title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1653 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Assessing the living and dead proportions of cold-water coral colonies: implications for deep-water Marine Protected Area monitoring in a changing ocean link: https://peerj.com/articles/3705 last-modified: 2017-10-05 description: Coral growth patterns result from an interplay of coral biology and environmental conditions. In this study colony size and proportion of live and dead skeletons in the cold-water coral (CWC) Lophelia pertusa (Linnaeus, 1758) were measured using video footage from Remotely Operated Vehicle (ROV) transects conducted at the inshore Mingulay Reef Complex (MRC) and at the offshore PISCES site (Rockall Bank) in the NE Atlantic. The main goal of this paper was to explore the development of a simple method to quantify coral growth and its potential application as an assessment tool of the health of these remote habitats. Eighteen colonies were selected and whole colony and dead/living layer size were measured. Live to dead layer ratios for each colony were then determined and analysed. The age of each colony was estimated using previously published data. Our paper shows that: (1) two distinct morphotypes can be described: at the MRC, colonies displayed a ‘cauliflower-shaped’ morphotype whereas at the PISCES site, colonies presented a more flattened ‘bush-shaped’ morphotype; (2) living layer size was positively correlated with whole colony size; (3) live to dead layer ratio was negatively correlated to whole colony size; (4) live to dead layer ratio never exceeded 0.27. These results suggest that as a colony develops and its growth rate slows down, the proportion of living polyps in the colony decreases. Furthermore, at least 73% of L. pertusa colonies are composed of exposed dead coral skeleton, vulnerable to ocean acidification and the associated shallowing of the aragonite saturation horizon, with significant implications for future deep-sea reef framework integrity. The clear visual contrast between white/pale living and grey/dark dead portions of the colonies also gives a new way by which they can be visually monitored over time. The increased use of marine autonomous survey vehicles offers an important new platform from which such a surveying technique could be applied to monitor deep-water marine protected areas in the future. creator: Johanne Vad creator: Covadonga Orejas creator: Juan Moreno-Navas creator: Helen S. Findlay creator: J. Murray Roberts uri: https://doi.org/10.7717/peerj.3705 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Vad et al. title: Impact of land reclamation and agricultural water regime on the distribution and conservation status of the endangered Dryophytes suweonensis link: https://peerj.com/articles/3872 last-modified: 2017-10-04 description: Knowledge about the distribution and habitat preferences of a species is critical for its conservation. The Suweon Treefrog (Dryophytes suweonensis) is an endangered species endemic to the Republic of Korea. We conducted surveys from 2014 to 2016 at 890 potentially suitable sites across the entire range of the species in South Korea. We then assessed whether D. suweonensis was found in the current and ancestral predicted ranges, reclaimed and protected areas, and how the presence of agricultural floodwater affected its occurrence. Our results describe a 120 km increase in the southernmost known distribution of the species, and the absence of the species at lower latitudes. We then demonstrate a putative constriction on the species ancestral range due to urban encroachment, and provide evidence for a significant increase in its coastal range due to the colonisation of reclaimed land by the species. In addition, we demonstrate that D. suweonensis is present in rice fields that are flooded with water originating from rivers as opposed to being present in rice fields that are irrigated from underground water. Finally, the non-overlap of protected areas and the occurrence of the species shows that only the edge of a single site where D. suweonensis occurs is legally protected. Based on our results and the literature, we suggest the design of a site fitting all the ecological requirements of the species, and suggest the use of such sites to prevent further erosion in the range of D. suweonensis. creator: Amaël Borzée creator: Kyungmin Kim creator: Kyongman Heo creator: Piotr G. Jablonski creator: Yikweon Jang uri: https://doi.org/10.7717/peerj.3872 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Borzée et al. title: Accuracy of microbial community diversity estimated by closed- and open-reference OTUs link: https://peerj.com/articles/3889 last-modified: 2017-10-04 description: Next-generation sequencing of 16S ribosomal RNA is widely used to survey microbial communities. Sequences are typically assigned to Operational Taxonomic Units (OTUs). Closed- and open-reference OTU assignment matches reads to a reference database at 97% identity (closed), then clusters unmatched reads using a de novo method (open). Implementations of these methods in the QIIME package were tested on several mock community datasets with 20 strains using different sequencing technologies and primers. Richness (number of reported OTUs) was often greatly exaggerated, with hundreds or thousands of OTUs generated on Illumina datasets. Between-sample diversity was also found to be highly exaggerated in many cases, with weighted Jaccard distances between identical mock samples often close to one, indicating very low similarity. Non-overlapping hyper-variable regions in 70% of species were assigned to different OTUs. On mock communities with Illumina V4 reads, 56% to 88% of predicted genus names were false positives. Biological inferences obtained using these methods are therefore not reliable. creator: Robert C. Edgar uri: https://doi.org/10.7717/peerj.3889 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Edgar title: Exceptional soft tissues preservation in a mummified frog-eating Eocene salamander link: https://peerj.com/articles/3861 last-modified: 2017-10-03 description: Fossils are almost always represented by hard tissues but we present here the exceptional case of a three-dimensionally preserved specimen that was ‘mummified’ (likely between 40 and 34 million years ago) in a terrestrial karstic environment. This fossil is the incomplete body of a salamander, Phosphotriton sigei, whose skeleton and external morphology are well preserved, as revealed by phase-contrast synchrotron X-ray microtomography. In addition, internal structures composed of soft tissues preserved in three dimensions are now identified: a lung, the spinal cord, a lumbosacral plexus, the digestive tract, muscles and urogenital organs that may be cloacal glands. These are among the oldest known cases of three-dimensional preservation of these organs in vertebrates and shed light on the ecology of this salamander. Indeed, the digestive tract contains remains of a frog, which represents the only known case of an extinct salamander that fed on a frog, an extremely rare type of predation in extant salamanders. These new data improve our scarce knowledge on soft tissue anatomy of early urodeles and should prove useful for future biologists and palaeontologists working on urodele evolutionary biology. We also suggest that the presence of bat guano and carcasses represented a close source of phosphorus, favouring preservation of soft tissues. Bone microanatomy indicates that P. sigei was likely amphibious or terrestrial, and was probably not neotenic. creator: Jérémy Tissier creator: Jean-Claude Rage creator: Michel Laurin uri: https://doi.org/10.7717/peerj.3861 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Tissier et al. title: Alpha-arylphorin is a mitogen in the Heliothis virescens midgut cell secretome upon Cry1Ac intoxication link: https://peerj.com/articles/3886 last-modified: 2017-10-03 description: Insecticidal crystal (Cry) proteins produced by the bacterium Bacillus thuringiensis (Bt) target cells in the midgut epithelium of susceptible larvae. While the mode of action of Cry toxins has been extensively investigated, the midgut response to Cry intoxication and its regulation are not well characterized. In this work, we describe the secreted proteome (secretome) of primary mature midgut cell cultures from Heliothis virescens larvae after exposure to Cry1Ac toxin compared to control buffer treatment. The Cry1Ac-induced secretome caused higher proliferation and differentiation and an overall reduction in total cell mortality over time in primary H. virescens midgut stem cell cultures when compared to treatment with control buffer secretome. Differential proteomics identified four proteins with significant differences in abundance comparing Cry1Ac-treated and control secretomes. The most significant difference detected in the Cry1Ac secretome was an arylphorin subunit alpha protein not detected in the control secretome. Feeding of purified alpha-arylphorin to H. virescens larvae resulted in midgut hyperplasia and significantly reduced susceptibility to Cry1Ac toxin compared to controls. These data identify alpha-arylphorin as a protein with a new putative role in the midgut regeneration process in response to Cry1Ac intoxication and possibly pathogen/abiotic stress, identifying alpha-arylphorin as a potential gene to target with insecticidal gene silencing for pest control. creator: Anais Castagnola creator: Jerreme Jackson creator: Omaththage P. Perera creator: Cris Oppert creator: Shigetoshi Eda creator: Juan Luis Jurat-Fuentes uri: https://doi.org/10.7717/peerj.3886 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Castagnola et al. title: Perch, Perca fluviatilis show a directional preference for, but do not increase attacks toward, prey in response to water-borne cortisol link: https://peerj.com/articles/3883 last-modified: 2017-10-03 description: In freshwater environments, chemosensory cues play an important role in predator-prey interactions. Prey use a variety of chemosensory cues to detect and avoid predators. However, whether predators use the chemical cues released by disturbed or stressed prey has received less attention. Here we tested the hypothesis that the disturbance cue cortisol, in conjunction with visual cues of prey, elevates predatory behavior. We presented predators (perch, Perca fluviatilis) with three chemosensory choice tests and recorded their location, orientation, and aggressive behavior. We compared the responses of predators when provided with (i) visual cues of prey only (two adjacent tanks containing sticklebacks); (ii) visual and natural chemical cues of prey vs. visual cues only; and (iii) visual cues of prey with cortisol vs. visual cues only. Perch spent a significantly higher proportion of time in proximity to prey, and orientated toward prey more, when presented with a cortisol stimulus plus visual cues, relative to presentations of visual and natural chemical cues of prey, or visual cues of prey only. There was a trend that perch directed a higher proportion of predatory behaviors (number of lunges) toward sticklebacks when presented with a cortisol stimulus plus visual cues, relative to the other chemosensory conditions. But they did not show a significant increase in total predatory behavior in response to cortisol. Therefore, it is not clear whether water-borne cortisol, in conjunction with visual cues of prey, affects predatory behavior. Our results provide evidence that cortisol could be a source of public information about prey state and/or disturbance, but further work is required to confirm this. creator: Lindsay J. Henderson creator: Mary R. Ryan creator: Hannah M. Rowland uri: https://doi.org/10.7717/peerj.3883 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Henderson et al. title: Segmentation and classification of colon glands with deep convolutional neural networks and total variation regularization link: https://peerj.com/articles/3874 last-modified: 2017-10-03 description: Segmentation of histopathology sections is a necessary preprocessing step for digital pathology. Due to the large variability of biological tissue, machine learning techniques have shown superior performance over conventional image processing methods. Here we present our deep neural network-based approach for segmentation and classification of glands in tissue of benign and malignant colorectal cancer, which was developed to participate in the GlaS@MICCAI2015 colon gland segmentation challenge. We use two distinct deep convolutional neural networks (CNN) for pixel-wise classification of Hematoxylin-Eosin stained images. While the first classifier separates glands from background, the second classifier identifies gland-separating structures. In a subsequent step, a figure-ground segmentation based on weighted total variation produces the final segmentation result by regularizing the CNN predictions. We present both quantitative and qualitative segmentation results on the recently released and publicly available Warwick-QU colon adenocarcinoma dataset associated with the GlaS@MICCAI2015 challenge and compare our approach to the simultaneously developed other approaches that participated in the same challenge. On two test sets, we demonstrate our segmentation performance and show that we achieve a tissue classification accuracy of 98% and 95%, making use of the inherent capability of our system to distinguish between benign and malignant tissue. Our results show that deep learning approaches can yield highly accurate and reproducible results for biomedical image analysis, with the potential to significantly improve the quality and speed of medical diagnoses. creator: Philipp Kainz creator: Michael Pfeiffer creator: Martin Urschler uri: https://doi.org/10.7717/peerj.3874 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Kainz et al. title: Development and validation of near-infrared spectroscopy for the prediction of forage quality parameters in Lolium multiflorum link: https://peerj.com/articles/3867 last-modified: 2017-10-03 description: Italian ryegrass (Lolium multiflorum) is an important cool-season, annual forage crop for the grassland rotation system in Southern China. The primary aim of breeding programs is always to seek to improve forage quality in the animal productivity system; however, it is time- and labor-consuming when analyzed excessive large number of samples. The main objectives of this study were to construct near-infrared reflectance spectroscopy (NIRS) models to predict the forage chemistry quality of Italian ryegrass including the concentrations of crude protein (CP), acid detergent fiber (ADF), neutral detergent fiber (NDF), and water soluble carbohydrate (WSC). The results showed that a broader range of CP, NDF, ADF and WSC contents (%DM) were obtained (4.45–30.60, 21.29–60.47, 11.66–36.17 and 3.95–51.52, respectively) from the samples selected for developing NIRS models. In addition, the critical wavelengths identified in this study to construct optimal NIRS models were located in 4,247–6,102 and 4,247–5,450 cm-1 for CP and NDF content, and both wavelengths 5,446–6,102 and 4,247–4,602 cm-1 could for ADF and WSC. Finally, the optimal models were developed based on the laboratory data and the spectral information by partial least squares (PLS) regression, with relatively high coefficients of determination (R2CV, CP = 0.99, NDF = 0.94, ADF = 0.92, WSC = 0.88), ratio of prediction to devitation (RPD, CP = 8.58, NDF = 4.25, ADF = 3.64, WSC = 3.10). The further statistics of prediction errors relative to laboratory (PRL) and the range error ratio (RER) give excellent assessments of the models with the PRL ratios lower than 2 and the RER values greater than 10. The NIRS models were validated using a completely independent set of samples and have coefficients of determination (R2V, CP = 0.99, NDF = 0.91, ADF = 0.95, WSC = 0.91) and ratio of prediction to deviation (RPD, CP = 9.37, NDF = 3.44, ADF = 4.40, WSC = 3.39). The result suggested that routine screening for forage quality parameters with large numbers of samples is available with the NIRS model in Italian ryegrass breeding programs, as well as facilitating graziers to monitor the forage development stage for improving grazing efficiency. creator: Zhongfu Yang creator: Gang Nie creator: Ling Pan creator: Yan Zhang creator: Linkai Huang creator: Xiao Ma creator: Xinquan Zhang uri: https://doi.org/10.7717/peerj.3867 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Yang et al. title: Assessment on the coupling effects of drip irrigation and organic fertilization based on entropy weight coefficient model link: https://peerj.com/articles/3855 last-modified: 2017-10-03 description: Water and fertilizer are two important factors influencing crop growth, development and yield formation. To investigate their combined effects on the soil-plant system, and to find out the optimal water and organic fertilizer coupling strategy for tomato (Solanum lycopersicum L), an experiment was carried out from May to October in 2016 in the south of China. The experiment consisted of three drip irrigation quotas (150, 180, 210 m3/ha) and three organic fertilizer application amounts (2,800, 3,600, 4,400 kg/ha). A water-fertilizer treatment (abbreviated as CK) that is in line with local practice was used for comparison. The tomato marketable yield, sugar/acid ratio (SAR) and irrigation water use efficiency (IWUE), as well as the soil salinity and available nutrient concentrations were measured. The results showed that the marketable yield was highly significantly (p < 0.01) affected by irrigation or fertilization. The SAR of tomato were significantly (p < 0.05) affected by irrigation or/and fertilization. The fertilization had an highly significant (p < 0.01) effect on the concentrations of soil nutrients (N, P, K), while the coupling effect of irrigation and fertilization was not pronounced. According to the multi-index analysis and the computed result by the entropy weight coefficient model, a 180 m3/ha irrigation quota in combination with 4,400 kg/ha organic fertilizer application amount was the optimal water-fertilizer coupling strategy which owned the most satisfactory comprehensive benefits. The marketable yield, SAR and IWUE under this optimal strategy were 122.4 t/ha, 9.2, 32.4 kg/m3, respectively, and by 28.0%, 29.6% and 28.1% higher compared to that under CK. creator: Fenglin Zhong creator: Maomao Hou creator: Bizhu He creator: Iouzen Chen uri: https://doi.org/10.7717/peerj.3855 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Zhong et al. title: A preliminary survey of zoantharian endosymbionts shows high genetic variation over small geographic scales on Okinawa-jima Island, Japan link: https://peerj.com/articles/3740 last-modified: 2017-10-03 description: Symbiotic dinoflagellates (genus Symbiodinium) shape the responses of their host reef organisms to environmental variability and climate change. To date, the biogeography of Symbiodinium has been investigated primarily through phylogenetic analyses of the ribosomal internal transcribed spacer 2 region. Although the marker can approximate species-level diversity, recent work has demonstrated that faster-evolving genes can resolve otherwise hidden species and population lineages, and that this diversity is often distributed over much finer geographical and environmental scales than previously recognized. Here, we use the noncoding region of the chloroplast psbA gene (psbAncr) to examine genetic diversity among clade C Symbiodinium associating with the common reef zoantharian Palythoa tuberculosa on Okinawa-jima Island, Japan. We identify four closely related Symbiodinium psbAncr lineages including one common generalist and two potential specialists that appear to be associated with particular microhabitats. The sea surface temperature differences that distinguish these habitats are smaller than those usually investigated, suggesting that future biogeographic surveys of Symbiodinium should incorporate fine scale environmental information as well as fine scale molecular data to accurately determine species diversity and their distributions. creator: Hatsuko Noda creator: John Everett Parkinson creator: Sung-Yin Yang creator: James Davis Reimer uri: https://doi.org/10.7717/peerj.3740 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Noda et al.