title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1014 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: The p53 signaling pathway of the large yellow croaker (Larimichthys crocea) responds to acute cold stress: evidence via spatiotemporal expression analysis of p53, p21, MDM2, IGF-1, Gadd45, Fas, and Akt link: https://peerj.com/articles/10532 last-modified: 2020-12-18 description: The p53 activation is induced by stressors, such as DNA damage, oxidative stress, and activated oncogenes, and can promote cell cycle arrest, cellular senescence, and apoptosis. The large yellow croaker (Larimichthys crocea) is an important warm temperate marine fish in the Chinese aquiculture industry. However, few studies have investigated the role of p53 in the response of L. crocea to environmental stressors. Therefore, the aim of the present study was to assess the spatiotemporal mRNA expression levels of genes involved in the p53 signaling pathway of the large yellow croaker in response to cold stress. The results showed significant changes in the expression levels of p53, p21, MDM2, IGF-1, Gadd45, Fas, and Akt in various tissues of the large yellow croaker in response to cold stress for different times. As compared to the control group, p53 mRNA expression was upregulated in most of the examined tissues at 24 h with the exception of the gill. In the liver, the expression levels of p53 and Fas were significantly decreased at 12 h, while those of p21, MDM2, IGF-1, Gadd45 were dramatically increased. Akt expression was notably changed in response to cold in several tissues. These results suggested that p53 was potentially a key gene in the large yellow croaker response to cold and possibly other environmental stressors. creator: Baoying Qian creator: Xin Qi creator: Yi Bai creator: Yubo Wu uri: https://doi.org/10.7717/peerj.10532 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Qian et al. title: Individual differences show that only some bats can cope with noise-induced masking and distraction link: https://peerj.com/articles/10551 last-modified: 2020-12-18 description: Anthropogenic noise is a widespread pollutant that has received considerable recent attention. While alarming effects on wildlife have been documented, we have limited understanding of the perceptual mechanisms of noise disturbance, which are required to understand potential mitigation measures. Likewise, individual differences in response to noise (especially via perceptual mechanisms) are likely widespread, but lacking in empirical data. Here we use the echolocating bat Phyllostomus discolor, a trained discrimination task, and experimental noise playback to explicitly test perceptual mechanisms of noise disturbance. We demonstrate high individual variability in response to noise treatments and evidence for multiple perceptual mechanisms. Additionally, we highlight that only some individuals were able to cope with noise, while others were not. We tested for changes in echolocation call duration, amplitude, and peak frequency as possible ways of coping with noise. Although all bats strongly increased call amplitude and showed additional minor changes in call duration and frequency, these changes could not explain the differences in coping and non-coping individuals. Our understanding of noise disturbance needs to become more mechanistic and individualistic as research knowledge is transformed into policy changes and conservation action. creator: Dylan G.E. Gomes creator: Holger R. Goerlitz uri: https://doi.org/10.7717/peerj.10551 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Gomes and Goerlitz title: Macrel: antimicrobial peptide screening in genomes and metagenomes link: https://peerj.com/articles/10555 last-modified: 2020-12-18 description: MotivationAntimicrobial peptides (AMPs) have the potential to tackle multidrug-resistant pathogens in both clinical and non-clinical contexts. The recent growth in the availability of genomes and metagenomes provides an opportunity for in silico prediction of novel AMP molecules. However, due to the small size of these peptides, standard gene prospection methods cannot be applied in this domain and alternative approaches are necessary. In particular, standard gene prediction methods have low precision for short peptides, and functional classification by homology results in low recall.ResultsHere, we present Macrel (for metagenomic AMP classification and retrieval), which is an end-to-end pipeline for the prospection of high-quality AMP candidates from (meta)genomes. For this, we introduce a novel set of 22 peptide features. These were used to build classifiers which perform similarly to the state-of-the-art in the prediction of both antimicrobial and hemolytic activity of peptides, but with enhanced precision (using standard benchmarks as well as a stricter testing regime). We demonstrate that Macrel recovers high-quality AMP candidates using realistic simulations and real data.AvailabilityMacrel is implemented in Python 3. It is available as open source at https://github.com/BigDataBiology/macrel and through bioconda. Classification of peptides or prediction of AMPs in contigs can also be performed on the webserver: https://big-data-biology.org/software/macrel. creator: Célio Dias Santos-Júnior creator: Shaojun Pan creator: Xing-Ming Zhao creator: Luis Pedro Coelho uri: https://doi.org/10.7717/peerj.10555 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Santos-Júnior et al. title: Quality of urban parks in the perception of city residents with mobility difficulties link: https://peerj.com/articles/10570 last-modified: 2020-12-18 description: Urban parks should be inclusive for all. Availability and accessibility of urban parks determine the quality of life in cities. The importance of access increases for residents with limited mobility who, facing obstacles due to inadequate adjustment of the surrounding physical space, are exposed to social exclusion. Five groups of respondents completed a survey questionnaire revealing their attitudes towards green areas and indicating barriers to parks’ accessibility. The groups were designed to include blind and vision impaired people, those who use a wheelchair, have a physical disability of any kind, their carers/assistants and parents pushing strollers. The results revealed more similarities than differences among the five groups (the differences included preferences towards the neighbourhood and destination parks, physical barriers in parks, as well as using assistive technology devices and mobile assistive applications). Overall, city residents with mobility difficulties find those green public spaces as an important element of their life quality. creator: Magdalena Błaszczyk creator: Marzena Suchocka creator: Magdalena Wojnowska-Heciak creator: Magdalena Muszyńska uri: https://doi.org/10.7717/peerj.10570 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Błaszczyk et al. title: Optimizing the amount of pig manure in the vermicomposting of spent mushroom (Lentinula) substrate link: https://peerj.com/articles/10584 last-modified: 2020-12-18 description: BackgroundThe mushroom industry produces a large amount of spent mushroom substrate (SMS), which requires a large geographical footprint and causes pollution.MethodsWe sought to optimize the C:N ratio of the initial feedstock used in vermicomposting of SMS by adding pig manure additions. We applied five treatments to the initial feedstock (S0, S1, S2, S3, and S4) with different C:N ratio of approximately 35, 30, 25, 20, and 15, respectively.ResultsOur results showed that lignin and cellulose in SMS were degraded after 56 days vermicomposting, especially in S2 (77.05% and 45.29%, respectively) and S3 (65.05% and 48.37%, respectively) treatments. We observed the degradation of the fibrous structure in SMS using pig manure treatments after vermicomposting by microscope and scanning electron microscope. Cellulase and polyphenol oxidase (PPO) were enhanced in pig manure treatments during vermicomposting, especially in the S2 and S3 treatments. The biomass of earthworms in the S2 treatments was at its highest level among all treatments at 28 to 56 days. The high level of PPO activity in the S2 treatment may protect cellulase and earthworms against the aromatic toxicity that is a byproduct of lignin degradation, particularly at 28 to 56 days of vermicomposting. Conclusively, it indicated that the C/N ratio of 25 in the S2 treatment was the optimal for SMS vermicomposting with the addition of pig manure. Our results provide a positive application for the recycling of both SMS and pig manure. creator: Yajing Shi creator: Zhenyu Wang creator: Yurong Wang uri: https://doi.org/10.7717/peerj.10584 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Shi et al. title: Previous oil exposure alters Gulf Killifish Fundulus grandis oil avoidance behavior link: https://peerj.com/articles/10587 last-modified: 2020-12-18 description: Oil spills threaten the structure and function of ecological communities. The Deepwater Horizon spill was predicted to have catastrophic consequences for nearshore fishes, but field studies indicate resilience in populations and communities. Previous research indicates many marsh fishes exhibit avoidance of oil contaminated areas, representing one potential mechanism for this resilience. Here, we test whether prior oil exposure of Gulf killifish Fundulus grandis alters this avoidance response. Using choice tests between unoiled and oiled sediments at one of three randomized concentrations (low: 0.1 L oil m−2, medium: 0.5 L oil m−2, or high: 3.0 L oil m−2), we found that, even at low prior exposure levels, killifish lose recognition of oiled sediments compared to control, unexposed fish. Preference for unoiled sediments was absent across all oil concentrations after oil exposure, and some evidence for preference of oiled sediments at high exposure was demonstrated. These results highlight the lack of response to toxic environments in exposed individuals, indicating altered behavior despite organism survival. Future research should document additional sublethal consequences that affect ecosystem and food web functioning. creator: Charles W. Martin creator: Ashley M. McDonald creator: Guillaume Rieucau creator: Brian J. Roberts uri: https://doi.org/10.7717/peerj.10587 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Martin et al. title: Time of night and moonlight structure vertical space use by insectivorous bats in a Neotropical rainforest: an acoustic monitoring study link: https://peerj.com/articles/10591 last-modified: 2020-12-18 description: BackgroundPrevious research has shown diverse vertical space use by various taxa, highlighting the importance of forest vertical structure. Yet, we know little about vertical space use of tropical forests, and we often fail to explore how this three-dimensional space use changes over time.MethodsHere we use canopy tower systems in French Guiana and passive acoustic monitoring to measure Neotropical bat activity above and below the forest canopy throughout nine nights. We use a Bayesian generalized linear mixed effect model and kernel density estimates to demonstrate patterns in space-use over time.ResultsWe found that different bats use both canopy and understory space differently and that these patterns change throughout the night. Overall, bats were more active above the canopy (including Cormura brevirostris, Molossus molossus, Peropteryx kappleri and Peropteryx macrotis), but multiple species or acoustic complexes (when species identification was impossible) were more active in the understory (such as Centronycteris maximiliani, Myotis riparius, Pteronotus alitonus and Pteronotus rubiginosus). We also found that most bats showed temporally-changing preferences in hourly activity. Some species were less active (e.g., P. kappleri and P. macrotis), whereas others were more active (Pteronotus gymnonotus, C. brevirostris, and M. molossus) on nights with higher moon illuminance.DiscussionHere we show that Neotropical bats use habitat above the forest canopy and within the forest understory differently throughout the night. While bats generally were more active above the forest canopy, we show that individual groups of bats use space differently over the course of a night, and some prefer the understory. This work highlights the need to consider diel cycles in studies of space use, as animals use different habitats during different periods of the day. creator: Dylan G.E. Gomes creator: Giulliana Appel creator: Jesse R. Barber uri: https://doi.org/10.7717/peerj.10591 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Gomes et al. title: Sesamoids in Caudata and Gymnophiona (Lissamphibia): absences and evidence link: https://peerj.com/articles/10595 last-modified: 2020-12-18 description: An integrative definition of sesamoid bones has been recently proposed, highlighting their relationship with tendons and ligaments, their genetic origin, the influence of epigenetic stimuli on their development, and their variable tissue composition. Sesamoid bones occur mainly associated with a large number of mobile joints in vertebrates, most commonly in the postcranium. Here, we present a survey of the distribution pattern of sesamoids in 256 taxa of Caudata and Gymnophiona and 24 taxa of temnospondyls and lepospondyls, based on dissections, high-resolution X-ray computed tomography from digital databases and literature data. These groups have a pivotal role in the interpretation of the evolution of sesamoids in Lissamphibia and tetrapods in general. Our main goals were: (1) to contribute to the knowledge of the comparative anatomy of sesamoids in Lissamphibia; (2) to assess the evolutionary history of selected sesamoids. We formally studied the evolution of the observed sesamoids by optimizing them in the most accepted phylogeny of the group. We identified only three bony or cartilaginous sesamoids in Caudata: the mandibular sesamoid, which is adjacent to the jaw articulation; one located on the mandibular symphysis; and one located in the posterior end of the maxilla. We did not observe any cartilaginous or osseous sesamoid in Gymnophiona. Mapping analyses of the sesamoid dataset of urodeles onto the phylogeny revealed that the very conspicuous sesamoid in the mandibular symphysis of Necturus beyeri and Amphiuma tridactylum is an independent acquisition of these taxa. On the contrary, the sesamoid located between the maxilla and the lower jaw is a new synapomorphy that supports the node of Hydromantes platycephalus and Karsenia coreana. The absence of a mandibular sesamoid is plesiomorphic to Caudata, whereas it is convergent in seven different families. The absence of postcranial sesamoids in salamanders might reveal a paedomorphic pattern that would be visible in their limb joints. creator: María Laura Ponssa creator: Virginia Abdala uri: https://doi.org/10.7717/peerj.10595 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Ponssa and Abdala title: Utilizing sponge spicules in taxonomic, ecological and environmental reconstructions: a review link: https://peerj.com/articles/10601 last-modified: 2020-12-18 description: Most sponges produce skeletons formed by spicules, structural elements that develop in a wide variety of sizes and tridimensional shapes. The morphologies of spicules are often unique to clade- or even species-level taxa which makes them particularly useful in taxonomic assignments. When dead sponge bodies disintegrate, spicules become incorporated into sediments and sometimes accumulate into enormous agglomerations called spicule mats or beds, or fossilize to form special type of rocks called the spiculites. The record of fossil and subfossil sponge spicules is extraordinarily rich and often serves as a basis for far-reaching reconstructions of sponge communities, though spicules are also bearers of significant ecological and environmental information. Specific requirements and preferences of sponges can be used to interpret the environment in which they lived, and reconstruct oscillations in water depths, pH, temperatures, and other parameters, providing snapshots of past climate conditions. In turn, the silicon isotope compositions in spicules (δ30Si) are being increasingly often used to estimate the level of silicic acid in the marine settings throughout the geological history, which enables to reconstruct the past silica cycle and ocean circulation. This contribution provides a review of the use of sponge spicules in reconstructions of sponge communities, their ecology, and environments, and aims to detect the pertinent gaps in their utilization. Even though spicules are well known for their significance as bearers of taxonomic, ecological, and environmental data, their potential remains to be fully exploited. creator: Magdalena Łukowiak uri: https://doi.org/10.7717/peerj.10601 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Łukowiak title: Mutational spectra of SARS-CoV-2 isolated from animals link: https://peerj.com/articles/10609 last-modified: 2020-12-18 description: Coronaviruses are ubiquitous and infect a wide spectrum of animals and humans. The newly emerged severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has become a worldwide pandemic. To address the role that animals may play in the evolution of SARS-CoV-2, the full genome sequences of SARS-CoV-2 isolated from animals were compared with SARS-CoV-2 human isolates from the same clade and geographic region. Phylogenetic analysis of SARS-CoV-2 isolated from the cat, dog, mink, mouse, and tiger revealed a close relationship with SARS-CoV-2 human isolates from the same clade and geographic region with sequence identities of 99.94–99.99%. The deduced amino acid sequence of spike (S) protein revealed the presence of a furin cleavage site (682RRAR▾685), which did not differ among all SARS-CoV-2 isolates from animals and humans. SARS-CoV-2 isolates from minks exhibited two amino acid substitutions (G261D, A262S) in the N-terminal domain of S protein and four (L452M, Y453F, F486L, N501T) in the receptor-binding motif (RBM). In the mouse, the S protein had two amino acid substitutions, one in the RBM (Q498H) and the other (N969S) in the heptad repeat 1. SARS-CoV-2 isolated from minks furtherly exhibited three unique amino acid substitutions in the nucleocapsid (N)protein. In the cat, two unique amino acid substitutions were discovered in the N (T247I) and matrix (T175M) proteins. Additionally, SARS-CoV-2 isolated from minks possessed sixteen, four, and two unique amino acid substitutions in the open reading frame 1ab (ORF1ab), ORF3a, and ORF6, respectively. Dog and cat SARS-CoV-2 isolates showed one and seven unique amino acid substitutions in ORF1ab, respectively. Further studies may be necessary to determine the pathogenic significance of these amino acid substitutions to understand the molecular epidemiology and evolution of SARS-CoV-2. creator: Ahmed Elaswad creator: Mohamed Fawzy creator: Shereen Basiouni creator: Awad A. Shehata uri: https://doi.org/10.7717/peerj.10609 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Elaswad et al.