Decline in coral cover and flattening of the reefs around Mauritius (1998–2010)
Coral reefs are degrading through the impacts of multiple anthropogenic stressors. How are coral reef communities going to change and how to protect them for future generations are important conservation questions. Using coral reef data from Mauritius, we examined changes in cover in 23 benthic groups for a 13-yr period and at 15 sites. Moreover, we determined which land-based stressor out of four (human population, agriculture, tourism, rainfall) correlated the most with the observed changes in coral reef cover. Among the stony corals, Acropora corals appeared to be the most impacted, decreasing in cover at many sites. However, the non-Acropora encrusting group increased in cover at several sites. The increase in abundance of dead corals and rubble at some sites also supported the observations of stony coral decline during the study period. Additionally, the decline in stony corals appeared to be more pronounced in second half of the study period for all sites suggesting that a global factor rather than a local factor was responsible for this decline. There was little change in cover for the other benthic groups, some of which were quite rare. Human population was significantly correlated with changes in coral reef cover for 11 sites, followed by tourism and agriculture. Rainfall, a proxy for runoff, did not appear to affect coral reef cover. Overall, our results showed that there has been a decline of stony coral cover especially the ones with complex morphologies, which in turn suggest that coral reefs around Mauritius have experienced a decline in habitat complexity during the study period. Our study also suggests that humans are an important factor contributing to the demise of coral reefs around the island.
Elliott et al. (2018) Decline in coral cover and flattening of the reefs around Mauritius (1998–2010). PeerJ 6:e6014 https://doi.org/10.7717/peerj.6014
The effect of insulin on equine lamellar basal epithelial cells mediated by the insulin-like growth factor-1 receptor
Background In horses and ponies, insulin dysregulation leading to hyperinsulinemia may be associated with increased risk of laminitis, and prolonged infusion of insulin can induce the condition. It is unclear whether insulin may have a direct or indirect effect on the lamellar tissues. Insulin is structurally related to insulin-like growth factor (IGF-1), and can bind the IGF-1 receptor, albeit at a lower affinity than IGF-1. Methods Immunohistochemistry was performed on formalin-fixed lamellar tissue sections from six normal horses, euthanised for non-research purposes, using an anti-IGF-1 receptor antibody. In further studies, lamellar epithelial cells were obtained by collagenase digestion from the hooves of 18 normal horses, also euthanised for non-research purposes, and incubated for 48 h in the presence of insulin (0–2,000 m IU/ml). The increase in cell numbers was determined using a cell proliferation assay, and compared to the effect of zero insulin using one-way ANOVA. Results Immunohistochemistry demonstrated IGF-1 receptors on lamellar epidermal epithelial cells. With cultured cells, insulin caused a concentration-dependent increase in cell proliferation compared to untreated cells (maximal effect 63.3 ± 12.8% more cells after 48 h with 1,000 m IU/ml insulin; P < 0.01). Co-incubation with a blocking antibody against the IGF-1 receptor significantly inhibited the proliferative effect of insulin (P < 0.01). Discussion These results demonstrate that IGF-1 receptors are present on lamellar epithelial cells. At high physiological concentrations, insulin may activate these cells, by a mechanism involving IGF-1 receptors, resulting in a proliferative effect. This mechanism could help to explain the link between hyperinsulinemia and laminitis.
Baskerville et al. (2018) The effect of insulin on equine lamellar basal epithelial cells mediated by the insulin-like growth factor-1 receptor. PeerJ 6:e5945 https://doi.org/10.7717/peerj.5945
ShapeGTB: the role of local DNA shape in prioritization of functional variants in human promoters with machine learning
Motivation The identification of functional sequence variations in regulatory DNA regions is one of the major challenges of modern genetics. Here, we report results of a combined multifactor analysis of properties characterizing functional sequence variants located in promoter regions of genes. Results We demonstrate that GC-content of the local sequence fragments and local DNA shape features play significant role in prioritization of functional variants and outscore features related to histone modifications, transcription factors binding sites, or evolutionary conservation descriptors. Those observations allowed us to build specialized machine learning classifier identifying functional single nucleotide polymorphisms within promoter regions—ShapeGTB. We compared our method with more general tools predicting pathogenicity of all non-coding variants. ShapeGTB outperformed them by a wide margin (average precision 0.93 vs. 0.47–0.55). On the external validation set based on ClinVar database it displayed worse performance but was still competitive with other methods (average precision 0.47 vs. 0.23–0.42). Such results suggest unique characteristics of mutations located within promoter regions and are a promising signal for the development of more accurate variant prioritization tools in the future.
Malkowska et al. (2018) ShapeGTB: the role of local DNA shape in prioritization of functional variants in human promoters with machine learning. PeerJ 6:e5742 https://doi.org/10.7717/peerj.5742
Disinfection effect of povidone-iodine in aquaculture water of swamp eel (Monopterus albus)
The swamp eel (Monopterus albus) is an important commercial farmed fish species in China. However, it is susceptible to Aeromonas hydrophila infections, resulting in high mortality and considerable economic loss. Povidone-iodine (PVP-I) is a widely used chemical disinfectant in aquaculture, which can decrease the occurrence of diseases and improve the survival. However, environmental organic matter could affect the bactericidal effectiveness of PVP-I, and the efficacy of PVP-I in aquaculture water is still unknown. In this paper, disinfection assays were conducted to evaluate the effectiveness of PVP-I against the A. hydrophila in different types of water. We found that the effective germicidal concentration of PVP-I in outdoor aquaculture water was 25 ppm for 12 h. In indoor aquaculture water with 105 CFU/mL bacteria, 10 ppm and 20 ppm of PVP-I could kill 99% and 100% of the bacteria, respectively. The minimal germicidal concentration of PVP-I in Luria-Bertani broth was 4,000 ppm. Available iodine content assay in LB solutions confirmed that the organic substance had negative impact on the effectiveness of PVP-I, which was consistent with the different efficacy of PVP-I in different water samples. Acute toxicity tests showed that the 24 h-LC50 of PVP-I to swamp eel was 173.82 ppm, which was much higher than the germicidal concentrations in outdoor and indoor aquaculture water, indicating its safety and effectivity to control the A. hydrophila. The results indicated PVP-I can be helpful for preventing the transmission of A. hydrophila in swamp eel aquaculture.
Chen et al. (2018) Disinfection effect of povidone-iodine in aquaculture water of swamp eel (Monopterus albus). PeerJ 6:e5523 https://doi.org/10.7717/peerj.5523
Chemical analysis and evaluation of antioxidant and antimicrobial activities of fruit fractions of Mauritia flexuosa L. f. (Arecaceae)
Background Fruit consumption is currently considered beyond the nutritional aspects because of the important roles in disease prevention and benefits to health. The objective of this study was to characterize the chemical profile and evaluate the antioxidant and antimicrobial properties of different fractions obtained from fruit pulps of Mauritia flexuosa (MFFs). Methods Initially, chloroform, ethyl acetate and ethanol fractions were obtained from the pulps. Quantifications of total phenols and flavonoids were performed using the methods of Folin-Ciocalteu and complexation with aluminum chloride, respectively. Standard samples were used to identify and quantify phenolic acids and flavonoids using high-performance liquid chromatography with a diode-array detector (HPLC-DAD). The antioxidant capacity of the fractions was verified by sequestration of the free radical 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid (ABTS) and iron chelating activity. The antimicrobial activity was determined using the microdilution method and the modulating activity was determined using sub-inhibitory concentrations of the fractions in association with antibiotics. Results The chemical analyzes revealed the presence of catechin, caffeic acid, rutin, orientin, quercetin, apigenin, luteolin and kaempferol, where all are present in the ethyl acetate fraction. The fractions exhibited moderate antioxidant and antimicrobial activities against Gram-positive and Candida strains in addition to modulating the activity of conventional antibiotics. The most expressive result was obtained from the association of the chloroform fraction with cefotaxime, which produced a synergistic effect, reducing the minimum inhibitory concentration (MIC) of the antibiotic from 1,024 to 256 μg/mL. Discussion The fractions presented a constitution rich in phenolic compounds, especially flavonoids. The data obtained demonstrated that the fractions presented moderate antioxidant activity by acting both as primary and secondary antioxidants. The fractions presented antimicrobial and antibiotic potentiating activities, being the first record of modulating effect of fractions of this species against the studied microbial strains, but failed in modulating the activity of antifungal drugs, indicating that this plant has the potential to be used in the development of therapeutic alternatives against resistant bacteria. The constitution phenolic the fractions may be responsible for their pharmacological properties in vitro.
Nonato et al. (2018) Chemical analysis and evaluation of antioxidant and antimicrobial activities of fruit fractions of Mauritia flexuosa L. f. (Arecaceae). PeerJ 6:e5991 https://doi.org/10.7717/peerj.5991
Taxonomic patterns in the zoonotic potential of mammalian viruses
Predicting and simplifying which pathogens may spill over from animals to humans is a major priority in infectious disease biology. Many efforts to determine which viruses are at risk of spillover use a subset of viral traits to find trait-based associations with spillover. We adapt a new method—phylofactorization—to identify not traits but lineages of viruses at risk of spilling over. Phylofactorization is used to partition the International Committee on Taxonomy of Viruses viral taxonomy based on non-human host range of viruses and whether there exists evidence the viruses have infected humans. We identify clades on a range of taxonomic levels with high or low propensities to spillover, thereby simplifying the classification of zoonotic potential of mammalian viruses. Phylofactorization by whether a virus is zoonotic yields many disjoint clades of viruses containing few to no representatives that have spilled over to humans. Phylofactorization by non-human host breadth yields several clades with significantly higher host breadth. We connect the phylogenetic factors above with life-histories of clades, revisit trait-based analyses, and illustrate how cladistic coarse-graining of zoonotic potential can refine trait-based analyses by illuminating clade-specific determinants of spillover risk.
Washburne et al. (2018) Taxonomic patterns in the zoonotic potential of mammalian viruses. PeerJ 6:e5979 https://doi.org/10.7717/peerj.5979
Effects of waste stream combinations from brewing industry on performance of Black Soldier Fly, Hermetia illucens (Diptera: Stratiomyidae)
Background In recent years, there has been a rapidly growing demand for readily accessible substrates for mass production of Black Soldier Fly, Hermetia illucens Linnaeus. Beer production results in various by-products that typically end up in uncontrolled dumpsites constituting pollution problems, which merits urgent attention. The present study investigated whether the 12 formulated diets composed of brewers’ spent grains (BSGs), brewers’ yeast and cane molasses can serve as substrate for H. illucens production. Methods Four different BSGs were selected and formulated into 12 diets, aiming at varying protein and net energy levels. The diets were offered to newly hatched (∼1 h old) H. illucens larvae and the influence on developmental duration, survival, wet weight, pre-oviposition time, fecundity, and longevity were compared. Results Developmental duration of the larvae (16–21 days) and pre-pupae (8–11 days) differed significantly across the different diets. The developmental duration of the pupae (8.7–9.1 days) was not affected by diet. The larval (86–99.2%), pre-pupal (71–95%), and pupal (65–91%) survival rates varied significantly between flies reared on the different diets. The pre-oviposition time was similar for flies provided with water (7–11 days) and 10% sugar solution (8–14 days) or across the different diets. The mean fecundity per female ranged from 324–787 eggs and did not differ between females provided with water or sugar solution. However, the number of eggs laid per female varied significantly across the different diets when provided with water. The longevity of starved H. illucens adults was significantly lower (5 days) compared to those provided with water (11–14 days) or sugar solution (14–15 days). Discussion The implications of these findings as part of a quality control procedure for commercial production of high-quality H. illucens larvae as an alternative protein ingredient in livestock and aquaculture feed are discussed.
Chia et al. (2018) Effects of waste stream combinations from brewing industry on performance of Black Soldier Fly, Hermetia illucens (Diptera: Stratiomyidae). PeerJ 6:e5885 https://doi.org/10.7717/peerj.5885
Cochlear impulse responses resolved into sets of gammatones: the case for beating of closely spaced local resonances
Gammatones have had a long history in auditory studies, and recent theoretical work suggests they may play an important role in cochlear mechanics as well. Following this lead, the present paper takes five examples of basilar membrane impulse responses and uses a curve-fitting algorithm to decompose them into a number of discrete gammatones. The limits of this ‘sum of gammatones’ (SOG) method to accurately represent the impulse response waveforms were tested and it was found that at least two and up to six gammatones could be isolated from each example. Their frequencies were stable and largely independent of stimulus parameters. The gammatones typically formed a regular series in which the frequency ratio between successive members was about 1.1. Adding together the first few gammatones in a set produced beating-like waveforms which mimicked waxing and waning, and the instantaneous frequencies of the waveforms were also well reproduced, providing an explanation for frequency glides. Consideration was also given to the impulse response of a pair of elastically coupled masses—the basis of two-degree-of-freedom models comprised of coupled basilar and tectorial membranes—and the resulting waveform was similar to a pair of beating gammatones, perhaps explaining why the SOG method seems to work well in describing cochlear impulse responses. A major limitation of the SOG method is that it cannot distinguish a waveform resulting from an actual physical resonance from one derived from overfitting, but taken together the method points to the presence of a series of closely spaced local resonances in the cochlea.
Bell et al. (2018) Cochlear impulse responses resolved into sets of gammatones: the case for beating of closely spaced local resonances. PeerJ 6:e6016 https://doi.org/10.7717/peerj.6016
Fast cyclic stimulus flashing modulates perception of bi-stable figure
Many experiments have demonstrated that the rhythms in the brain influence the initial perceptual information processing. We investigated whether the alternation rate of the perception of a Necker cube depends on the frequency and duration of a flashing Necker cube. We hypothesize that synchronization between the external rhythm of a flashing stimulus and the internal rhythm of neuronal processing should change the alternation rate of a Necker cube. Knowing how a flickering stimulus with a given frequency and duration affects the alternation rate of bistable perception, we could estimate the frequency of the internal neuronal processing. Our results show that the perception time of the dominant stimulus depends on the frequency or duration of the flashing stimuli. The duration of the stimuli, at which the duration of the perceived image was maximal, was repeated periodically at 4 ms intervals. We suppose that such results could be explained by the existence of an internal rhythm of 125 cycles/s for bistable visual perception. We can also suppose that it is not the stimulus duration but the precise timing of the moments of switching on of external stimuli to match the internal stimuli which explains our experimental results. Similarity between the effects of flashing frequency on alternation rate of stimuli perception in present and previously performed experiment on binocular rivalry support the existence of a common mechanism for binocular rivalry and monocular perception of ambiguous figures.
Vaitkevicius et al. (2018) Fast cyclic stimulus flashing modulates perception of bi-stable figure. PeerJ 6:e6011 https://doi.org/10.7717/peerj.6011
DockerBIO: web application for efficient use of bioinformatics Docker images
Background and Objective Docker is a light containerization program that shows almost the same performance as a local environment. Recently, many bioinformatics tools have been distributed as Docker images that include complex settings such as libraries, configurations, and data if needed, as well as the actual tools. Users can simply download and run them without making the effort to compile and configure them, and can obtain reproducible results. In spite of these advantages, several problems remain. First, there is a lack of clear standards for distribution of Docker images, and the Docker Hub often provides multiple images with the same objective but different uses. For these reasons, it can be difficult for users to learn how to select and use them. Second, Docker images are often not suitable as a component of a pipeline, because many of them include big data. Moreover, a group of users can have difficulties when sharing a pipeline composed of Docker images. Users of a group may modify scripts or use different versions of the data, which causes inconsistent results. Methods and Results To handle the problems described above, we developed a Java web application, DockerBIO, which provides reliable, verified, light-weight Docker images for various bioinformatics tools and for various kinds of reference data. With DockerBIO, users can easily build a pipeline with tools and data registered at DockerBIO, and if necessary, users can easily register new tools or data. Built pipelines are registered in DockerBIO, which provides an efficient running environment for the pipelines registered at DockerBIO. This enables user groups to run their pipelines without expending much effort to copy and modify them.
Kwon et al. (2018) DockerBIO: web application for efficient use of bioinformatics Docker images. PeerJ 6:e5954 https://doi.org/10.7717/peerj.5954