results: We found that one SNP displayed a nominal evidence of association with a continuous trait: rs1800871 (IL-10) with LDL (beta = −0.068 ± 1.006, P = 0.01). Subsequently, we found one nominal association with a binary trait: rs7305618 (HNF1A) with family history of hypertension (odds-ratio = 1.389 [1.054–1.829], P = 0.02). However, no P-value passed the Bonferroni correction for multiple testing.Discussion: Our data in a Mexican children population are consistent with previous reports in European adults in failing to demonstrate an association between inflammation-associated single nucleotide polymorphisms (SNPs) and metabolic traits. creator: Neeti Vashi creator: Carolina Stryjecki creator: Jesus Peralta-Romero creator: Fernando Suarez creator: Jaime Gomez-Zamudio creator: Ana I. Burguete-Garcia creator: Miguel Cruz creator: David Meyre uri: https://doi.org/10.7717/peerj.2090 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Vashi et al. title: The in vitro and in vivo effects of constitutive light expression on a bioluminescent strain of the mouse enteropathogen Citrobacter rodentium link: https://peerj.com/articles/2130 last-modified: 2016-06-22 description: Bioluminescent reporter genes, such as those from fireflies and bacteria, let researchers use light production as a non-invasive and non-destructive surrogate measure of microbial numbers in a wide variety of environments. As bioluminescence needs microbial metabolites, tagging microorganisms with luciferases means only live metabolically active cells are detected. Despite the wide use of bioluminescent reporter genes, very little is known about the impact of continuous (also called constitutive) light expression on tagged bacteria. We have previously made a bioluminescent strain of Citrobacter rodentium, a bacterium which infects laboratory mice in a similar way to how enteropathogenic Escherichia coli (EPEC) and enterohaemorrhagic E. coli (EHEC) infect humans. In this study, we compared the growth of the bioluminescent C. rodentium strain ICC180 with its non-bioluminescent parent (strain ICC169) in a wide variety of environments. To understand more about the metabolic burden of expressing light, we also compared the growth profiles of the two strains under approximately 2,000 different conditions. We found that constitutive light expression in ICC180 was near-neutral in almost every non-toxic environment tested. However, we also found that the non-bioluminescent parent strain has a competitive advantage over ICC180 during infection of adult mice, although this was not enough for ICC180 to be completely outcompeted. In conclusion, our data suggest that constitutive light expression is not metabolically costly to C. rodentium and supports the view that bioluminescent versions of microbes can be used as a substitute for their non-bioluminescent parents to study bacterial behaviour in a wide variety of environments. creator: Hannah M. Read creator: Grant Mills creator: Sarah Johnson creator: Peter Tsai creator: James Dalton creator: Lars Barquist creator: Cristin G. Print creator: Wayne M. Patrick creator: Siouxsie Wiles uri: https://doi.org/10.7717/peerj.2130 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Read et al. title: Preserving and vouchering butterflies and moths for large-scale museum-based molecular research link: https://peerj.com/articles/2160 last-modified: 2016-06-22 description: Butterflies and moths (Lepidoptera) comprise significant portions of the world’s natural history collections, but a standardized tissue preservation protocol for molecular research is largely lacking. Lepidoptera have traditionally been spread on mounting boards to display wing patterns and colors, which are often important for species identification. Many molecular phylogenetic studies have used legs from pinned specimens as the primary source for DNA in order to preserve a morphological voucher, but the amount of available tissue is often limited. Preserving an entire specimen in a cryogenic freezer is ideal for DNA preservation, but without an easily accessible voucher it can make specimen identification, verification, and morphological work difficult. Here we present a procedure that creates accessible and easily visualized “wing vouchers” of individual Lepidoptera specimens, and preserves the remainder of the insect in a cryogenic freezer for molecular research. Wings are preserved in protective holders so that both dorsal and ventral patterns and colors can be easily viewed without further damage. Our wing vouchering system has been implemented at the University of Maryland (AToL Lep Collection) and the University of Florida (Florida Museum of Natural History, McGuire Center of Lepidoptera and Biodiversity), which are among two of the largest Lepidoptera molecular collections in the world. creator: Soowon Cho creator: Samantha W. Epstein creator: Kim Mitter creator: Chris A. Hamilton creator: David Plotkin creator: Charles Mitter creator: Akito Y. Kawahara uri: https://doi.org/10.7717/peerj.2160 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Cho et al. title: In vitro evaluation of antifungal activity of monolaurin against Candida albicans biofilms link: https://peerj.com/articles/2148 last-modified: 2016-06-22 description: Monolaurin (also known as glycerol monolaurate) is a natural compound found in coconut oil and is known for its protective biological activities as an antimicrobial agent. The nature of oral candidiasis and the increased antifungal resistance demand the search for novel antifungal therapeutic agents. In this study, we examine the antifungal activity of monolaurin against Candida albicans biofilms (strain ATCC:SC5314/MYA2876) in vitro and investigate whether monolaurin can alter gene expression of host inflammatory cytokines, IL-1α and IL-1β. In a co-culture model, oral fibroblast cells were cultured simultaneously with C. albicans for 24 hrs followed by the exposure to treatments of monolaurin (3.9–2,500 µM), positive control fluconazole (32.2 µM), and vehicle control group (1% ethanol), which was a model used to evaluate the cytotoxicity of monolaurin on fibroblasts as well as to analyze morphological characteristics of biofilms through fluorescence microscopy. In addition, the co-culture model was used for RNA extraction of oral fibroblasts to assess gene expression of host inflammatory cytokines, using quantitative real-time PCR. Our results showed the MIC and MFC of monolaurin were in the range 62.5–125 µM and 125–250 µM, respectively. Biofilm antifungal assay showed significant reduction in Log (CFU/ml) of biofilms treated with 1,250 and 2,500 µM of 1-monolaurin when compared to the control groups . There was also a significant down-regulation of IL-1α and IL-1β in the co-culture treated with monolaurin. It can be concluded that monolaurin has a potential antifungal activity against C. albicans and can modulate the pro-inflammatory response of the host. creator: Dalia Seleem creator: Emily Chen creator: Bruna Benso creator: Vanessa Pardi creator: Ramiro M. Murata uri: https://doi.org/10.7717/peerj.2148 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Seleem et al. title: Simple approach for ranking structure determining residues link: https://peerj.com/articles/2136 last-modified: 2016-06-22 description: Mutating residues has been a common task in order to study structural properties of the protein of interest. Here, we propose and validate a simple method that allows the identification of structural determinants; i.e., residues essential for preservation of the stability of global structure, regardless of the protein topology. This method evaluates all of the residues in a 3D structure of a given globular protein by ranking them according to their connectivity and movement restrictions without topology constraints. Our results matched up with sequence-based predictors that look up for intrinsically disordered segments, suggesting that protein disorder can also be described with the proposed methodology. creator: Oscar D. Luna-Martínez creator: Abraham Vidal-Limón creator: Miryam I. Villalba-Velázquez creator: Rosalba Sánchez-Alcalá creator: Ramón Garduño-Juárez creator: Vladimir N. Uversky creator: Baltazar Becerril uri: https://doi.org/10.7717/peerj.2136 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Luna-Martínez et al. title: Potential ecosystem service delivery by endemic plants in New Zealand vineyards: successes and prospects link: https://peerj.com/articles/2042 last-modified: 2016-06-22 description: Vineyards worldwide occupy over 7 million hectares and are typically virtual monocultures, with high and costly inputs of water and agro-chemicals. Understanding and enhancing ecosystem services can reduce inputs and their costs and help satisfy market demands for evidence of more sustainable practices. In this New Zealand work, low-growing, endemic plant species were evaluated for their potential benefits as Service Providing Units (SPUs) or Ecosystem Service Providers (ESPs). The services provided were weed suppression, conservation of beneficial invertebrates, soil moisture retention and microbial activity. The potential Ecosystem Dis-services (EDS) from the selected plant species by hosting the larvae of a key vine moth pest, the light-brown apple moth (Epiphyas postvittana), was also quantified. Questionnaires were used to evaluate winegrowers’ perceptions of the value of and problems associated with such endemic plant species in their vineyards. Growth and survival rates of the 14 plant species, in eight families, were evaluated, with Leptinella dioica (Asteraceae) and Acaena inermis ‘purpurea’ (Rosaceae) having the highest growth rates in terms of area covered and the highest survival rate after 12 months. All 14 plant species suppressed weeds, with Leptinella squalida, Geranium sessiliforum (Geraniaceae), Hebe chathamica (Plantaginaceae), Scleranthus uniflorus (Caryophyllaceae) and L. dioica, each reducing weed cover by >95%. Plant species also differed in the diversity of arthropods that they supported, with the Shannon Wiener diversity index (H′) for these taxa ranging from 0 to 1.3. G. sessiliforum and Muehlenbeckia axillaris (Polygonaceae) had the highest invertebrate diversity. Density of spiders was correlated with arthropod diversity and G. sessiliflorum and H. chathamica had the highest densities of these arthropods. Several plant species associated with higher soil moisture content than in control plots. The best performing species in this context were A. inermis ‘purpurea’ and Lobelia angulata (Lobeliaceae). Soil beneath all plant species had a higher microbial activity than in control plots, with L. dioica being highest in this respect. Survival proportion to the adult stage of the moth pest, E. postvittana, on all plant species was poor (<0.3). When judged by a ranking combining multiple criteria, the most promising plant species were (in decreasing order) G. sessiliflorum, A. inermis ‘purpurea’, H. chathamica, M. axillaris, L. dioica, L. angulata, L. squalida and S. uniflorus. Winegrowers surveyed said that they probably would deploy endemic plants around their vines. This research demonstrates that enhancing plant diversity in vineyards can deliver SPUs, harbour ESPs and therefore deliver ES. The data also shows that growers are willing to follow these protocols, with appropriate advice founded on sound research. creator: Morgan W. Shields creator: Jean-Marie Tompkins creator: David J. Saville creator: Colin D. Meurk creator: Stephen Wratten uri: https://doi.org/10.7717/peerj.2042 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Shields et al. title: Towards evenly distributed grazing patterns: including social context in sheep management strategies link: https://peerj.com/articles/2152 last-modified: 2016-06-21 description: Background. A large proportion of natural grasslands around the world is exposed to overgrazing resulting in land degradation and biodiversity loss. Although there is an increasing effort in the promotion of sustainable livestock management, rangeland degradation still occurs because animals’ foraging behaviour is highly selective at different spatial scales. The assessment of the ecological mechanisms modulating the spatial distribution of grazing and how to control it has critical implications for long term conservation of resources and the sustainability of livestock production. Considering the relevance of social interactions on animals’ space use patterns, our aim was to explore the potential effects of including animals’ social context into management strategies using domestic sheep grazing in rangelands as case study.Methods. We used GPS data from 19 Merino sheep (approximately 10% of the flock) grazing on three different paddocks (with sizes from 80 to 1000 Ha) during a year, to estimate resource selection functions of sheep grazing in flocks of different levels of heterogeneity. We assessed the effects of sheep class (i.e., ewes, wethers, and hoggets), age, body condition and time since release on habitat selection patterns.Results. We found that social rank was reflected on sheep habitat use, where dominant individuals (i.e., reproductive females) used more intensively the most preferred areas and low-ranked (i.e., yearlings) used less preferred areas. Our results showed that when sheep grazed on more heterogeneous flocks, grazing patterns were more evenly distributed at all the paddocks considered in this study. On the other hand, when high-ranked individuals were removed from the flock, low-ranked sheep shifted their selection patterns by increasing the use of the most preferred areas and strongly avoided to use less preferred sites (i.e., a highly selective grazing behaviour).Discussion. Although homogenization and segregation of flocks by classes are common practices to increase flock productivity, we are proposing an alternative that employs behavioural interactions in heterogeneous flocks to generate more evenly distributed grazing patterns. This practice can be combined with other practices such as rotational grazing and guardian dogs (to decrease mortality levels that may be generated by sheep grazing on more risky habitats). This does not imply any modifications of livestock stocking rates and densities or any additional investments for labour and materials. Considering livestock behaviour is critical for the design of sustainable management practices that balance landscape conservation and livestock productivity. creator: Agustina di Virgilio creator: Juan Manuel Morales uri: https://doi.org/10.7717/peerj.2152 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 di Virgilio and Morales title: First records of Canis dirus and Smilodon fatalis from the late Pleistocene Tule Springs local fauna, upper Las Vegas Wash, Nevada link: https://peerj.com/articles/2151 last-modified: 2016-06-21 description: Late Pleistocene groundwater discharge deposits (paleowetlands) in the upper Las Vegas Wash north of Las Vegas, Nevada, have yielded an abundant and diverse vertebrate fossil assemblage, the Tule Springs local fauna (TSLF). The TSLF is the largest open-site vertebrate fossil assemblage dating to the Rancholabrean North American Land Mammal Age in the southern Great Basin and Mojave Desert. Over 600 discrete body fossil localities have been recorded from the wash, including an area that now encompasses Tule Springs Fossil Beds National Monument (TUSK). Paleowetland sediments exposed in TUSK named the Las Vegas Formation span the last 250 ka, with fossiliferous sediments spanning ∼100–13 ka. The recovered fauna is dominated by remains of Camelopsand Mammuthus, and also includes relatively common remains of extinct Equusand Bisonas well as abundant vertebrate microfaunal fossils. Large carnivorans are rare, with only Puma concolor and Panthera atrox documented previously. Postcranial remains assigned to the species Canis dirus (dire wolf) and Smilodon fatalis (sabre-toothed cat) represent the first confirmed records of these species from the TSLF, as well as the first documentation of Canis dirus in Nevada and the only known occurrence of Smilodonin southern Nevada. The size of the recovered canid fossil precludes assignment to other Pleistocene species of Canis. The morphology of the felid elements differentiates them from other large predators such as Panthera, Homotherium, and Xenosmilus, and the size of the fossils prevents assignment to other species of Smilodon. The confirmed presence of S. fatalis in the TSLF is of particular interest, indicating that this species inhabited open habitats. In turn, this suggests that the presumed preference of S. fatalis for closed-habitat environments hunting requires further elucidation. creator: Eric Scott creator: Kathleen B. Springer uri: https://doi.org/10.7717/peerj.2151 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Scott and Springer title: Interrater reliability of quantitative ultrasound using force feedback among examiners with varied levels of experience link: https://peerj.com/articles/2146 last-modified: 2016-06-21 description: Background. Quantitative ultrasound measures are influenced by multiple external factors including examiner scanning force. Force feedback may foster the acquisition of reliable morphometry measures under a variety of scanning conditions. The purpose of this study was to determine the reliability of force-feedback image acquisition and morphometry over a range of examiner-generated forces using a muscle tissue-mimicking ultrasound phantom.Methods. Sixty material thickness measures were acquired from a muscle tissue mimicking phantom using B-mode ultrasound scanning by six examiners with varied experience levels (i.e., experienced, intermediate, and novice). Estimates of interrater reliability and measurement error with force feedback scanning were determined for the examiners. In addition, criterion-based reliability was determined using material deformation values across a range of examiner scanning forces (1–10 Newtons) via automated and manually acquired image capture methods using force feedback.Results. All examiners demonstrated acceptable interrater reliability (intraclass correlation coefficient, ICC = .98, p < .001) for material thickness measures obtained using force feedback. Individual examiners exhibited acceptable reliability with the criterion-based reference measures (ICC > .90, p < .001), independent of their level of experience. The measurement error among all examiners was 1.5%–2.9% across all applied stress conditions.Conclusion. Manual image capture with force feedback may aid the reliability of morphometry measures across a range of examiner scanning forces, and allow for consistent performance among examiners with differing levels of experience. creator: Michael O. Harris-Love creator: Catheeja Ismail creator: Reza Monfaredi creator: Haniel J. Hernandez creator: Donte Pennington creator: Paula Woletz creator: Valerie McIntosh creator: Bernadette Adams creator: Marc R. Blackman uri: https://doi.org/10.7717/peerj.2146 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: Clinical and prognostic value of preoperative hydronephrosis in upper tract urothelial carcinoma: a systematic review and meta-analysis link: https://peerj.com/articles/2144 last-modified: 2016-06-21 description: Background. Epidemiological studies have reported various results relating preoperative hydronephrosis to upper tract urothelial carcinoma (UTUC). However, the clinical significance and prognostic value of preoperative hydronephrosis in UTUC remains controversial. The aim of this study was to provide a comprehensive meta-analysis of the extent of the possible association between preoperative hydronephrosis and the risk of UTUC.Methods. We searched PubMed, ISI Web of Knowledge, and Embase to identify eligible studies written in English. Summary odds ratios (ORs) or hazard ratios (HRs) and 95% confidence intervals (CIs) were calculated using fixed-effects or random-effects models. Results. Nineteen relevant studies, which had a total of 5,782 UTUC patients enrolled, were selected for statistical analysis. The clinicopathological and prognostic relevance of preoperative hydronephrosis was evaluated in the UTUC patients. The results showed that all tumor stages, lymph node status and tumor location, as well as the risk of cancer-specific survival (CSS), overall survival (OS), recurrence-free survival (RFS) and metastasis-free survival (MFS) were significantly different between UTUC patients with elevated preoperative hydronephrosis and those with low preoperative hydronephrosis. High preoperative hydronephrosis indicated a poor prognosis. Additionally, significant correlations between preoperative hydronephrosis and tumor grade (high grade vs. low grade) were observed in UTUC patients; however, no significant difference was observed for tumor grading (G1 vs. G2 + G3 and G1 + G2 vs. G3). In contrast, no such correlations were evident for recurrence status or gender in UTUC patients.Conclusions. The results of this meta-analysis suggest that preoperative hydronephrosis is associated with increased risk and poor survival in UTUC patients. The presence of preoperative hydronephrosis plays an important role in the carcinogenesis and prognosis of UTUC. creator: Yuejun Tian creator: Yuwen Gong creator: Yangyang Pang creator: Zhiping Wang creator: Mei Hong uri: https://doi.org/10.7717/peerj.2144 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Tian et al. title: Diversity of Fusarium species isolated from UK forage maize and the population structure of F. graminearum from maize and wheat link: https://peerj.com/articles/2143 last-modified: 2016-06-21 description: Pre-harvest contamination of forage maize by mycotoxin producing Fusarium species was investigated in the UK in 2011 and 2012. A total of 15 Fusarium species were identified from a collection of 1,761 Fusarium isolates recovered from maize stalks and kernels. This study characterized the diversity of Fusarium species present in forage maize in the UK. The predominant species detected were F. graminearum (32.9%) and F. culmorum (34.1%). Along with those species; F. avenacem, F. cerealis, F. equiseti, F. langsethiae, F. napiforme, F. oxysporum, F. poae, F. proliferatum, F. scripi, F. solani, F. subglutinans, F. tricinctum and, F. verticillioides were occasionally isolated. The trichothecene genotypes for F. graminearum were determined to be 84.9% deoxynivalenol (DON) and 15.0% nivalenol (NIV) while F. culmorum isolates were determined to have 24.9% DON and 75.1% NIV genotypes. A Bayesian model-based clustering method with nine variable number of tandem repeat markers was used to evaluate the population genetic structure of 277 F. graminearum isolates from the maize and wheat in the UK. There were three genetic clusters detected which were DON in maize, NIV in maize and DON in wheat. There were high admixture probabilities for 14.1% of the isolates in the populations. In conclusion, increased maize production in the UK and the high admixture rates in a significant portion of F. graminearum populations in maize and wheat will contribute to a new pathogen population which will further complicate breeding strategies for tolerance or resistance to this pathogen in both crops. creator: Ryan Basler uri: https://doi.org/10.7717/peerj.2143 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Basler title: The impact of an invasive ambrosia beetle on the riparian habitats of the Tijuana River Valley, California link: https://peerj.com/articles/2141 last-modified: 2016-06-21 description: The Tijuana River Valley is the first natural habitat in California to be substantially invaded by the Kuroshio Shot Hole Borer (KSHB, Euwallacea sp.), an ambrosia beetle native to Southeast Asia. This paper documents the distribution of the KSHB in the riparian vegetation in the valley and assesses the damage done to the vegetation as of early 2016, approximately six months after the beetle was first observed in the valley. I divided the riparian habitats into 29 survey units so that the vegetation within each unit was relatively homogenous in terms of plant species composition, age and density. From a random point within each unit, I examined approximately 60 individuals of the dominant plant species for evidence of KSHB infestation and evidence of major damage such as limb breakage. In the 22 forested units,I examined the dominant arroyo and black willows (Salix lasiolepis Benth. and S. gooddingii C.R. Ball), and in the seven scrub units, I examined mule fat (Baccharis salicifolia (Ruiz & Pav.) Pers.). Evidence of KSHB infestation was found in 25 of the 29 units. In the forest units, infestation rates ranged from 0 to 100% and were high (>60%) in 16 of the units. In the scrub units, infestation rates ranged from 0 to 33%. Infestation rates were significantly correlated with the wetness of a unit; wetter units had higher infestation rates. Evidence of major physical damage was found in 24 units, and dense stands of willows were reduced to broken trunks in several areas. Overall, I estimated that more than 280,000 (70%) of the willows in the valley were infested, and more than 140,000 had suffered major limb damage. In addition, I recorded evidence of KSHB infestation in the other common plant species in the valley; of the 23 species examined, 14 showed evidence of beetle attack. The four species with the highest rates of infestation were native trees in the Salicaceae family. The three species considered to be the worst invasive plants in the valley, Ricinus communis L., Tamarix ramosissima Ledeb. and Arundo donax L., had low rates of infestation. Several findings from this study have significance for resource managers: (1) the KSHB attack caused extensive mortality of trees soon after being first discovered so, if managers are to control the spread of the beetle, they will need to develop an effective early detection and rapid response program; (2) infestation rates were highest in units that were wet, so resource managers trying to detect the beetle in other areas should thoroughly search trees near water, particularly nutrient-enriched water; (3) the infestation appears to be a novel form of disturbance, and the affected forests may need special management actions in order to recover; and (4) the infestation has altered the structure of the forest canopy, and this is likely to promote the growth of invasive plant species that were relatively inconspicuous in the forests prior to the beetle attack but will now need more attention. creator: John M. Boland uri: https://doi.org/10.7717/peerj.2141 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Boland title: An exploratory pilot study of mechanisms of action within normative feedback for adult drinkers link: https://peerj.com/articles/2114 last-modified: 2016-06-21 description: Background. Normative feedback (NF), or receiving information about one’s drinking compared to peer drinking norms, is one of the most widely used brief interventions for prevention and intervention for hazardous alcohol use. NF has demonstrated predominantly small but significant effect sizes for intention to change and other drinking related outcomes. Identifying mechanisms of action may improve the effectiveness of NF; however, few studies have examined NF’s mechanisms of action, particularly among adults.Objective. This study is an exploratory analysis of two theorized mechanisms of NF: discrepancy (specifically personal dissonance—the affective response to feedback) and belief in the accuracy of feedback.Method. Using Amazon’s Mechanical Turk, 87 men (n = 56) and women (n = 31) completed an online survey during which they were asked about their perceptions about their drinking and actual drinking behaviors. Then participants were provided tailored NF and evaluated for their reactions. Severity of discrepancy was measured by the difference between one’s estimated percentile ranking of drinking compared to peers and actual percentile ranking. Surprise and worry reported due to the discrepancy were proxies for personal dissonance. Participants were also asked if they believed the feedback and if they had any plans to change their drinking. Mediation analyses were implemented, exploring whether surprise, worry, or belief in the accuracy of feedback mediated severity of discrepancy’s impact on plan for change.Results. Among this sample of adult drinkers, severity of discrepancy did not predict plan for change, and personal dissonance did not mediate severity of discrepancy. Severity of discrepancy was mediated by belief in the accuracy of feedback. In addition, viewing one’s drinking as a problem prior to feedback and post-NF worry both predicted plan for change independently.Conclusions. Results revealed that NF may not work to create personal dissonance through discrepancy, but belief in the accuracy of feedback may be important. It appears the more one believes the feedback, the more one makes a plan for change, suggesting practitioners should be mindful of how information within feedback is presented. Findings also indicate NF may work by validating a preexisting perception that drinking is a problem instead of creating concern related to discrepancy where none existed. Limitations regarding generalizability are discussed. creator: Alexis Kuerbis creator: Frederick J. Muench creator: Rufina Lee creator: Juan Pena creator: Lisa Hail uri: https://doi.org/10.7717/peerj.2114 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Kuerbis et al. title: The impact of feature selection on one and two-class classification performance for plant microRNAs link: https://peerj.com/articles/2135 last-modified: 2016-06-21 description: MicroRNAs (miRNAs) are short nucleotide sequences that form a typical hairpin structure which is recognized by a complex enzyme machinery. It ultimately leads to the incorporation of 18–24 nt long mature miRNAs into RISC where they act as recognition keys to aid in regulation of target mRNAs. It is involved to determine miRNAs experimentally and, therefore, machine learning is used to complement such endeavors. The success of machine learning mostly depends on proper input data and appropriate features for parameterization of the data. Although, in general, two-class classification (TCC) is used in the field; because negative examples are hard to come by, one-class classification (OCC) has been tried for pre-miRNA detection. Since both positive and negative examples are currently somewhat limited, feature selection can prove to be vital for furthering the field of pre-miRNA detection. In this study, we compare the performance of OCC and TCC using eight feature selection methods and seven different plant species providing positive pre-miRNA examples. Feature selection was very successful for OCC where the best feature selection method achieved an average accuracy of 95.6%, thereby being ∼29% better than the worst method which achieved 66.9% accuracy. While the performance is comparable to TCC, which performs up to 3% better than OCC, TCC is much less affected by feature selection and its largest performance gap is ∼13% which only occurs for two of the feature selection methodologies. We conclude that feature selection is crucially important for OCC and that it can perform on par with TCC given the proper set of features. creator: Waleed Khalifa creator: Malik Yousef creator: Müşerref Duygu Saçar Demirci creator: Jens Allmer uri: https://doi.org/10.7717/peerj.2135 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Khalifa et al. title: Utilizing mutual information for detecting rare and common variants associated with a categorical trait link: https://peerj.com/articles/2139 last-modified: 2016-06-16 description: Background. Genome-wide association studies have succeeded in detecting novel common variants which associate with complex diseases. As a result of the fast changes in next generation sequencing technology, a large number of sequencing data are generated, which offers great opportunities to identify rare variants that could explain a larger proportion of missing heritability. Many effective and powerful methods are proposed, although they are usually limited to continuous, dichotomous or ordinal traits. Notice that traits having nominal categorical features are commonly observed in complex diseases, especially in mental disorders, which motivates the incorporation of the characteristics of the categorical trait into association studies with rare and common variants.Methods. We construct two simple and intuitive nonparametric tests, MIT and aMIT, based on mutual information for detecting association between genetic variants in a gene or region and a categorical trait. MIT and aMIT can gauge the difference among the distributions of rare and common variants across a region given every categorical trait value. If there is little association between variants and a categorical trait, MIT or aMIT approximately equals zero. The larger the difference in distributions, the greater values MIT and aMIT have. Therefore, MIT and aMIT have the potential for detecting functional variants.Results.We checked the validity of proposed statistics and compared them to the existing ones through extensive simulation studies with varied combinations of the numbers of variants of rare causal, rare non-causal, common causal, and common non-causal, deleterious and protective, various minor allele frequencies and different levels of linkage disequilibrium. The results show our methods have higher statistical power than conventional ones, including the likelihood based score test, in most cases: (1) there are multiple genetic variants in a gene or region; (2) both protective and deleterious variants are present; (3) there exist rare and common variants; and (4) more than half of the variants are neutral. The proposed tests are applied to the data from Collaborative Studies on Genetics of Alcoholism, and a competent performance is exhibited therein.Discussion. As a complementary to the existing methods mainly focusing on quantitative traits, this study provides the nonparametric tests MIT and aMIT for detecting variants associated with categorical trait. Furthermore, we plan to investigate the association between rare variants and multiple categorical traits. creator: Leiming Sun creator: Chan Wang creator: Yue-Qing Hu uri: https://doi.org/10.7717/peerj.2139 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Sun et al. title: The Size-Weight Illusion is not anti-Bayesian after all: a unifying Bayesian account link: https://peerj.com/articles/2124 last-modified: 2016-06-16 description: When we lift two differently-sized but equally-weighted objects, we expect the larger to be heavier, but the smaller feels heavier. However, traditional Bayesian approaches with “larger is heavier” priors predict the smaller object should feel lighter; this Size-Weight Illusion (SWI) has thus been labeled “anti-Bayesian” and has stymied psychologists for generations. We propose that previous Bayesian approaches neglect the brain’s inference process about density. In our Bayesian model, objects’ perceived heaviness relationship is based on both their size and inferred density relationship: observers evaluate competing, categorical hypotheses about objects’ relative densities, the inference about which is then used to produce the final estimate of weight. The model can qualitatively and quantitatively reproduce the SWI and explain other researchers’ findings, and also makes a novel prediction, which we confirmed. This same computational mechanism accounts for other multisensory phenomena and illusions; that the SWI follows the same process suggests that competitive-prior Bayesian inference can explain human perception across many domains. creator: Megan A.K. Peters creator: Wei Ji Ma creator: Ladan Shams uri: https://doi.org/10.7717/peerj.2124 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Peters et al. title: Nest survival patterns in Eurasian Bittern: effect of nest age, time and habitat variables link: https://peerj.com/articles/2047 last-modified: 2016-06-16 description: Determining the key factors affecting the reproductive success of nesting birds is crucial in order to better understand the population dynamics of endangered species and to introduce effective conservation programmes for them. Inhabiting a variety of wetland habitats, aquatic birds actively select safe nesting sites so as to protect their nests against predators. The main aim of the present work was to assess the effect of temporal and habitat variables on the daily nest survival rate of Eurasian Bitterns colonizing semi–natural fishpond habitat in eastern Poland. MARK software was used for the modelling. Eurasian Bittern nests were most vulnerable to depredation at the beginning of the breeding season. This was probably because the reedbed vegetation at this time was not yet dense enough to effectively conceal the nests. There was a positive relationship between nest age and the daily survival rate. Two of the habitat variables analysed were of the greatest significance: water depth and vegetation density. In the Eurasian Bittern population studied here, nests built over deep water and in dense vegetation had the best chances of survival. The results of this work may be useful in the preparation of plans for the conservation and management of populations of this rare and endangered species. Conservation and restoration efforts that attempt to maintain high water levels will be especially beneficial to this avian species that is dependent on wetland ecosystems for breeding. creator: Marcin Polak uri: https://doi.org/10.7717/peerj.2047 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Polak title: The systematics of the Mongolepidida (Chondrichthyes) and the Ordovician origins of the clade link: https://peerj.com/articles/1850 last-modified: 2016-06-16 description: The Mongolepidida is an Order of putative early chondrichthyan fish, originally erected to unite taxa from the Lower Silurian of Mongolia. The present study reassesses mongolepid systematics through the examination of the developmental, histological and morphological characteristics of scale-based specimens from the Upper Ordovician Harding Sandstone (Colorado, USA) and the Upper Llandovery–Lower Wenlock Yimugantawu (Tarim Basin, China), Xiushan (Guizhou Province, China) and Chargat (north-western Mongolia) Formations. The inclusion of the Mongolepidida within the Class Chondrichthyes is supported on the basis of a suite of scale attributes (areal odontode deposition, linear odontocomplex structure and lack of enamel, cancellous bone and hard-tissue resorption) shared with traditionally recognized chondrichthyans (euchondrichthyans, e.g., ctenacanthiforms). The mongolepid dermal skeleton exhibits a rare type of atubular dentine (lamellin) that is regarded as one of the diagnostic features of the Order within crown gnathostomes. The previously erected Mongolepididae and Shiqianolepidae families are revised, differentiated by scale-base histology and expanded to include the genera Rongolepisand Xinjiangichthys, respectively. A newly described mongolepid species (Solinalepis levis gen. et sp. nov.) from the Ordovician of North America is treated as family incertae sedis, as it possesses a type of basal bone tissue (acellular and vascular) that has yet to be documented in other mongolepids. This study extends the stratigraphic and palaeogeographic range of Mongolepidida and adds further evidence for an early diversification of the Chondrichthyes in the Ordovician Period, 50 million years prior to the first recorded appearance of euchondrichthyan teeth in the Lower Devonian. creator: Plamen Andreev creator: Michael I. Coates creator: Valentina Karatajūtė-Talimaa creator: Richard M. Shelton creator: Paul R. Cooper creator: Nian-Zhong Wang creator: Ivan J. Sansom uri: https://doi.org/10.7717/peerj.1850 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Andreev et al. title: Freshwater gastropods diversity hotspots: three new species from the Uruguay River (South America) link: https://peerj.com/articles/2138 last-modified: 2016-06-15 description: Background: The Atlantic Forest is globally one of the priority ecoregions for biodiversity conservation. In Argentina, it is represented by the Paranense Forest, which covers a vast area of Misiones Province between the Paraná and Uruguay rivers. The Uruguay River is a global hotspot of freshwater gastropod diversity, here mainly represented by Tateidae (genus Potamolithus) and to a lesser extent Chilinidae. The family Chilinidae (Gastropoda, Hygrophila) includes 21 species currently recorded in Argentina, and three species in the Uruguay River. The species of Chilinidae occur in quite different types of habitats, but generally in clean oxygenated water recording variable temperature ranges. Highly oxygenated freshwater environments (waterfalls and rapids) are the most vulnerable continental environments. We provide here novel information on three new species of Chilinidae from environments containing waterfalls and rapids in the Uruguay River malacological province of Argentina.Materials and Methods: The specimens were collected in 2010. We analyzed shell, radula, and nervous and reproductive systems, and determined the molecular genetics. The genetic distance was calculated for two mitochondrial markers (cytochrome c oxidase subunit I–COI- and cytochrome b -Cyt b-) for these three new species and the species recorded from the Misionerean, Uruguay River and Lower Paraná-Río de la Plata malacological provinces. In addition, the COI data were analyzed phylogenetically by the neighbor-joining and Bayesian inference techniques.Results: The species described here are different in terms of shell, radula and nervous and reproductive systems, mostly based on the sculpture of the penis sheath. Phylogenetic analyses grouped the three new species with those present in the Lower Paraná-Río de la Plata and Uruguay River malacological provinces.Discussion: Phylogenetic analyses confirm the separation between the Uruguay River and the Misionerean malacological provinces in northeast Argentina. These new endemic species from the Uruguay River add further support to the suggestion that this river is a diversity hotspot of freshwater gastropods (with 54 species present in this basin, 15 of them endemic). These endemic species from environments with rapids and waterfalls should be taken into account by government agencies before the construction of dams that modify those ecologic niches in the Uruguay River. creator: Diego E. Gutiérrez Gregoric creator: Micaela de Lucía uri: https://doi.org/10.7717/peerj.2138 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Gutiérrez Gregoric & de Lucía title: Screening for drought tolerance in cultivars of the ornamental genus Tagetes (Asteraceae) link: https://peerj.com/articles/2133 last-modified: 2016-06-15 description: Drought tolerance was evaluated in twelve cultivars of three ornamental Tagetes species (T. patula, T. tenuifolia and T. erecta). A stress treatment was performed by completely stopping watering of plants maintained in controlled greenhouse conditions. After three weeks, several plant growth parameters (stem length (SL), fresh weight (FW) and water content (WC)), photosynthetic pigments (chlorophylls and carotenoids (Car)), osmolytes (proline (Pro), glycine betaine (GB) and total soluble sugars (TSS)), an oxidative stress maker (malondialdehyde (MDA)) and antioxidants (total phenolic compounds (TPC) and total flavonoids (TF)) were measured. Considerable differences in the evaluated traits were found among the control and drought-stressed plants. Drought stress generally caused a marked reduction in plant growth and carotenoid pigments, and an increase in soluble solutes and oxidative stress. For most cultivars, proline levels in stressed plants increased between 30 and 70-fold compared to the corresponding controls. According to the different measured parameters, on average T. erecta proved to be more tolerant to drought than T. patula and T. tenuifolia. However, a considerable variation in the tolerance to drought was found within each species. The traits with greater association to drought tolerance as well as the most tolerant cultivars could be clearly identified in a principal components analysis (PCA). Overall, our results indicate that drought tolerant cultivars of Tagetes can be identified at early stages using a combination of plant growth and biochemical markers. creator: Raluca Cicevan creator: Mohamad Al Hassan creator: Adriana F. Sestras creator: Jaime Prohens creator: Oscar Vicente creator: Radu E. Sestras creator: Monica Boscaiu uri: https://doi.org/10.7717/peerj.2133 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Cicevan et al. title: Identification, expression and variation of the GNPDA2 gene, and its association with body weight and fatness traits in chicken link: https://peerj.com/articles/2129 last-modified: 2016-06-15 description: Background. The GNPDA2 (glucosamine-6-phosphate deaminase 2) gene is a member of Glucosamine-6-phosphate (GlcN6P) deaminase subfamily, which encoded an allosteric enzyme of GlcN6P. Genome-wide association studies (GWAS) have shown that variations of human GNPDA2 are associated with body mass index and obesity risk, but its function and metabolic implications remain to be elucidated.The object of this study was to characterize the gene structure, expression, and biological functions of GNPDA2 in chickens.Methods. Variant transcripts of chicken GNPDA2 and their expression were investigated using rapid amplification of cDNA ends (RACE) system and real-time quantitative PCR technology. We detected the GNPDA2 expression in hypothalamic, adipose, and liver tissue of Xinghua chickens with fasting and high-glucose-fat diet treatments, and performed association analysis of variations of GNPDA2 with productive traits in chicken. The function of GNPDA2 was further studied by overexpression and small interfering RNA (siRNA) methods in chicken preadipocytes.Results.Four chicken GNPDA2 transcripts (cGNPDA2-a∼cGNPDA2-d) were identified in this study. The complete transcript GNPDA2-a was predominantly expressed in adipose tissue (subcutaneous fat and abdominal fat), hypothalamus, and duodenum. In fasting chickens, the mRNA level of GNPDA2 was decreased by 58.8% (P < 0.05) in hypothalamus, and returned to normal level after refeeding. Chicken fed a high-glucose-fat diet increased GNPDA2 gene expression about 2-fold higher in adipose tissue (P < 0.05) than that in the control (fed a basal diet), but decreased its expression in hypothalamus. Two single-nucleotide polymorphisms of the GNPDA2 gene were significantly associated with body weight and a number of fatness traits in chicken (P < 0.05).Conclusion. Our findings indicated that the GNPDA2 gene has a potential role in the regulation of body weight, fat and energy metabolism in chickens. creator: Hongjia Ouyang creator: Huan Zhang creator: Weimin Li creator: Sisi Liang creator: Endashaw Jebessa creator: Bahareldin A. Abdalla creator: Qinghua Nie uri: https://doi.org/10.7717/peerj.2129 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Ouyang et al. title: Myiarchus flycatchers are the primary seed dispersers of Bursera longipes in a Mexican dry forest link: https://peerj.com/articles/2126 last-modified: 2016-06-15 description: We evaluated the seed dispersal of Bursera longipes by birds along a successional gradient of tropical dry forest (TDF) in southwestern Mexico. B. longipes is an endemic tree to the TDF in the Balsas basin. The relative abundance of frugivorous birds, their frequency of visits to B. longipes and the number of removed fruits were recorded at three study sites with different stages of forest succession (early, intermediate and mature) characterized by distinct floristic and structural elements. Flycatchers of the Myiarchus and Tyrannus genera removed the majority of fruits at each site. Overall, visits to B. longipes were less frequent at the early successional site. Birds that function as legitimate dispersers by consuming whole seeds and regurgitating or defecating intact seeds in the process also remove the pseudoaril from seeds, thereby facilitating the germination process. The highest germination percentages were recorded for seeds that passed through the digestive system of two migratory flycatchers: M. cinerascens and M. nutingii. Perch plants, mainly composed of legumes (e.g., Eysenhardtia polystachya, Acacia cochliacantha, Calliandra eryophylla, Mimosa polyantha), serve also as nurse plants since the number of young individuals recruited from B. longipes was higher under these than expected by chance. This study shows that Myiarchus flycatchers are the most efficient seed dispersers of B. longipes across all successional stages. This suggests a close mutualistic relationship derived from adaptive processes and local specializations throughout the distribution of both taxa, as supported by the geographic mosaic theory of coevolution. creator: R. Carlos Almazán-Núñez creator: Luis E. Eguiarte creator: María del Coro Arizmendi creator: Pablo Corcuera uri: https://doi.org/10.7717/peerj.2126 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Almazán-Núñez et al. title: Integrated microRNA, gene expression and transcription factors signature in papillary thyroid cancer with lymph node metastasis link: https://peerj.com/articles/2119 last-modified: 2016-06-15 description: Background. Papillary thyroid carcinoma (PTC) is the commonest thyroid malignancy originating from the follicle cells in the thyroid. Despite a good overall prognosis, certain high-risk cases as in those with lymph node metastasis (LNM) have progressive disease and poorer prognosis. MicroRNAs are a class of non-protein-coding, 19–24 nucleotides single-stranded RNAs which regulate gene expression and these molecules have been shown to play a role in LNM. The integrated analysis of miRNAs and gene expression profiles together with transcription factors (TFs) has been shown to improve the identification of functional miRNA-target gene-TF relationships, providing a more complete view of molecular events underlying metastasis process.Objectives. We reanalyzed The Cancer Genome Atlas (TCGA) datasets on PTC to identify differentially expressed miRNAs/genes in PTC patients with LNM-positive (LNM-P) versus lymph node negative (LNN) PTC patients and to investigate the miRNA-gene-TF regulatory circuit that regulate LNM in PTC.Results. PTC patients with LNM (PTC LNM-P) have a significantly shorter disease-free survival rate compared to PTC patients without LNM (PTC LNN) (Log-rank Mantel Cox test, p = 0.0049). We identified 181 significantly differentially expressed miRNAs in PTC LNM-P versus PTC LNN; 110 were upregulated and 71 were downregulated. The five topmost deregulated miRNAs were hsa-miR-146b, hsa-miR-375, hsa-miR-31, hsa-miR-7-2 and hsa-miR-204. In addition, 395 miRNAs were differentially expressed between PTC LNM-P and normal thyroid while 400 miRNAs were differentially expressed between PTC LNN and normal thyroid. We found four significant enrichment pathways potentially involved in metastasis to the lymph nodes, namely oxidative phosphorylation (OxPhos), cell adhesion molecules (CAMs), leukocyte transendothelial migration and cytokine–cytokine receptor interaction. OxPhos was the most significantly perturbed pathway (p = 4.70E−06) involving downregulation of 90 OxPhos-related genes. Significant interaction of hsa-miR-301b with HLF, HIF and REL/NFkB transcription factors were identified exclusively in PTC LNM-P versus PTC LNN.Conclusion. We found evidence of five miRNAs differentially expressed in PTC LNM-P. Alteration in OxPhos pathway could be the central event in metastasis to the lymph node in PTC. We postulate that hsa-miR-301b might be involved in regulating LNM in PTC via interactions with HLF, HIF and REL/NFkB. To the best of our knowledge, the roles of these TFs have been studied in PTC but the precise role of this miRNA with these TFs in LNM in PTC has not been investigated. creator: Nurul-Syakima Ab Mutalib creator: Sri Noraima Othman creator: Azliana Mohamad Yusof creator: Shahrun Niza Abdullah Suhaimi creator: Rohaizak Muhammad creator: Rahman Jamal uri: https://doi.org/10.7717/peerj.2119 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Ab Mutalib et al. title: Development of a cost-effective metabarcoding strategy for analysis of the marine phytoplankton community link: https://peerj.com/articles/2115 last-modified: 2016-06-15 description: We developed a cost-effective metabarcoding strategy to analyze phytoplankton community structure using the Illumina MiSeq system. The amplicons (404–411 bp) obtained by end-pairing of two reads were sufficiently long to distinguish algal species and provided barcode data equivalent to those generated with the Roche 454 system, but at less than 1/20th of the cost. The original universal primer sequences targeting the 23S rDNA region and the PCR strategy were both modified, and this resulted in higher numbers of eukaryotic algal sequences by excluding non-photosynthetic proteobacterial sequences supporting effectiveness of this strategy. The novel strategy was used to analyze the phytoplankton community structure of six water samples from the East/Japan Sea: surface and 50 m depths at coastal and open-sea sites, with collections in May and July 2014. In total, 345 operational taxonomic units (OTUs) were identified, which covered most of the prokaryotic and eukaryotic algal phyla, including Dinophyta, Rhodophyta, Ochrophyta, Chlorophyta, Streptophyta, Cryptophyta, Haptophyta, and Cyanophyta. This highlights the importance of plastid 23S primers, which perform better than the currently used 16S primers for phytoplankton community surveys. The findings also revealed that more efforts should be made to update 23S rDNA sequences as well as those of 16S in the databases. Analysis of algal proportions in the six samples showed that community structure differed depending on location, depth and season. Across the six samples evaluated, the numbers of OTUs in each phylum were similar but their relative proportions varied. This novel strategy would allow laboratories to analyze large numbers of samples at reasonable expense, whereas this has not been possible to date due to cost and time. In addition, we expect that this strategy will generate a large amount of novel data that could potentially change established methods and tools that are currently used in the realms of oceanography and marine ecology. creator: Tae-Ho Yoon creator: Hye-Eun Kang creator: Chang-Keun Kang creator: Sang Heon Lee creator: Do-Hwan Ahn creator: Hyun Park creator: Hyun-Woo Kim uri: https://doi.org/10.7717/peerj.2115 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Yoon et al. title: A unique mating strategy without physical contact during fertilization in Bombay Night Frogs (Nyctibatrachus humayuni) with the description of a new form of amplexus and female call link: https://peerj.com/articles/2117 last-modified: 2016-06-14 description: Anurans show the highest diversity in reproductive modes of all vertebrate taxa, with a variety of associated breeding behaviours. One striking feature of anuran reproduction is amplexus. During this process, in which the male clasps the female, both individuals’ cloacae are juxtaposed to ensure successful external fertilization. Several types of amplexus have evolved with the diversification of anurans, and secondary loss of amplexus has been reported in a few distantly related taxa. Within Nyctibatrachus, a genus endemic to the Western Ghats of India, normal axillary amplexus, a complete loss of amplexus, and intermediate forms of amplexus have all been suggested to occur, but many species remain unstudied. Here, we describe the reproductive behaviour of N. humayuni, including a new type of amplexus. The dorsal straddle, here defined as a loose form of contact in which the male sits on the dorsum of the female prior to oviposition but without clasping her, is previously unreported for anurans. When compared to known amplexus types, it most closely resembles the form of amplexus observed in Mantellinae. Furthermore, we prove that, opposed to the situation in most anurans, male semen release happens before egg deposition. We hypothesize that the male ejaculates on the female’s dorsum and that sperm subsequently runs from her back and hind legs before fertilizing the eggs. A second feature characterizing anuran breeding is the advertisement call, mostly produced solely by males. Despite recent descriptions of several new Nyctibatrachus species, few studies have explored their vocal repertoire. We describe both the male advertisement call and a female call for N. humayuni. The presence of a female call has not been reported within Nyctibatrachidae, and has been reported in less than 0.5% of anuran species. Altogether, our results highlight a striking diversity and several unique aspects of Nyctibatrachus breeding behaviour. creator: Bert Willaert creator: Robin Suyesh creator: Sonali Garg creator: Varad B. Giri creator: Mark A. Bee creator: S.D. Biju uri: https://doi.org/10.7717/peerj.2117 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Willaert et al. title: Transient turbid water mass reduces temperature-induced coral bleaching and mortality in Barbados link: https://peerj.com/articles/2118 last-modified: 2016-06-14 description: Global warming is seen as one of the greatest threats to the world’s coral reefs and, with the continued rise in sea surface temperature predicted into the future, there is a great need for further understanding of how to prevent and address the damaging impacts. This is particularly so for countries whose economies depend heavily on healthy reefs, such as those of the eastern Caribbean. Here, we compare the severity of bleaching and mortality for five dominant coral species at six representative reef sites in Barbados during the two most significant warm-water events ever recorded in the eastern Caribbean, i.e., 2005 and 2010, and describe prevailing island-scale sea water conditions during both events. In so doing, we demonstrate that coral bleaching and subsequent mortality were considerably lower in 2010 than in 2005 for all species, irrespective of site, even though the anomalously warm water temperature profiles were very similar between years. We also show that during the 2010 event, Barbados was engulfed by a transient dark green turbid water mass of riverine origin coming from South America. We suggest that reduced exposure to high solar radiation associated with this transient water mass was the primary contributing factor to the lower bleaching and mortality observed in all corals. We conclude that monitoring these episodic mesoscale oceanographic features might improve risk assessments of southeastern Caribbean reefs to warm-water events in the future. creator: Hazel A. Oxenford creator: Henri Vallès uri: https://doi.org/10.7717/peerj.2118 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Oxenford and Vallés title: Transcriptional similarity in couples reveals the impact of shared environment and lifestyle on gene regulation through modified cytosines link: https://peerj.com/articles/2123 last-modified: 2016-06-14 description: Gene expression is a complex and quantitative trait that is influenced by both genetic and non-genetic regulators including environmental factors. Evaluating the contribution of environment to gene expression regulation and identifying which genes are more likely to be influenced by environmental factors are important for understanding human complex traits. We hypothesize that by living together as couples, there can be commonly co-regulated genes that may reflect the shared living environment (e.g., diet, indoor air pollutants, behavioral lifestyle). The lymphoblastoid cell lines (LCLs) derived from unrelated couples of African ancestry (YRI, Yoruba people from Ibadan, Nigeria) from the International HapMap Project provided a unique model for us to characterize gene expression pattern in couples by comparing gene expression levels between husbands and wives. Strikingly, 778 genes were found to show much smaller variances in couples than random pairs of individuals at a false discovery rate (FDR) of 5%. Since genetic variation between unrelated family members in a general population is expected to be the same assuming a random-mating society, non-genetic factors (e.g., epigenetic systems) are more likely to be the mediators for the observed transcriptional similarity in couples. We thus evaluated the contribution of modified cytosines to those genes showing transcriptional similarity in couples as well as the relationships these CpG sites with other gene regulatory elements, such as transcription factor binding sites (TFBS). Our findings suggested that transcriptional similarity in couples likely reflected shared common environment partially mediated through cytosine modifications. creator: Ke Tang creator: Wei Zhang uri: https://doi.org/10.7717/peerj.2123 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Tang and Zhang title: Geriatric syndromes are potential determinants of the medication adherence status in prevalent dialysis patients link: https://peerj.com/articles/2122 last-modified: 2016-06-14 description: Background. Geriatric syndromes (GS) exhibit high prevalence in patients with end-stage renal disease (ESRD) under chronic dialysis irrespective of age. We sought to determine whether GS influences medication adherence in ESRD patients.Methods. A prospective cohort of chronic dialysis patients was assembled. The presence of GS components, including frailty/prefrailty, polypharmacy, and malnutrition, were ascertained through a validated questionnaire, electronic records and chart abstraction, and laboratory tests. The severity of medication non-adherence was defined using the eight-item Morisky Medication Adherence Scale (MMAS). Multiple logistic regression analysis was performed targeting MMAS results and incorporating relevant clinical features and GS.Results. The prevalence of frailty/pre-frailty, polypharmacy, and hypoalbuminemia/ malnutrition among the enrolled participants was 66.7%, 94%, and 14%, respectively. The average MMAS scores in these dialysis patients were 2 ± 1.7 (range, 0–6), with only 15.7% exhibiting high medication adherence. Multiple regression analyses showed that the absence of frailty/pre-frailty (P = 0.01) were significantly associated with poorer medication adherence, while the presence of polypharmacy (P = 0.02) and lower serum albumin, a potential sign of malnutrition (P = 0.03), were associated with poor adherence in another model.Conclusion. This study is among the very few reports addressing GS and medication adherence, especially in ESRD patients. Interventions targeting frailty, polypharmacy, and malnutrition might potentially improve the medication non-adherence and symptom control in these pill-burdened patients. creator: Chia-Ter Chao creator: Jenq-Wen Huang uri: https://doi.org/10.7717/peerj.2122 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Chao et al. title: Phosphorus mobilizing consortium Mammoth P™ enhances plant growth link: https://peerj.com/articles/2121 last-modified: 2016-06-14 description: Phosphorus (P) is a critical nutrient used to maximize plant growth and yield. Current agriculture management practices commonly experience low plant P use efficiency due to natural chemical sorption and transformations when P fertilizer is applied to soils. A perplexing challenge facing agriculture production is finding sustainable solutions to deliver P more efficiently to plants. Using prescribed applications of specific soil microbial assemblages to mobilize soil bound—P to improve crop nutrient uptake and productivity has rarely been employed. We investigated whether inoculation of soils with a bacterial consortium developed to mobilize soil P, named Mammoth PTM, could increase plant productivity. In turf, herbs, and fruits, the combination of conventional inorganic fertilizer combined with Mammoth PTM increased productivity up to twofold compared to the fertilizer treatments without the Mammoth PTM inoculant. Jalapeño plants were found to bloom more rapidly when treated with either Mammoth P. In wheat trials, we found that Mammoth PTM by itself was able to deliver yields equivalent to those achieved with conventional inorganic fertilizer applications and improved productivity more than another biostimulant product. Results from this study indicate the substantial potential of Mammoth PTM to enhance plant growth and crop productivity. creator: Peter Baas creator: Colin Bell creator: Lauren M. Mancini creator: Melanie N. Lee creator: Richard T. Conant creator: Matthew D. Wallenstein uri: https://doi.org/10.7717/peerj.2121 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Baas et al. title: A time-lapse photography method for monitoring salmon (Oncorhynchus spp.) passage and abundance in streams link: https://peerj.com/articles/2120 last-modified: 2016-06-14 description: Accurately estimating population sizes is often a critical component of fisheries research and management. Although there is a growing appreciation of the importance of small-scale salmon population dynamics to the stability of salmon stock-complexes, our understanding of these populations is constrained by a lack of efficient and cost-effective monitoring tools for streams. Weirs are expensive, labor intensive, and can disrupt natural fish movements. While conventional video systems avoid some of these shortcomings, they are expensive and require excessive amounts of labor to review footage for data collection. Here, we present a novel method for quantifying salmon in small streams (<15 m wide, <1 m deep) that uses both time-lapse photography and video in a model-based double sampling scheme. This method produces an escapement estimate nearly as accurate as a video-only approach, but with substantially less labor, money, and effort. It requires servicing only every 14 days, detects salmon 24 h/day, is inexpensive, and produces escapement estimates with confidence intervals. In addition to escapement estimation, we present a method for estimating in-stream salmon abundance across time, data needed by researchers interested in predator--prey interactions or nutrient subsidies. We combined daily salmon passage estimates with stream specific estimates of daily mortality developed using previously published data. To demonstrate proof of concept for these methods, we present results from two streams in southwest Kodiak Island, Alaska in which high densities of sockeye salmon spawn. creator: William W. Deacy creator: William B. Leacock creator: Lisa A. Eby creator: Jack A. Stanford uri: https://doi.org/10.7717/peerj.2120 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Deacy et al. title: Characterizing the adult and larval transcriptome of the multicolored Asian lady beetle, Harmonia axyridis link: https://peerj.com/articles/2098 last-modified: 2016-06-14 description: The reasons for the evolution and maintenance of striking visual phenotypes are as widespread as the species that display these phenotypes. While study systems such as Heliconius and Dendrobatidae have been well characterized and provide critical information about the evolution of these traits, a breadth of new study systems, in which the phenotype of interest can be easily manipulated and quantified, are essential for gaining a more general understanding of these specific evolutionary processes. One such model is the multicolored Asian lady beetle, Harmonia axyridis, which displays significant elytral spot and color polymorphism. Using transcriptome data from two life stages, adult and larva, we characterize the transcriptome, thereby laying a foundation for further analysis and identification of the genes responsible for the continual maintenance of spot variation in H. axyridis. creator: Lindsay A. Havens creator: Matthew D. MacManes uri: https://doi.org/10.7717/peerj.2098 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Havens and MacManes title: Climate change may threaten habitat suitability of threatened plant species within Chinese nature reserves link: https://peerj.com/articles/2091 last-modified: 2016-06-14 description: Climate change has the potential to alter the distributions of threatened plant species, and may therefore diminish the capacity of nature reserves to protect threatened plant species. Chinese nature reserves contain a rich diversity of plant species that are at risk of becoming more threatened by climate change. Hence, it is urgent to identify the extent to which future climate change may compromise the suitability of threatened plant species habitats within Chinese nature reserves. Here, we modelled the climate suitability of 82 threatened plant species within 168 nature reserves across climate change scenarios. We used Maxent modelling based on species occurrence localities and evaluated climate change impacts using the magnitude of change in climate suitability and the degree of overlap between current and future climatically suitable habitats. There was a significant relationship between overlap with current and future climate suitability of all threatened plant species habitats and the magnitude of changes in climate suitability. Our projections estimate that the climate suitability of more than 60 threatened plant species will decrease and that climate change threatens the habitat suitability of plant species in more than 130 nature reserves under the low, medium, and high greenhouse gas concentration scenarios by both 2050s and 2080s. Furthermore, future climate change may substantially threaten tree plant species through changes in annual mean temperature. These results indicate that climate change may threaten plant species that occur within Chinese nature reserves. Therefore, we suggest that climate change projections should be integrated into the conservation and management of threatened plant species within nature reserves. creator: Chunjing Wang creator: Chengzhu Liu creator: Jizhong Wan creator: Zhixiang Zhang uri: https://doi.org/10.7717/peerj.2091 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Wang et al. title: Observed shifts in the contact zone between two forms of the diving beetle Hydroporus memnonius are consistent with predictions from sexual conflict link: https://peerj.com/articles/2089 last-modified: 2016-06-14 description: Sexual conflict drives both inter- and intrasexual dimorphisms in many diving beetles, where male persistence and female resistance traits co-evolve in an antagonistic manner. To date most studies have focussed on species where rough and smooth females and their associated males typically co-occur within populations, where phenotype matching between morphs may maintain forms as stable polymorphisms. The Palaearctic diving beetle Hydroporus memnonius is characterised by having dimorphic (rough var. castaneus and smooth, shining) females and associated males which differ in persistence traits; the two forms being largely distributed parapatrically. In this species, instead of mating trade-offs between morphs, males associated with castaneus females should have a mating advantage with both this form and shining females, due to their increased persistence abilities on either cuticular surface. This may be expected to lead to the replacement of the shining form with castaneus in areas where the two come into contact. Using data collected over a thirty year period, we show that this process of population replacement is indeed occurring, castaneus having expanded significantly at the expense of the shining female form. Whilst populations of both forms close to the contact zone appear to differ in their thermal physiology, these differences are minor and suggest that the expansion of castaneus is not linked to climatic warming in recent decades. Instead we argue that the observed spread of castaneus and its associated male may result from the dynamics of sexually antagonistic coevolution in this beetle. creator: David T. Bilton creator: Garth N. Foster uri: https://doi.org/10.7717/peerj.2089 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Bilton and Foster title: Aberrant methylation of PCDH10 and RASSF1A genes in blood samples for non-invasive diagnosis and prognostic assessment of gastric cancer link: https://peerj.com/articles/2112 last-modified: 2016-06-09 description: Background. Assessment of DNA methylation of specific genes is one approach to the diagnosis of cancer worldwide. Early stage detection is necessary to reduce the mortality rate of cancers, including those occurring in the stomach. For this purpose, tumor cells in circulating blood offer promising candidates for non-invasive diagnosis. Transcriptional inactivation of tumor suppressor genes, like PCDH10 and RASSF1A, by methylation is associated with progression of gastric cancer, and such methylation can therefore be utilized as a biomarker.Methods. The present research was conducted to evaluate DNA methylation in these two genes using blood samples of gastric cancer cases. Clinicopathological data were also analyzed and cumulative survival rates generated for comparison.Results. High frequencies of PCDH10 and RASSF1A methylations in the gastric cancer group were noted (94.1% and 83.2%, respectively, as compared to 2.97% and 5.45% in 202 matched controls). Most patients (53.4%) were in severe stage of the disease, with a median survival time of 8.4 months after diagnosis. Likewise, the patients with metastases, or RASSF1A and PCDH10 methylations, had median survival times of 7.3, 7.8, and 8.4 months, respectively. A Kaplan–Meier analysis showed that cumulative survival was significantly lower in those cases positive for methylation of RASSF1A than in their negative counterparts. Similarly, whereas almost 100% of patients positive for PCDH10 methylation had died after five years, none of the negative cases died over this period. Notably, the methylations of RASSF1A and PCDH10 were found to be higher in the late-stage patients and were also significantly correlated with metastasis and histology.Conclusions.PCDH10 and RASSF1A methylations in blood samples can serve as potential non-invasive diagnostic indicators in blood for gastric cancer. In addition to RASSF1A methylation, tumor stage proved to be a major prognostic factor in terms of survival rates. creator: Charinya Pimson creator: Tipaya Ekalaksananan creator: Chamsai Pientong creator: Supannee Promthet creator: Nuntiput Putthanachote creator: Krittika Suwanrungruang creator: Surapon Wiangnon uri: https://doi.org/10.7717/peerj.2112 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Pimson et al. title: Genetic, morphological and growth characterisation of a new Roseofilum strain (Oscillatoriales, Cyanobacteria) associated with coral black band disease link: https://peerj.com/articles/2110 last-modified: 2016-06-09 description: Black band disease (BBD) is a common disease of reef-building corals with a worldwide distribution that causes tissue loss at a rate of up to 3 cm/day. Critical for a mechanistic understanding of the disease’s aetiology is the cultivation of its proposed pathogen, filamentous cyanobacteria (genus Roseofilum). Here, we optimise existing protocols for the isolation and cultivation of Roseofilum cyanobacteria using a new strain from the central Great Barrier Reef. We demonstrate that the isolation of this bacterium via inoculation onto agar plates was highly effective with a low percentage agar of 0.6% and that growth monitoring was most sensitive with fluorescence measurements of chlorophyll-a (440/685 nm). Cell growth curves in liquid and solid media were generated for the first time for this cyanobacterium and showed best growth rates for the previously untested L1-medium (growth rate k = 0.214 biomass/day; doubling time tgen = 4.67 days). Our results suggest that the trace metals contained in L1-medium maximise biomass increase over time for this cyanobacterium. Since the newly isolated Roseofilum strain is genetically closest to Pseudoscillatoria coralii, but in terms of pigmentation and cell size closer to Roseofilumreptotaenium, we formally merge the two species into a single taxon by providing an emended species description, Roseofilum reptotaenium (Rasoulouniriana) Casamatta emend. Following this optimized protocol is recommended for fast isolation and cultivation of Roseofilum cyanobacteria, for growth curve generation in strain comparisons and for maximisation of biomass in genetic studies. creator: Patrick Buerger creator: Carlos Alvarez-Roa creator: Karen D. Weynberg creator: Sebastien Baekelandt creator: Madeleine J.H. van Oppen uri: https://doi.org/10.7717/peerj.2110 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Buerger et al. title: Does ecophysiology mediate reptile responses to fire regimes? Evidence from Iberian lizards link: https://peerj.com/articles/2107 last-modified: 2016-06-09 description: Background. Reptiles are sensitive to habitat disturbance induced by wildfires but species frequently show opposing responses. Functional causes of such variability have been scarcely explored. In the northernmost limit of the Mediterranean bioregion, lizard species of Mediterranean affinity (Psammodromus algirus and Podarcis guadarramae) increase in abundance in burnt areas whereas Atlantic species (Lacerta schreiberi and Podarcis bocagei) decrease. Timon lepidus, the largest Mediterranean lizard in the region, shows mixed responses depending on the locality and fire history. We tested whether such interspecific differences are of a functional nature, namely, if ecophysiological traits may determine lizard response to fire. Based on the variation in habitat structure between burnt and unburnt sites, we hypothesise that Mediterranean species, which increase density in open habitats promoted by frequent fire regimes, should be more thermophile and suffer lower water losses than Atlantic species.Methods. We submitted 6–10 adult males of the five species to standard experiments for assessing preferred body temperatures (Tp) and evaporativewater loss rates (EWL), and examined the variation among species and along time by means of repeated-measures AN(C)OVAs.Results. Results only partially supported our initial expectations, since the medium-sized P. algirus clearly attained higher Tp and lower EWL. The two small wall lizards (P. bocagei and P. guadarramae) displayed low Tp and high EWL while the two large green lizards (T. lepidus and L. schreiberi) displayed intermediate values for both parameters.Discussion. The predicted differences according to the biogeographic affinities within each pair were not fully confirmed. We conclude that ecophysiology may help to understand functional reptile responses to fire but other biological traits are also to be considered. creator: Catarina C. Ferreira creator: Xavier Santos creator: Miguel A. Carretero uri: https://doi.org/10.7717/peerj.2107 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Ferreira et al. title: Detection of antibiotic-resistant bacteria endowed with antimicrobial activity from a freshwater lake and their phylogenetic affiliation link: https://peerj.com/articles/2103 last-modified: 2016-06-09 description: Antimicrobial resistance poses a serious challenge to global public health. In this study, fifty bacterial strains were isolated from the sediments of a freshwater lake and were screened for antibiotic resistance. Out of fifty isolates, thirty-three isolates showed resistance against at least two of the selected antibiotics. Analysis of 16S rDNA sequencing revealed that the isolates belonged to ten different genera, namely Staphylococcus(n = 8), Bacillus(n = 7), Lysinibacillus(n = 4), Achromobacter(n=3), bacterium(n = 3), Methylobacterium(n = 2), Bosea(n = 2), Aneurinibacillus(n = 2), Azospirillum(n = 1), Novosphingobium(n = 1). Enterobacterial repetitive intergenic consensus (ERIC) and BOX-PCR markers were used to study the genetic relatedness among the antibiotic resistant isolates. Further, the isolates were screened for their antimicrobial activity against bacterial pathogens viz., Staphylococcus aureus(MTCC-96), Pseudomonas aeruginosa(MTCC-2453) and Escherichia coli(MTCC-739), and pathogenic fungi viz., Fusarium proliferatum (MTCC-286), Fusarium oxysporum (CABI-293942) and Fusarium oxy. ciceri (MTCC-2791). In addition, biosynthetic genes (polyketide synthase II (PKS-II) and non-ribosomal peptide synthetase (NRPS)) were detected in six and seven isolates, respectively. This is the first report for the multifunctional analysis of the bacterial isolates from a wetland with biosynthetic potential, which could serve as potential source of useful biologically active metabolites. creator: Zothanpuia creator: Ajit K. Passari creator: Vijai K. Gupta creator: Bhim P. Singh uri: https://doi.org/10.7717/peerj.2103 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Zothanpuia et al. title: Symptoms of depression, sadness and sense of coherence (coping) among cognitively intact older people with cancer living in nursing homes—a mixed-methods study link: https://peerj.com/articles/2096 last-modified: 2016-06-09 description: Background: Symptoms of depression are often reported among patients with a cancer diagnosis. Strong sense of coherence (SOC) is shown to be associated with less depression in the general older population and among nursing homes (NH) residents in particular. Knowledge about mixed-methods perspectives that examine symptoms of depression and SOC among cognitively intact NH residents with cancer is scarce.Aim: To investigate symptoms of depression and SOC among NH residents who are cognitively intact and have cancer.Methods: We used a quantitatively driven mixed-methods design with sequential supplementary qualitative components. We facilitated the collection of quantitative survey data of 60 NH residents (≥ 65 years) with cancer using the Geriatric Depression Scale (GDS) and SOC scale. The supplementary psychosocial component comprised qualitative research interviews about experiences related to depression with nine respondents from the same cohort.Results: In fully adjusted multiple regression analysis of the sociodemographic variables, the GDS was significantly correlated with SOC (P < 0.001). The experience of sadness was identified by the following theme: sadness. Coping with the experience of symptoms of depression was dominated by coping with sadness.Conclusion: More than half the NH residents reported symptoms of depression, and the SOC was associated with reduced symptoms. A mixed-methods design contributed to nuanced and detailed information about the meaning of depression, and the supplementary component informs and supports the core component. To improve the situation of NH residents with cancer, more attention should be paid to the residents’ experience of symptoms of depression and their SOC. creator: Jorunn Drageset creator: Geir Egil Eide creator: Solveig Hauge uri: https://doi.org/10.7717/peerj.2096 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Drageset et al. title: The oral microbiome of patients with axial spondyloarthritis compared to healthy individuals link: https://peerj.com/articles/2095 last-modified: 2016-06-09 description: Background. A loss of mucosal tolerance to the resident microbiome has been postulated in the aetiopathogenesis of spondyloarthritis, thus the purpose of these studies was to investigate microbial communities that colonise the oral cavity of patients with axial spondyloarthritis (AxSpA) and to compare these with microbial profiles of a matched healthy population.Methods. Thirty-nine participants, 17 patients with AxSpA and 22 age and gender-matched disease-free controls were recruited to the study. For patients with AxSpA, disease activity was assessed using the Bath Ankylosing Spondylitis Disease Activity Index (BASDAI). All participants underwent a detailed dental examination to assess oral health, including the presence of periodontal disease assessed using probing pocket depth (PPD). Plaque samples were obtained and their bacterial populations were profiled using Ion Torrent sequencing of the V6 region of the 16S rRNA gene.Results.Patients with AxSpA had active disease (BASDAI 4.1 ± 2.1 [mean ± SD]), and a significantly greater prevalence of periodontitis (PPD ≥ 4 mm at ≥4 sites) than controls. Bacterial communities did not differ between the two groups with multiple metrics of α and β diversity considered. Analysis of operational taxonomic units (OTUs) and higher levels of taxonomic assignment did not provide strong evidence of any single taxa associated with AxSpA in the subgingival plaque.Discussion. Although 16S rRNA gene sequencing did not identify specific bacterial profiles associated with AxSpA, there remains the potential for the microbiota to exert functional and metabolic influences in the oral cavity which could be involved in the pathogenesis of AxSpA. creator: Jordan E. Bisanz creator: Praema Suppiah creator: W. Murray Thomson creator: Trudy Milne creator: Nigel Yeoh creator: Anita Nolan creator: Grace Ettinger creator: Gregor Reid creator: Gregory B. Gloor creator: Jeremy P. Burton creator: Mary P. Cullinan creator: Simon M. Stebbings uri: https://doi.org/10.7717/peerj.2095 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Bisanz et al. title: Salt taste after bariatric surgery and weight loss in obese persons link: https://peerj.com/articles/2086 last-modified: 2016-06-09 description: Background. Little is known about the perception of salty taste in obese patients, especially after bariatric surgery. Therefore, the aim of this study was to analyse possible differences in salt detection thresholds and preferences for foods differing in salt content in obese persons before and after bariatric surgery with weight loss compared to non-obese individuals.Methods. Sodium chloride detection thresholds and liking for cream soups with different salt concentrations were studied with established tests. Moreover, a brief salt food questionnaire was assessed to identify the usage and awareness of salt in food.Results. The results showed similar mean sodium chloride detection thresholds between non-obese and obese participants. After bariatric surgery a non-significant increase in the salt detection threshold was observed in the obese patients (mean ± SD: 0.44 ± 0.24 g NaCl/L before OP vs. 0.64 ± 0.47 g NaCl/L after OP, p = 0.069). Cream soup liking between controls and obese patients were not significantly different. However, significant sex specific differences were detected with the tested women not liking the soups (p < 0.001). Results from the food questionnaire were similar between the groups.Conclusion. No differences between non-obese persons and obese patients were shown regarding the salt detection threshold. However, due to highly significant differences in soup liking, sex should be taken into consideration when conducting similar sensory studies. creator: Cem Ekmekcioglu creator: Julia Maedge creator: Linda Lam creator: Gerhard Blasche creator: Soheila Shakeri-Leidenmühler creator: Michael Kundi creator: Bernhard Ludvik creator: Felix B. Langer creator: Gerhard Prager creator: Karin Schindler creator: Klaus Dürrschmid uri: https://doi.org/10.7717/peerj.2086 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Ekmekcioglu et al. title: Different RNA splicing mechanisms contribute to diverse infective outcome of classical swine fever viruses of differing virulence: insights from the deep sequencing data in swine umbilical vein endothelial cells link: https://peerj.com/articles/2113 last-modified: 2016-06-08 description: Molecular mechanisms underlying RNA splicing regulation in response to viral infection are poorly understood. Classical swine fever (CSF), one of the most economically important and highly contagious swine diseases worldwide, is caused by classical swine fever virus (CSFV). Here, we used high-throughput sequencing to obtain the digital gene expression (DGE) profile in swine umbilical vein endothelial cells (SUVEC) to identify different response genes for CSFV by using both Shimen and C strains. The numbers of clean tags obtained from the libraries of the control and both CSFV-infected libraries were 3,473,370, 3,498,355, and 3,327,493 respectively. In the comparison among the control, CSFV-C, and CSFV-Shimen groups, 644, 158, and 677 differentially expressed genes (DEGs) were confirmed in the three groups. Pathway enrichment analysis showed that many of these DEGs were enriched in spliceosome, ribosome, proteasome, ubiquitin-mediated proteolysis, cell cycle, focal adhesion, Wnt signalling pathway, etc., where the processes differ between CSFV strains of differing virulence. To further elucidate important mechanisms related to the differential infection by the CSFV Shimen and C strains, we identified four possible profiles to assess the significantly expressed genes only by CSFV Shimen or CSFV C strain. GO analysis showed that infection with CSFV Shimen and C strains disturbed ‘RNA splicing’ of SUVEC, resulting in differential ‘gene expression’ in SUVEC. Mammalian target of rapamycin (mTOR) was identified as a significant response regulator contributed to impact on SUVEC function for CSFV Shimen. This computational study suggests that CSFV of differing virulence could induce alterations in RNA splicing regulation in the host cell to change cell metabolism, resulting in acute haemorrhage and pathological damage or infectious tolerance. creator: Pengbo Ning creator: Yulu Zhou creator: Wulong Liang creator: Yanming Zhang uri: https://doi.org/10.7717/peerj.2113 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Ning et al. title: Geometric morphometric analysis of intratrackway variability: a case study on theropod and ornithopod dinosaur trackways from Münchehagen (Lower Cretaceous, Germany) link: https://peerj.com/articles/2059 last-modified: 2016-06-08 description: A profound understanding of the influence of trackmaker anatomy, foot movements and substrate properties is crucial for any interpretation of fossil tracks. In this case study we analyze variability of footprint shape within one large theropod (T3), one medium-sized theropod (T2) and one ornithopod (I1) trackway from the Lower Cretaceous of Münchehagen (Lower Saxony, Germany) in order to determine the informativeness of individual features and measurements for ichnotaxonomy, trackmaker identification, and the discrimination between left and right footprints. Landmark analysis is employed based on interpretative outline drawings derived from photogrammetric data, allowing for the location of variability within the footprint and the assessment of covariation of separate footprint parts. Objective methods to define the margins of a footprint are tested and shown to be sufficiently accurate to reproduce the most important results. The lateral hypex and the heel are the most variable regions in the two theropod trackways. As indicated by principal component analysis, a posterior shift of the lateral hypex is correlated with an anterior shift of the margin of the heel. This pattern is less pronounced in the ornithopod trackway, indicating that variation patterns can differ in separate trackways. In all trackways, hypices vary independently from each other, suggesting that their relative position a questionable feature for ichnotaxonomic purposes. Most criteria commonly employed to differentiate between left and right footprints assigned to theropods are found to be reasonably reliable. The described ornithopod footprints are asymmetrical, again allowing for a left–right differentiation. Strikingly, 12 out of 19 measured footprints of the T2 trackway are stepped over the trackway midline, rendering the trackway pattern a misleading left–right criterion for this trackway. Traditional measurements were unable to differentiate between the theropod and the ornithopod trackways. Geometric morphometric analysis reveals potential for improvement of existing discriminant methods. creator: Jens N. Lallensack creator: Anneke H. van Heteren creator: Oliver Wings uri: https://doi.org/10.7717/peerj.2059 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Lallensack et al. title: New lower jaw and teeth referred to Maxakalisaurus topai (Titanosauria: Aeolosaurini) and their implications for the phylogeny of titanosaurid sauropods link: https://peerj.com/articles/2054 last-modified: 2016-06-08 description: Sauropod dinosaurs compose a diversified, well known, and worldwide distributed clade, with a stereotyped body plan: deep trunk, elongated neck and tail, columnar limbs and very small skull. In Brazil, the group is represented by ten formally described Cretaceous species, mostly titanosaurs. This is the case of Maxakalisaurus topai, known based on an incomplete and disarticulated skeleton, unearthed from deposits of the Adamantina Formation in Minas Gerais. Here, we report a partial right dentary, including five isolated teeth, collected from the same site as the type-series of M. topai and tentatively referred to that taxon. The bone is gently curved medially, the functional teeth are set on an anterolingual position, and two replacement teeth are seen per alveoli. New morphological data gathered from that specimen was employed to conduct a comprehensive phylogenetic analysis of Titanosauria (with 42 taxa and 253 characters), based on previous studies. The Aeolosaurini clade was recovered, with Gondwanatitan and Aelosaurus as sister taxa, and Maxakalisaurus, Panamericansaurus, and Rinconsaurus forming a basal polytomy. creator: Marco A.G. França creator: Júlio C. de A. Marsola creator: Douglas Riff creator: Annie S. Hsiou creator: Max C. Langer uri: https://doi.org/10.7717/peerj.2054 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 França et al. title: Temporal changes in the structure of a plant-frugivore network are influenced by bird migration and fruit availability link: https://peerj.com/articles/2048 last-modified: 2016-06-08 description: Background. Ecological communities are dynamic collections whose composition and structure change over time, making up complex interspecific interaction networks. Mutualistic plant–animal networks can be approached through complex network analysis; these networks are characterized by a nested structure consisting of a core of generalist species, which endows the network with stability and robustness against disturbance. Those mutualistic network structures can vary as a consequence of seasonal fluctuations and food availability, as well as the arrival of new species into the system that might disorder the mutualistic network structure (e.g., a decrease in nested pattern). However, there is no assessment on how the arrival of migratory species into seasonal tropical systems can modify such patterns. Emergent and fine structural temporal patterns are adressed here for the first time for plant-frugivorous bird networks in a highly seasonal tropical environment.Methods. In a plant-frugivorous bird community, we analyzed the temporal turnover of bird species comprising the network core and periphery of ten temporal interaction networks resulting from different bird migration periods. Additionally, we evaluated how fruit abundance and richness, as well as the arrival of migratory birds into the system, explained the temporal changes in network parameters such as network size, connectance, nestedness, specialization, interaction strength asymmetry and niche overlap. The analysis included data from 10 quantitative plant-frugivorous bird networks registered from November 2013 to November 2014.Results. We registered a total of 319 interactions between 42 plant species and 44 frugivorous bird species; only ten bird species were part of the network core. We witnessed a noteworthy turnover of the species comprising the network periphery during migration periods, as opposed to the network core, which did not show significant temporal changes in species composition. Our results revealed that migration and fruit richness explain the temporal variations in network size, connectance, nestedness and interaction strength asymmetry. On the other hand, fruit abundance only explained connectance and nestedness.Discussion. By means of a fine-resolution temporal analysis, we evidenced for the first time how temporal changes in the interaction network structure respond to the arrival of migratory species into the system and to fruit availability. Additionally, few migratory bird species are important links for structuring networks, while most of them were peripheral species. We showed the relevance of studying bird–plant interactions at fine temporal scales, considering changing scenarios of species composition with a quantitative network approach. creator: Michelle Ramos-Robles creator: Ellen Andresen creator: Cecilia Díaz-Castelazo uri: https://doi.org/10.7717/peerj.2048 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Ramos-Robles et al. title: Sparc: a sparsity-based consensus algorithm for long erroneous sequencing reads link: https://peerj.com/articles/2016 last-modified: 2016-06-08 description: Motivation. The third generation sequencing (3GS) technology generates long sequences of thousands of bases. However, its current error rates are estimated in the range of 15–40%, significantly higher than those of the prevalent next generation sequencing (NGS) technologies (less than 1%). Fundamental bioinformatics tasks such as de novo genome assembly and variant calling require high-quality sequences that need to be extracted from these long but erroneous 3GS sequences.Results. We describe a versatile and efficient linear complexity consensus algorithm Sparc to facilitate de novo genome assembly. Sparc builds a sparse k-mer graph using a collection of sequences from a targeted genomic region. The heaviest path which approximates the most likely genome sequence is searched through a sparsity-induced reweighted graph as the consensus sequence. Sparc supports using NGS and 3GS data together, which leads to significant improvements in both cost efficiency and computational efficiency. Experiments with Sparc show that our algorithm can efficiently provide high-quality consensus sequences using both PacBio and Oxford Nanopore sequencing technologies. With only 30× PacBio data, Sparc can reach a consensus with error rate <0.5%. With the more challenging Oxford Nanopore data, Sparc can also achieve similar error rate when combined with NGS data. Compared with the existing approaches, Sparc calculates the consensus with higher accuracy, and uses approximately 80% less memory and time.Availability. The source code is available for download at https://github.com/yechengxi/Sparc. creator: Chengxi Ye creator: Zhanshan (Sam) Ma uri: https://doi.org/10.7717/peerj.2016 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Ye and Ma title: On causality of extreme events link: https://peerj.com/articles/2111 last-modified: 2016-06-07 description: Multiple metrics have been developed to detect causality relations between data describing the elements constituting complex systems, all of them considering their evolution through time. Here we propose a metric able to detect causality within static data sets, by analysing how extreme events in one element correspond to the appearance of extreme events in a second one. The metric is able to detect non-linear causalities; to analyse both cross-sectional and longitudinal data sets; and to discriminate between real causalities and correlations caused by confounding factors. We validate the metric through synthetic data, dynamical and chaotic systems, and data representing the human brain activity in a cognitive task. We further show how the proposed metric is able to outperform classical causality metrics, provided non-linear relationships are present and large enough data sets are available. creator: Massimiliano Zanin uri: https://doi.org/10.7717/peerj.2111 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Zanin title: What flowers do we like? The influence of shape and color on the rating of flower beauty link: https://peerj.com/articles/2106 last-modified: 2016-06-07 description: There is no doubt that people find flowers beautiful. Surprisingly, we know very little about the actual properties which make flowers so appealing to humans. Although the evolutionary aesthetics provides some theories concerning generally preferred flower traits, empirical evidence is largely missing. In this study, we used an online survey in which residents of the Czech Republic (n = 2006) rated the perceived beauty of 52 flower stimuli of diverse shapes and colors. Colored flowers were preferred over their uncolored versions. When controlling for flower shape, we found an unequal preference for different flower colors, blue being the most and yellow the least preferred. In the overall assessment of beauty, shape was more important than color. Prototypical flowers, i.e., radially symmetrical flowers with low complexity, were rated as the most beautiful. We also found a positive effect of sharp flower contours and blue color on the overall rating of flower beauty. The results may serve as a basis for further studies in some areas of the people-plant interaction research. creator: Martin Hůla creator: Jaroslav Flegr uri: https://doi.org/10.7717/peerj.2106 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Hůla and Flegr title: 1H NMR studies distinguish the water soluble metabolomic profiles of untransformed and RAS-transformed cells link: https://peerj.com/articles/2104 last-modified: 2016-06-07 description: Metabolomic profiling is an increasingly important method for identifying potential biomarkers in cancer cells with a view towards improved diagnosis and treatment. Nuclear magnetic resonance (NMR) provides a potentially noninvasive means to accurately characterize differences in the metabolomic profiles of cells. In this work, we use 1H NMR to measure the metabolomic profiles of water soluble metabolites extracted from isogenic control and oncogenic HRAS-, KRAS-, and NRAS-transduced BEAS2B lung epithelial cells to determine the robustness of NMR metabolomic profiling in detecting differences between the transformed cells and their untransformed counterparts as well as differences among the RAS-transformed cells. Unique metabolomic signatures between control and RAS-transformed cell lines as well as among the three RAS isoform-transformed lines were found by applying principal component analysis to the NMR data. This study provides a proof of principle demonstration that NMR-based metabolomic profiling can robustly distinguish untransformed and RAS-transformed cells as well as cells transformed with different RAS oncogenic isoforms. Thus, our data may potentially provide new diagnostic signatures for RAS-transformed cells. creator: Vered Marks creator: Anisleidys Munoz creator: Priyamvada Rai creator: Jamie D. Walls uri: https://doi.org/10.7717/peerj.2104 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Marks et al. title: Transcriptome analysis of immature xylem in the Chinese fir at different developmental phases link: https://peerj.com/articles/2097 last-modified: 2016-06-07 description: Background.Chinese fir [Cunninghamia lanceolata (Lamb.) Hook.] is one of the most important native tree species for timber production in southern China. An understanding of overall fast growing stage, stem growth stage and senescence stage cambium transcriptome variation is lacking. We used transcriptome sequencing to identify the repertoire of genes expressed during development of xylem tissue in Chinese fir, aiming to delineate the molecular mechanisms of wood formation. Results. We carried out transcriptome sequencing at three different cultivation ages (7Y, 15Y and 21Y) generating 68.71 million reads (13.88 Gbp). A total of 140,486 unigenes with a mean size of 568.64 base pairs (bp) were obtained via de novo assembly. Of these, 27,427 unigenes (19.52%) were further annotated by comparison to public protein databases. A total of 5,331 (3.79%) unigenes were mapped into 118 pathways by searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG). Differentially expressed genes (DEG) analysis identified 3, 16 and 5,899 DEGs from the comparison of 7Y vs. 15Y, 7Y vs. 21Y and 15Y vs. 21Y, respectively, in the immature xylem tissues, including 2,638 significantly up-regulated and 3,280 significantly down-regulated genes. Besides, five NAC transcription factors, 190 MYB transcription factors, and 34 WRKY transcription factors were identified respectively from Chinese fir transcriptome.Conclusion. Our results revealed the active transcriptional pathways and identified the DEGs at different cultivation phases of Chinese fir wood formation. This transcriptome dataset will aid in understanding and carrying out future studies on the molecular basis of Chinese fir wood formation and contribute to future artificial production and applications. creator: Yunxing Zhang creator: Xiaojiao Han creator: Jian Sang creator: Xuelian He creator: Mingying Liu creator: Guirong Qiao creator: Renying Zhuo creator: Guiping He creator: Jianjun Hu uri: https://doi.org/10.7717/peerj.2097 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Zhang et al. title: Consequences for selected high-elevation butterflies and moths from the spread of Pinus mugo into the alpine zone in the High Sudetes Mountains link: https://peerj.com/articles/2094 last-modified: 2016-06-07 description: Due to changes in the global climate, isolated alpine sites have become one of the most vulnerable habitats worldwide. The indigenous fauna in these habitats is threatened by an invasive species, dwarf pine (Pinus mugo), which is highly competitive and could be important in determining the composition of the invertebrate community. In this study, the association of species richness and abundance of butterflies with the extent of Pinus mugo cover at individual alpine sites was determined. Butterflies at alpine sites in the High Sudetes Mountains (Mts.) were sampled using Moericke yellow water traps. The results of a Canonical Correspondence Analysis (CCA) indicated that at a local scale the area of alpine habitats is the main limiting factor for native species of alpine butterflies. Butterfly assemblages are associated with distance to the tree-line with the optimum situated in the lower forest zone. In addition the CCA revealed that biotic factors (i.e. Pinus mugo and alpine tundra vegetation) accounted for a significant amount of the variability in species data. Regionally, the CCA identified that the species composition of butterflies and moths is associated with presence and origin of Pinus mugo. Our study provides evidence that the structure of the Lepidopteran fauna that formed during the postglacial period and also the present composition of species assemblages is associated with the presence of Pinus mugo. With global warming, Pinus mugo has the potential to spread further into alpine areas and negatively affect the local species communities. creator: Karolína Bílá creator: Jan Šipoš creator: Pavel Kindlmann creator: Tomáš Kuras uri: https://doi.org/10.7717/peerj.2094 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Bílá et al. title: Potential urinary aging markers of 20-month-old rats link: https://peerj.com/articles/2058 last-modified: 2016-06-07 description: Urine is a very good source for biomarker discovery because it accumulates changes in the body. However, a major challenge in urinary biomarker discovery is the fact that the urinary proteome is influenced by various elements. To circumvent these problems, simpler systems, such as animal models, can be used to establish associations between physiological or pathological conditions and alterations in the urinary proteome. In this study, the urinary proteomes of young (two months old) and old rats (20 months old; nine in each group) were analyzed using LC-MS/MS and quantified using the Progenesis LC-MS software. A total of 371 proteins were identified, 194 of which were shared between the young and old rats. Based on criteria of a fold change ≥2, P < 0.05 and identification in each rat of the high-abundance group, 33 proteins were found to be changed (15 increased and 18 decreased in old rats). By adding a more stringent standard (protein spectral counts from every rat in the higher group greater than those in the lower group), eight proteins showed consistent changes in all rats of the groups; two of these proteins are also altered in the urinary proteome of aging humans. However, no shared proteins between our results and the previous aging plasma proteome were identified. Twenty of the 33 (60%) altered proteins have been reported to be disease biomarkers, suggesting that aging may share similar urinary changes with some diseases. The 33 proteins corresponded to 28 human orthologs which, according to the Human Protein Atlas, are strongly expressed in the kidney, intestine, cerebellum and lung. Therefore, the urinary proteome may reflect aging conditions in these organs. creator: Xundou Li creator: Youhe Gao uri: https://doi.org/10.7717/peerj.2058 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Li and Gao title: Uropygial gland and bib colouration in the house sparrow link: https://peerj.com/articles/2102 last-modified: 2016-06-02 description: Birds frequently signal different qualities by plumage colouration, mainly during mating. However, plumage colouration is determined during the moult, and therefore it would indicate the quality of individual birds during the moult, not its current quality. Recent studies, however, suggest that birds could modify plumage colouration by using cosmetic preen oil produced by the uropygial gland. In this study, I show that bib colouration is related to uropygial gland size and body condition in male house sparrows (Passer domesticus). Moreover, I conducted an experiment in which a group of sparrows were inoculated with an antigen, mimicking an illness. In control birds, short-term changes in bib colouration were related to both body condition and change in uropygial gland size. Therefore, birds that reduced uropygial gland size showed a greater colouration change. However, bib colouration did not change with the change in uropygial gland size in experimental birds inoculated with the antigen. Given that the experiment did not affect preen oil production or consumption, this finding tentatively suggests that the immune challenge provoked a change in the composition of preen oil, affecting its cosmetic properties. In short, the results of this study suggest that (1) male house sparrows produce cosmetic preen oil that alters the colouration of their bibs; (2) the more change in uropygial gland size, the more change in bib colouration; and (3) in this way, bib colouration has the potential to signal current health status, since less healthy birds showed less capacity to change bib colouration. creator: Gregorio Moreno-Rueda uri: https://doi.org/10.7717/peerj.2102 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Moreno-Rueda title: A closer look at four-dot masking of a foveated target link: https://peerj.com/articles/2068 last-modified: 2016-06-02 description: Four-dot masking with a common onset mask was recently demonstrated in a fully attended and foveated target (Filmer, Mattingley & Dux, 2015). Here, we replicate and extend this finding by directly comparing a four-dot mask with an annulus mask while probing masking as a function of mask duration, and target-mask separation. Our results suggest that while an annulus mask operates via spatially local contour interactions, a four-dot mask operates through spatially global mechanisms. We also measure how the visual system’s representation of an oriented bar is impacted by a four-dot mask, and find that masking here does not degrade the precision of perceived targets, but instead appears to be driven exclusively by rendering the target completely invisible. creator: Marwan Daar creator: Hugh R. Wilson uri: https://doi.org/10.7717/peerj.2068 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Daar and Wilson title: European adults’ physical activity socio-demographic correlates: a cross-sectional study from the European Social Survey link: https://peerj.com/articles/2066 last-modified: 2016-06-02 description: Background. From a public health perspective, the study of socio-demographic factors related to physical activity is important in order to identify subgroups for intervention programs.Objective. This study aimed to identify the prevalence of, and the socio-demographic correlates related to, the achievement of recommended physical activity levels.Methods. Using data from the European Social Survey round 6, physical activity and socio-demographic characteristics were collected, in 2012, from 39,278 European adults (18,272 men, 21,006 women), aged 18–65 years, from 28 countries. The question of meeting physical activity guidelines was assessed using World Health Organization criteria.Results. A total of 64.50% (63.36% men, 66.49% women) attained physical activity recommended levels. The likelihood of attaining physical activity recommendations was higher in the 55–64 years age group (men: OR = 1.22, p < 0.05; women: OR = 1.66, p < 0.001), among those who had secondary education (men: OR = 1.28, p < 0.01; women: OR = 1.26, p < 0.05), among those who lived in rural areas (men: OR = 1.20, p < 0.001; women: OR = 1.10, p < 0.05), and among those who had three or more people living at home (men: OR = 1.40, p < 0.001; women: OR = 1.43, p < 0.001). On the other hand, attaining physical activity recommendations was negatively associated with being unemployed (men: OR = 0.70, p < 0.001; women: OR = 0.87, p < 0.05), being a student (OR = 0.56, p < 0.001; women: OR = 0.64, p < 0.01), being a retired person (men: OR = 0.86, p < 0.05) and with having a higher household income (OR = 0.80, p < 0.001; women: OR = 0.81, p < 0.01).Conclusions. This research helped clarify that, as the promotion of physical activity is critical to sustain health and prevent disease, socio-demographic factors are important to consider when planning the increase of physical activity. creator: Adilson Marques creator: João Martins creator: Miguel Peralta creator: Ricardo Catunda creator: Luís Saboga Nunes uri: https://doi.org/10.7717/peerj.2066 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Marques et al. title: Microfungal oasis in an oligotrophic desert: diversity patterns and community structure in three freshwater systems of Cuatro Ciénegas, Mexico link: https://peerj.com/articles/2064 last-modified: 2016-06-02 description: The Cuatro Ciénegas Basin (CCB) comprises several oligotrophic aquatic ecosystems limited by phosphorus. These aquatic systems are dominated by a high prokaryotic diversity, shaped by the stress of low nutrient supplies and interspecific competition. Although fungi constitute a diverse and important component of microbial diversity, the microfungal diversity in the CCB remains to be unveiled. With the aim to explore microfungal diversity and ecological patterns in this area, we present the first investigation analyzing cultivable taxa from sediment and water, as well as lignocellulolytic taxa obtained from incubated submerged plant debris, and wood panels in three contrasting freshwater systems in the CCB: Churince, Becerra and Pozas Rojas. We chose a culture-based approach to analyze sediment and water samples in order to obtain fungal cultures, providing opportunities for a posteriori studies, and the possibility of ex situ preservation of the diversity. We evaluated sequence data from the nuclear ribosomal internal transcribed spacer including the 5.8 rDNA region for 126 isolates, revealing 37 OTUs. These OTUs were phylogenetically affiliated to several genera in the fungal phyla: Zygomycota, Basidiomycota, and Ascomycota. We recorded two OTUs with saline affinity, agreeing with previous findings on the prokaryotic communities with ancestral marine resemblances. All the studied systems showed moderate diversity levels, however discrepancies among the diversity indexes were observed, due to the occurrence of abundant taxa in the samples. Our results indicated that lignocellulolytic microfungal communities are dominated by transient fungal taxa, as resident species were not recorded perhaps as a result of the long-term strong competition with the highly adapted prokaryotic community. Moreover, the obtained microfungal taxa occurred mostly on the resident plant debris, rather than submerged wood panels, perhaps as a result of the high adaptation to specific environmental conditions. In conclusion, the CCB possess a moderate taxonomical diversity compared to other arid environments, probably as a result of high selective pressures. Nonetheless, due to high spatial and temporal heterogeneity, the functional fungal diversity was considerable as predicted by the intermediate disturbance hypothesis. Decisively, the assessment of microfungal diversity freshwater systems is relevant, since this ecological group of microorganisms represents an important indicator of trophic complexity and biotic interactions among microbial communities, having important implications for understanding eukaryotic survival at the oligotrophic limit for life. creator: Patricia Velez creator: Jaime Gasca-Pineda creator: Edmundo Rosique-Gil creator: Luis E. Eguiarte creator: Laura Espinosa-Asuar creator: Valeria Souza uri: https://doi.org/10.7717/peerj.2064 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Velez et al. title: Potential problems of removing one invasive species at a time: a meta-analysis of the interactions between invasive vertebrates and unexpected effects of removal programs link: https://peerj.com/articles/2029 last-modified: 2016-06-02 description: Although the co-occurrence of nonnative vertebrates is a ubiquitous global phenomenon, the study of interactions between invaders is poorly represented in the literature. Limited understanding of the interactions between co-occurring vertebrates can be problematic for predicting how the removal of only one invasive—a common management scenario—will affect native communities. We suggest a trophic food web framework for predicting the effects of single-species management on native biodiversity. We used a literature search and meta-analysis to assess current understanding of how the removal of one invasive vertebrate affects native biodiversity relative to when two invasives are present. The majority of studies focused on the removal of carnivores, mainly within aquatic systems, which highlights a critical knowledge gap in our understanding of co-occurring invasive vertebrates. We found that removal of one invasive vertebrate caused a significant negative effect on native species compared to when two invasive vertebrates were present. These unexpected results could arise because of the positioning and hierarchy of the co-occurring invasives in the food web (e.g., carnivore–carnivore or carnivore–herbivore). We consider that there are important knowledge gaps to determinate the effects of multiple co-existing invaders on native ecosystems, and this information could be precious for management. creator: Sebastián A. Ballari creator: Sara E. Kuebbing creator: Martin A. Nuñez uri: https://doi.org/10.7717/peerj.2029 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Ballari et al. title: Experimental warming decreases arbuscular mycorrhizal fungal colonization in prairie plants along a Mediterranean climate gradient link: https://peerj.com/articles/2083 last-modified: 2016-06-01 description: Background: Arbuscular mycorrhizal fungi (AMF) provide numerous services to their plant symbionts. Understanding climate change effects on AMF, and the resulting plant responses, is crucial for predicting ecosystem responses at regional and global scales. We investigated how the effects of climate change on AMF-plant symbioses are mediated by soil water availability, soil nutrient availability, and vegetation dynamics.Methods: We used a combination of a greenhouse experiment and a manipulative climate change experiment embedded within a Mediterranean climate gradient in the Pacific Northwest, USA to examine this question. Structural equation modeling (SEM) was used to determine the direct and indirect effects of experimental warming on AMF colonization.Results: Warming directly decreased AMF colonization across plant species and across the climate gradient of the study region. Other positive and negative indirect effects of warming, mediated by soil water availability, soil nutrient availability, and vegetation dynamics, canceled each other out.Discussion: A warming-induced decrease in AMF colonization would likely have substantial consequences for plant communities and ecosystem function. Moreover, predicted increases in more intense droughts and heavier rains for this region could shift the balance among indirect causal pathways, and either exacerbate or mitigate the negative, direct effect of increased temperature on AMF colonization. creator: Hannah Wilson creator: Bart R. Johnson creator: Brendan Bohannan creator: Laurel Pfeifer-Meister creator: Rebecca Mueller creator: Scott D. Bridgham uri: https://doi.org/10.7717/peerj.2083 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Wilson et al. title: Snapshot fecal survey of domestic animals in rural Ghana for Mycobacterium ulcerans link: https://peerj.com/articles/2065 last-modified: 2016-06-01 description: Identifying the source reservoirs of Mycobacterium ulcerans is key to understanding the mode of transmission of this pathogen and controlling the spread of Buruli ulcer (BU). In Australia, the native possum can harbor M. ulcerans in its gastrointestinal tract and shed high concentrations of the bacteria in its feces. To date, an analogous animal reservoir in Africa has not been identified. Here we tested the hypothesis that common domestic animals in BU endemic villages of Ghana are reservoir species analogous to the Australian possum. Using linear-transects at 10-meter intervals, we performed systematic fecal surveys across four BU endemic villages and one non-endemic village in the Asante Akim North District of Ghana. One hundred and eighty fecal specimens from a single survey event were collected and analyzed by qPCR for the M. ulcerans diagnostic DNA targets IS2404 and KR-B. Positive and negative controls performed as expected but all 180 test samples were negative. This structured snapshot survey suggests that common domestic animals living in and around humans do not shed M. ulcerans in their feces. We conclude that, unlike the Australian native possum, domestic animals in rural Ghana are unlikely to be major reservoirs of M. ulcerans. creator: Nicholas J. Tobias creator: Nana Ama Ammisah creator: Evans K. Ahortor creator: John R. Wallace creator: Anthony Ablordey creator: Timothy P. Stinear uri: https://doi.org/10.7717/peerj.2065 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Tobias et al. title: Assessing Illumina technology for the high-throughput sequencing of bacteriophage genomes link: https://peerj.com/articles/2055 last-modified: 2016-06-01 description: Bacteriophages are the most abundant biological entities on the planet, playing crucial roles in the shaping of bacterial populations. Phages have smaller genomes than their bacterial hosts, yet there are currently fewer fully sequenced phage than bacterial genomes. We assessed the suitability of Illumina technology for high-throughput sequencing and subsequent assembly of phage genomes. In silico datasets reveal that 30× coverage is sufficient to correctly assemble the complete genome of ~98.5% of known phages, with experimental data confirming that the majority of phage genomes can be assembled at 30× coverage. Furthermore, in silico data demonstrate it is possible to co-sequence multiple phages from different hosts, without introducing assembly errors. creator: Branko Rihtman creator: Sean Meaden creator: Martha R.J. Clokie creator: Britt Koskella creator: Andrew D. Millard uri: https://doi.org/10.7717/peerj.2055 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Rihtman et al. title: Living to the range limit: consumer isotopic variation increases with environmental stress link: https://peerj.com/articles/2034 last-modified: 2016-06-01 description: Background: Theoretically, each species’ ecological niche is phylogenetically-determined and expressed spatially as the species’ range. However, environmental stress gradients may directly or indirectly decrease individual performance, such that the precise process delimiting a species range may not be revealed simply by studying abundance patterns. In the intertidal habitat the vertical ranges of marine species may be constrained by their abilities to tolerate thermal and desiccation stress, which may act directly or indirectly, the latter by limiting the availability of preferred trophic resources. Therefore, we expected individuals at greater shore heights to show greater variation in diet alongside lower indices of physiological condition.Methods: We sampled the grazing gastropod Echinolittorina peruviana from the desert coastline of northern Chile at three shore heights, across eighteen regionally-representative shores. Stable isotope values (δ13C and δ15N) were extracted from E. peruviana and its putative food resources to estimate Bayesian ellipse area, carbon and nitrogen ranges and diet. Individual physiological condition was tracked by muscle % C and % N.Results: There was an increase in isotopic variation at high shore levels, where E. peruviana’s preferred resource, tide-deposited particulate organic matter (POM), appeared to decrease in dietary contribution, and was expected to be less abundant. Both muscle % C and % N of individuals decreased with height on the shore.Discussion: Individuals at higher stress levels appear to be less discriminating in diet, likely because of abiotic forcing, which decreases both consumer mobility and the availability of a preferred resource. Abiotic stress might be expected to increase trophic variation in other selective dietary generalist species. Where this coincides with a lower physiological condition may be a direct factor in setting their range limit. creator: Carl J. Reddin creator: Nessa E. O’Connor creator: Chris Harrod uri: https://doi.org/10.7717/peerj.2034 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Reddin et al.