title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=1744
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Are sawfishes still present in Mozambique? A baseline ecological study
link: https://peerj.com/articles/2950
last-modified: 2017-02-02
description: Sawfishes (Pristidae) were formerly abundant in the western Indian Ocean, but current data on sawfish presence and distribution are lacking for most of the region. This paper summarises historical records of sawfishes in Mozambican waters and presents the findings of the first assessment of the presence and status of sawfishes in Mozambique. A countrywide baseline assessment was undertaken between May and July 2014, using interviews with artisanal, semi-industrial and industrial fishers, fish traders and fisheries monitoring staff as the primary source of information on sawfish distribution, recent catches, socio-economic value and cultural importance. Additional interviews were conducted via email or telephone with individuals running sport fishing operations or who otherwise had considerable experience interacting with the fishing sectors or the marine environment in Mozambique. Where encountered, sawfish rostra were photographed and a series of measurements and associated data were collected. In total, 200 questionnaire surveys and seven interviews with recreational fishing and dive operators were conducted, and 19 rostra were documented from museum archives and private collections, belonging to two sawfish species, the Largetooth Sawfish (Pristis pristis) and Green Sawfish (P. zijsron). The most recent captures of sawfishes were reported to have occurred in 2014. Two key sites were identified where both recent encounters were reported and numerous Largetooth Sawfish rostra were documented. Gill nets were the fishing gear most commonly attributed to sawfish catches. Sawfishes did not hold any cultural importance in Mozambique, but they have at least some socio-economic importance to artisanal fishers, primarily through the sale of their fins. The meat did not appear to be held in high regard and was usually consumed locally. Sampling and further research is now required to confirm the presence of sawfishes and to assess the primary threats to sawfishes in those areas. At one site where a number of rostra were present and where fishers stated that they still catch sawfish, gill nets are being provided to fishers as an alternative to beach seining. This may have a serious impact on the local sawfish population and more broadly for other elasmobranchs in the area. Immediate action is required to develop a landings monitoring programme in this and other key habitats, and to encourage fishers to release sawfishes alive.
creator: Ruth H. Leeney
uri: https://doi.org/10.7717/peerj.2950
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Leeney

title: Comparison of admission random glucose, fasting glucose, and glycated hemoglobin in predicting the neurological outcome of acute ischemic stroke: a retrospective study
link: https://peerj.com/articles/2948
last-modified: 2017-02-02
description: BackgroundHyperglycemia is a known predictor of negative outcomes in stroke. Several glycemic measures, including admission random glucose, fasting glucose, and glycated hemoglobin (HbA1c), have been associated with bad neurological outcomes in acute ischemic stroke, particularly in nondiabetic patients. However, the predictive power of these glycemic measures is yet to be investigated.MethodsThis retrospective study enrolled 484 patients with acute ischemic stroke from January 2009 to March 2013, and complete records of initial stroke severity, neurological outcomes at three months, and glycemic measures were evaluated. We examined the predictive power of admission random glucose, fasting glucose, and HbA1c for neurological outcomes in acute ischemic stroke. Furthermore, subgroup analyses of nondiabetic patients and patients with diabetes were performed separately.ResultsReceiver operating characteristic (ROC) analysis revealed that admission random glucose and fasting glucose were significant predictors of poor neurological outcomes, whereas HbA1c was not (areas under the ROC curve (AUCs): admission random glucose = 0.564, p = 0.026; fasting glucose = 0.598, p = 0.001; HbA1c = 0.510, p = 0.742). Subgroup analyses of nondiabetic patients and those with diabetes revealed that only fasting glucose predicts neurological outcomes in patients with diabetes, and the AUCs of these three glycemic measures did not differ between the two groups. A multivariate logistic regression analysis of the study patients indicated that only age, initial stroke severity, and fasting glucose were independent predictors of poor neurological outcomes, whereas admission random glucose and HbA1c were not (adjusted odds ratio: admission random glucose = 1.002, p = 0.228; fasting glucose = 1.005, p = 0.039; HbA1c = 1.160, p = 0.076). Furthermore, subgroup multivariate logistic regression analyses of nondiabetic patients and those with diabetes indicated that none of the three glycemic measures were associated with poor neurological outcomes.DiscussionFasting glucose is an independent predictor of poor neurological outcomes in patients with acute ischemic stroke and had greater predictive power than that of admission random glucose and HbA1c. The predictive power of glycemic measures for poor neurological outcomes did not differ significantly between the nondiabetic patients and those with diabetes.
creator: Jia-Ying Sung
creator: Chin-I Chen
creator: Yi-Chen Hsieh
creator: Yih-Ru Chen
creator: Hsin-Chiao Wu
creator: Lung Chan
creator: Chaur-Jong Hu
creator: Han-Hwa Hu
creator: Hung-Yi Chiou
creator: Nai-Fang Chi
uri: https://doi.org/10.7717/peerj.2948
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Sung et al.

title: Do syntopic host species harbour similar symbiotic communities? The case of Chaetopterus spp. (Annelida: Chaetopteridae)
link: https://peerj.com/articles/2930
last-modified: 2017-02-02
description: To assess whether closely related host species harbour similar symbiotic communities, we studied two polychaetes, Chaetopterus sp. (n = 11) and Chaetopterus cf. appendiculatus (n = 83) living in soft sediments of Nhatrang Bay (South China Sea, Vietnam). The former harboured the porcellanid crabs Polyonyx cf. heok and Polyonyx sp., the pinnotherid crab Tetrias sp. and the tergipedid nudibranch Phestilla sp. The latter harboured the polynoid polychaete Ophthalmonoe pettiboneae, the carapid fish Onuxodon fowleri and the porcellanid crab Eulenaios cometes, all of which, except O. fowleri, seemed to be specialized symbionts. The species richness and mean intensity of the symbionts were higher in Chaetopterus sp. than in C. cf. appendiculatus (1.8 and 1.02 species and 3.0 and 1.05 individuals per host respectively). We suggest that the lower density of Chaetopterus sp. may explain the higher number of associated symbionts observed, as well as the 100% prevalence (69.5% in C. cf. appenciculatus). Most Chaetopterus sp. harboured two symbiotic species, which was extremely rare in C. cf. appendiculatus, suggesting lower interspecific interactions in the former. The crab and nudibranch symbionts of Chaetopterus sp. often shared a host and lived in pairs, thus partitioning resources. This led to the species coexisting in the tubes of Chaetopterus sp., establishing a tightly packed community, indicating high species richness and mean intensity, together with a low species dominance. In contrast, the aggressive, strictly territorial species associated with C. cf. appendiculatus established a symbiotic community strongly dominated by single species and, thus, low species richness and mean intensity. Therefore, we suggest that interspecific interactions are determining species richness, intensity and dominance, while intraspecific interactions are influencing only intensity and abundance. It is possible that species composition may have influenced the differences in community structure observed. We hypothesize that both host species could originally be allopatric. The evolutionary specialization of the symbiotic communities would occur in separated geographical areas, while the posterior disappearance of the existing geographical barriers would lead to the overlapped distribution.
creator: Temir A. Britayev
creator: Elena Mekhova
creator: Yury Deart
creator: Daniel Martin
uri: https://doi.org/10.7717/peerj.2930
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Britayev et al.

title: The embryonic life history of the tropical sea hare Stylocheilus striatus (Gastropoda: Opisthobranchia) under ambient and elevated ocean temperatures
link: https://peerj.com/articles/2956
last-modified: 2017-02-01
description: Ocean warming represents a major threat to marine biota worldwide, and forecasting ecological ramifications is a high priority as atmospheric carbon dioxide (CO2) emissions continue to rise. Fitness of marine species relies critically on early developmental and reproductive stages, but their sensitivity to environmental stressors may be a bottleneck in future warming oceans. The present study focuses on the tropical sea hare, Stylocheilus striatus (Gastropoda: Opisthobranchia), a common species found throughout the Indo-West Pacific and Atlantic Oceans. Its ecological importance is well-established, particularly as a specialist grazer of the toxic cyanobacterium, Lyngbya majuscula. Although many aspects of its biology and ecology are well-known, description of its early developmental stages is lacking. First, a detailed account of this species’ life history is described, including reproductive behavior, egg mass characteristics and embryonic development phases. Key developmental features are then compared between embryos developed in present-day (ambient) and predicted end-of-century elevated ocean temperatures (+3 °C). Results showed developmental stages of embryos reared at ambient temperature were typical of other opisthobranch species, with hatching of planktotrophic veligers occurring 4.5 days post-oviposition. However, development times significantly decreased under elevated temperature, with key embryonic features such as the velum, statocysts, operculum, eyespots and protoconch developing approximately 24 h earlier when compared to ambient temperature. Although veligers hatched one day earlier under elevated temperature, their shell size decreased by approximately 20%. Our findings highlight how an elevated thermal environment accelerates planktotrophic development of this important benthic invertebrate, possibly at the cost of reducing fitness and increasing mortality.
creator: Rael Horwitz
creator: Matthew D. Jackson
creator: Suzanne C. Mills
uri: https://doi.org/10.7717/peerj.2956
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Horwitz et al.

title: What has been missed for predicting human attention in viewing driving clips?
link: https://peerj.com/articles/2946
last-modified: 2017-02-01
description: Recent research progress on the topic of human visual attention allocation in scene perception and its simulation is based mainly on studies with static images. However, natural vision requires us to extract visual information that constantly changes due to egocentric movements or dynamics of the world. It is unclear to what extent spatio-temporal regularity, an inherent regularity in dynamic vision, affects human gaze distribution and saliency computation in visual attention models. In this free-viewing eye-tracking study we manipulated the spatio-temporal regularity of traffic videos by presenting them in normal video sequence, reversed video sequence, normal frame sequence, and randomised frame sequence. The recorded human gaze allocation was then used as the ‘ground truth’ to examine the predictive ability of a number of state-of-the-art visual attention models. The analysis revealed high inter-observer agreement across individual human observers, but all the tested attention models performed significantly worse than humans. The inferior predictability of the models was evident from indistinguishable gaze prediction irrespective of stimuli presentation sequence, and weak central fixation bias. Our findings suggest that a realistic visual attention model for the processing of dynamic scenes should incorporate human visual sensitivity with spatio-temporal regularity and central fixation bias.
creator: Jiawei Xu
creator: Shigang Yue
creator: Federica Menchinelli
creator: Kun Guo
uri: https://doi.org/10.7717/peerj.2946
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Xu et al.

title: Epidermal cell death in frogs with chytridiomycosis
link: https://peerj.com/articles/2925
last-modified: 2017-02-01
description: BackgroundAmphibians are declining at an alarming rate, and one of the major causes of decline is the infectious disease chytridiomycosis. Parasitic fungal sporangia occur within epidermal cells causing epidermal disruption, but these changes have not been well characterised. Apoptosis (planned cell death) can be a damaging response to the host but may alternatively be a mechanism of pathogen removal for some intracellular infections.MethodsIn this study we experimentally infected two endangered amphibian species Pseudophryne corroboree and Litoria verreauxii alpina with the causal agent of chytridiomycosis. We quantified cell death in the epidermis through two assays: terminal transferase-mediated dUTP nick end-labelling (TUNEL) and caspase 3/7.ResultsCell death was positively associated with infection load and morbidity of clinically infected animals. In infected amphibians, TUNEL positive cells were concentrated in epidermal layers, correlating to the localisation of infection within the skin. Caspase activity was stable and low in early infection, where pathogen loads were light but increasing. In animals that recovered from infection, caspase activity gradually returned to normal as the infection cleared. Whereas, in amphibians that did not recover, caspase activity increased dramatically when infection loads peaked.DiscussionIncreased cell death may be a pathology of the fungal parasite, likely contributing to loss of skin homeostatic functions, but it is also possible that apoptosis suppression may be used initially by the pathogen to help establish infection. Further research should explore the specific mechanisms of cell death and more specifically apoptosis regulation during fungal infection.
creator: Laura A. Brannelly
creator: Alexandra A. Roberts
creator: Lee F. Skerratt
creator: Lee Berger
uri: https://doi.org/10.7717/peerj.2925
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Brannelly et al.

title: Untargeted metabolomics approach for unraveling robust biomarkers of nutritional status in fasted gilthead sea bream (Sparus aurata)
link: https://peerj.com/articles/2920
last-modified: 2017-02-01
description: A metabolomic study has been performed to identify sensitive and robust biomarkers of malnutrition in farmed fish, using gilthead sea bream (Sparus aurata) as a model. The metabolomic fingerprinting of serum from fasted fish was assessed by means of ultra-high performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry. More than 15,000 different m/z ions were detected and Partial Least Squares–Discriminant analysis allowed a clear differentiation between the two experimental groups (fed and 10-day fasted fish) with more than 90% of total variance explained by the two first components. The most significant metabolites (up to 45) were elucidated on the basis of their tandem mass spectra with a broad representation of amino acids, oligopeptides, urea cycle metabolites, L-carnitine-related metabolites, glutathione-related metabolites, fatty acids, lysophosphatidic acids, phosphatidylcholines as well as biotin- and noradrenaline-related metabolites. This untargeted approach highlighted important adaptive responses in energy and oxidative metabolism, contributing to identify robust and nutritionally-regulated biomarkers of health and metabolic condition that will serve to assess the welfare status of farmed fish.
creator: Ruben Gil-Solsona
creator: Jaime Nácher-Mestre
creator: Leticia Lacalle-Bergeron
creator: Juan Vicente Sancho
creator: Josep Alvar Calduch-Giner
creator: Félix Hernández
creator: Jaume Pérez-Sánchez
uri: https://doi.org/10.7717/peerj.2920
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Gil-Solsona et al.

title: Successive DNA extractions improve characterization of soil microbial communities
link: https://peerj.com/articles/2915
last-modified: 2017-02-01
description: Currently, characterization of soil microbial communities relies heavily on the use of molecular approaches. Independently of the approach used, soil DNA extraction is a crucial step, and success of downstream procedures will depend on how well DNA extraction was performed. Often, studies describing and comparing soil microbial communities are based on a single DNA extraction, which may not lead to a representative recovery of DNA from all organisms present in the soil. The use of successive DNA extractions might improve soil microbial characterization, but the benefit of this approach has only been limitedly studied. To determine whether successive DNA extractions of the same soil sample would lead to different observations in terms of microbial abundance and community composition, we performed three successive extractions, with two widely used commercial kits, on a range of clay and sandy soils. Successive extractions increased DNA yield considerably (1–374%), as well as total bacterial and fungal abundances in most of the soil samples. Analysis of the 16S and 18S ribosomal RNA genes using 454-pyrosequencing, revealed that microbial community composition (taxonomic groups) observed in the successive DNA extractions were similar. However, successive DNA extractions did reveal several additional microbial groups. For some soil samples, shifts in microbial community composition were observed, mainly due to shifts in relative abundance of a number of microbial groups. Our results highlight that performing successive DNA extractions optimize DNA yield, and can lead to a better picture of overall community composition.
creator: Mauricio R. Dimitrov
creator: Annelies J. Veraart
creator: Mattias de Hollander
creator: Hauke Smidt
creator: Johannes A. van Veen
creator: Eiko E. Kuramae
uri: https://doi.org/10.7717/peerj.2915
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2017 Dimitrov et al.

title: Boxer crabs induce asexual reproduction of their associated sea anemones by splitting and intraspecific theft
link: https://peerj.com/articles/2954
last-modified: 2017-01-31
description: Crabs of the genus Lybia have the remarkable habit of holding a sea anemone in each of their claws. This partnership appears to be obligate, at least on the part of the crab. The present study focuses on Lybia leptochelis from the Red Sea holding anemones of the genus Alicia (family Aliciidae). These anemones have not been found free living, only in association with L. leptochelis. In an attempt to understand how the crabs acquire them, we conducted a series of behavioral experiments and molecular analyses. Laboratory observations showed that the removal of one anemone from a crab induces a “splitting” behavior, whereby the crab tears the remaining anemone into two similar parts, resulting in a complete anemone in each claw after regeneration. Furthermore, when two crabs, one holding anemones and one lacking them, are confronted, the crabs fight, almost always leading to the “theft” of a complete anemone or anemone fragment by the crab without them. Following this, crabs “split” their lone anemone into two. Individuals of Alicia sp. removed from freshly collected L. leptochelis were used for DNA analysis. By employing AFLP (Fluorescence Amplified Fragments Length Polymorphism) it was shown that each pair of anemones from a given crab is genetically identical. Furthermore, there is genetic identity between most pairs of anemone held by different crabs, with the others showing slight genetic differences. This is a unique case in which one animal induces asexual reproduction of another, consequently also affecting its genetic diversity.
creator: Yisrael Schnytzer
creator: Yaniv Giman
creator: Ilan Karplus
creator: Yair Achituv
uri: https://doi.org/10.7717/peerj.2954
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Schnytzer et al.

title: Catchments catch all in South African coastal lowlands: topography and palaeoclimate restricted gene flow in Nymania capensis (Meliaceae)—a multilocus phylogeographic and distribution modelling approach
link: https://peerj.com/articles/2965
last-modified: 2017-01-31
description: BackgroundThis study investigates orbitally-forced range dynamics at a regional scale by exploring the evolutionary history of Nymania capensis (Meliaceae) across the deeply incised landscapes of the subescarpment coastal lowlands of South Africa; a region that is home to three biodiversity hotspots (Succulent Karoo, Fynbos, and Maputaland-Pondoland-Albany hotspots).MethodsA range of methods are used including: multilocus phylogeography (chloroplast and high- and low-copy nuclear DNA), molecular dating and species distribution modelling (SDM).ResultsThe results support an ‘evolutionarily distinct catchment’ hypothesis where: (1) different catchments contain genetically distinct lineages, (2) limited genetic structuring was detected within basins whilst high structuring was detected between basins, and (3) within primary catchment populations display a high degree of genealogical lineage sorting. In addition, the results support a glacial refugia hypothesis as: (a) the timing of chloroplast lineage diversification is restricted to the Pleistocene in a landscape that has been relatively unchanged since the late Pliocene, and (b) the projected LGM distribution of suitable climate for N. capensis suggest fragmentation into refugia that correspond to the current phylogeographic populations.DiscussionThis study highlights the interaction of topography and subtle Pleistocene climate variations as drivers limiting both seed and pollen flow along these lowlands. This lends support to the region’s large-scale conservation planning efforts, which used catchments as foundational units for conservation as these are likely to be evolutionarily significant units.
creator: Alastair J. Potts
uri: https://doi.org/10.7717/peerj.2965
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Potts