title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=980 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: A new elasmosaurid (Sauropterygia: Plesiosauria) from the non-marine to paralic Dinosaur Park Formation of southern Alberta, Canada link: https://peerj.com/articles/10720 last-modified: 2021-02-11 description: Elasmosaurid plesiosaurian remains have been documented from non-marine to paralic (fluvial to estuarine) sediments of the upper Campanian Dinosaur Park Formation (DPF) of southern Alberta since 1898. Despite this long collection history, this material has received relatively little research attention, largely due to the highly fragmentary nature of most recovered specimens. However, this assemblage is significant, as it constitutes a rare occurrence of plesiosaurian remains in a non-marine depositional environment. This study reports on a recently collected and prepared specimen, which represents the most complete elasmosaurid yet collected from the DPF. This specimen preserves the trunk region, the base of the neck and tail, a partial fore and hind limb, and tooth, and is sufficiently complete to be assigned as the holotype of a new genus and species. This new taxon is diagnosed by a distinctive character state combination including a boomerang-shaped clavicular arch with acute anterior process, convex anterolateral margin, deeply embayed posterior margin, and pronounced ventral keel, together with the presence of 22 dorsal vertebrae, and the anterior dorsal centra bearing a ventral notch. The DPF plesiosaurian fossils were recovered from both estuarine/bay and fluvial palaeochannel sediments. The holotype skeleton represents an osteologically mature individual with an estimated body length of around 5 m, although the largest referred DPF elasmosaurid might have been closer to 7 m, which is considerably larger than other plesiosaurians reported from non-marine deposits. This suggests small-body lengths relative to typical elasmosaurids from marine settings, but is consistent with other plesiosaurians recovered from non-marine sediments. The identification of a distinct elasmosaurid taxon in the DPF might be evidence of niche-partitioning among the predominantly oceanic members of the ubiquitous plesiosaurian clade. creator: James A. Campbell creator: Mark T. Mitchell creator: Michael J. Ryan creator: Jason S. Anderson uri: https://doi.org/10.7717/peerj.10720 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Campbell et al. title: Transcriptomic analysis of nonylphenol effect on Saccharomyces cerevisiae link: https://peerj.com/articles/10794 last-modified: 2021-02-11 description: Nonylphenol (NP) is a bioaccumulative environmental estrogen that is widely used as a nonionic surfactant. We have previously examined short-term effects of NP on yeast cells using microarray technology. In the present study, we investigated the adaptive response of Saccharomyces cerevisiae BY4742 cells to NP exposure by analyzing genome-wide transcriptional profiles using RNA-sequencing. We used 2 mg/L NP concentration for 40 days of exposure. Gene expression analysis showed that a total of 948 genes were differentially expressed. Of these, 834 genes were downregulated, while 114 genes were significantly upregulated. GO enrichment analysis revealed that 369 GO terms were significantly affected by NP exposure. Further analysis showed that many of the differentially expressed genes were associated with oxidative phosphorylation, iron and copper acquisition, autophagy, pleiotropic drug resistance and cell cycle progression related processes such as DNA and mismatch repair, chromosome segregation, spindle checkpoint activity, and kinetochore organization. Overall, these results provide considerable information and a comprehensive understanding of the adaptive response to NP exposure at the gene expression level. creator: Ceyhun Bereketoglu creator: Gozde Nacar creator: Tugba Sari creator: Bulent Mertoglu creator: Ajay Pradhan uri: https://doi.org/10.7717/peerj.10794 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Bereketoglu et al. title: Low pH alleviated salinity stress of ginger seedlings by enhancing photosynthesis, fluorescence, and mineral element contents link: https://peerj.com/articles/10832 last-modified: 2021-02-11 description: We investigated the effects of low pH on the photosynthesis, chlorophyll fluorescence, and mineral contents of the leaves of ginger plants under salt stress. This experiment involved four treatments: T1 (pH 6, 0 salinity), T2 (pH 4, 0 salinity), T3 (pH 6, 100 mmol L−1 salinity) and T4 (pH 4, 100 mmol L−1 salinity). This study showed that photosynthesis (Pn, Gs, WUE and Tr) and chlorophyll fluorescence (qP, Φ PSII, and Fv/Fm) significantly decreased under salt stress; however, all the parameters of the ginger plants under the low-pH treatment and salt stress recovered. Moreover, low pH reduced the content of Na and enhanced the contents of K, Mg, Fe and Zn in the leaves of ginger plants under salt stress. Taken together, these results suggest that low pH improves photosynthesis efficiency and nutrient acquisition and reduces the absorption of Na, which could enhance the salt tolerance of ginger. creator: Fengman Yin creator: Shanying Zhang creator: Bili Cao creator: Kun Xu uri: https://doi.org/10.7717/peerj.10832 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Yin et al. title: Using natural history collections to investigate changes in pangolin (Pholidota: Manidae) geographic ranges through time link: https://peerj.com/articles/10843 last-modified: 2021-02-11 description: Pangolins, often considered the world’s most trafficked wild mammals, have continued to experience rapid declines across Asia and Africa. All eight species are classed as either Vulnerable, Endangered or Critically Endangered by the International Union for Conservation of Nature (IUCN) Red List. Alongside habitat loss, they are threatened mainly by poaching and/or legal hunting to meet the growing consumer demand for their meat and keratinous scales. Species threat assessments heavily rely on changes in species distributions which are usually expensive and difficult to monitor, especially for rare and cryptic species like pangolins. Furthermore, recent assessments of the threats to pangolins focus on characterising their trade using seizure data which provide limited insights into the true extent of global pangolin declines. As the consequences of habitat modifications and poaching/hunting on species continues to become apparent, it is crucial that we frequently update our understanding of how species distributions change through time to allow effective identification of geographic regions that are in need of urgent conservation actions. Here we show how georeferencing pangolin specimens from natural history collections can reveal how their distributions are changing over time, by comparing overlap between specimen localities and current area of habitat maps derived from IUCN range maps. We found significant correlations in percentage area overlap between species, continent, IUCN Red List status and collection year, but not ecology (terrestrial or arboreal/semi-arboreal). Human population density (widely considered to be an indication of trafficking pressure) and changes in primary forest cover, were weakly correlated with percentage overlap. Our results do not suggest a single mechanism for differences among historical distributions and present-day ranges, but rather show that multiple explanatory factors must be considered when researching pangolin population declines as variations among species influence range fluctuations. We also demonstrate how natural history collections can provide temporal information on distributions and discuss the limitations of collecting and using historical data. creator: Emily Buckingham creator: Jake Curry creator: Charles Emogor creator: Louise Tomsett creator: Natalie Cooper uri: https://doi.org/10.7717/peerj.10843 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Buckingham et al. title: Arousal modulates the motor interference effect stimulated by pictures of threatening animals link: https://peerj.com/articles/10876 last-modified: 2021-02-11 description: Previous research related to the motor interference effect from dangerous objects indicated that delayed responses to dangerous objects were associated with more positive parietal P3 amplitudes, suggesting that great attentional resources were allocated to evaluate the level of danger (i.e., negative valence). However, arousal covaried with valence in this research. Together with previous studies in which the P3 amplitude was found to be increased along with a higher arousal level in the parietal lobe, we raised the issue that more positive parietal P3 amplitudes might also be affected by a high arousal level. To clarify whether valence or arousal impacted the motor interference effect, this study used a motor priming paradigm mixed with a Go/NoGo task and manipulated the valence (negative, neutral and positive) and arousal (medium and high) of target stimuli. Analysis of the behavioral results identified a significant motor interference effect (longer reaction times (RTs) in the negative valence condition than in the neutral valence condition) at the medium arousal level and an increased effect size (increment of RT difference) at the high arousal level. The results indicated that negative valence stimuli may interfere with the prime elicited motor preparation more strongly at the high arousal level than at the medium arousal level. The ERP results identified larger centroparietal P3 amplitudes for the negative valence condition than for the neutral valence condition at a high arousal level. However, the inverse result, i.e., lower centroparietal P3 amplitudes for the negative valence condition than for the neutral valence condition, was observed at a medium arousal level. The ERP results further indicated that the effect size of the behavioral motor interference effect increased because subjects are more sensitive to the negative valence stimuli at the high arousal level than at the medium arousal level. Furthermore, the motor interference effect is related to the negative valence rather than emotionality of the target stimuli because different result patterns emerged between the positive and negative valence conditions. Detailed processes underlying the interaction between valence and arousal effects are discussed. creator: Gai Cao creator: Peng Liu uri: https://doi.org/10.7717/peerj.10876 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Cao and Liu title: Characterization and complete genome sequence of Privateer, a highly prolate Proteus mirabilis podophage link: https://peerj.com/articles/10645 last-modified: 2021-02-10 description: The Gram-negative bacterium Proteus mirabilis causes a large proportion of catheter-associated urinary tract infections, which are among the world’s most common nosocomial infections. Here, we characterize P. mirabilis bacteriophage Privateer, a prolate podophage of the C3 morphotype isolated from Texas wastewater treatment plant activated sludge. Basic characterization assays demonstrated Privateer has a latent period of ~40 min and average burst size around 140. In the 90.7 kb Privateer genome, 43 functions were assigned for the 144 predicted protein-coding genes. Genes encoding DNA replication proteins, DNA modification proteins, four tRNAs, lysis proteins, and structural proteins were identified. Cesium-gradient purified Privateer particles analyzed via LC-MS/MS verified the presence of several predicted structural proteins, including a longer, minor capsid protein apparently produced by translational frameshift. Comparative analysis demonstrated Privateer shares 83% nucleotide similarity with Cronobacter phage vB_CsaP_009, but low nucleotide similarity with other known phages. Predicted structural proteins in Privateer appear to have evolutionary relationships with other prolate podophages, in particular the Kuraviruses creator: James E. Corban creator: Jolene Ramsey uri: https://doi.org/10.7717/peerj.10645 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Corban and Ramsey title: A validation of Illumina EPIC array system with bisulfite-based amplicon sequencing link: https://peerj.com/articles/10762 last-modified: 2021-02-10 description: The Illumina Infinium® MethylationEPIC BeadChip system (hereafter EPIC array) is considered to be the current gold standard detection method for assessing DNA methylation at the genome-wide level. EPIC arrays are often used for hypothesis generation or pilot studies, the natural conclusion to which is to validate methylation candidates and expand these in a larger cohort, in a targeted manner. As such, an accurate smaller-scale, targeted technique, that generates data at the individual CpG level that is equivalent to the EPIC array, is needed. Here, we tested an alternative DNA methylation detection technique, known as bisulfite-based amplicon sequencing (BSAS), to determine its ability to validate CpG sites detected in EPIC array studies. BSAS was able to detect differential DNA methylation at CpG sites to a degree which correlates highly with the EPIC array system at some loci. However, BSAS correlated less well with EPIC array data in some instances, and most notably, when the magnitude of change via EPIC array was greater than 5%. Therefore, our data suggests that BSAS can be used to validate EPIC array data, but each locus must be compared on an individual basis, before being taken forward into large scale screening. Further, BSAS does offer advantages compared to the probe-based EPIC array; BSAS amplifies a region of the genome (∼500 bp) around a CpG of interest, allowing analyses of other CpGs in the region that may not be present on the EPIC array, aiding discovery of novel CpG sites and differentially methylated regions of interest. We conclude that BSAS offers a valid investigative tool for specific regions of the genome that are currently not contained on the array system. creator: Alexandra J. Noble creator: John F. Pearson creator: Joseph M. Boden creator: L. John Horwood creator: Neil J. Gemmell creator: Martin A. Kennedy creator: Amy J. Osborne uri: https://doi.org/10.7717/peerj.10762 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Noble et al. title: Comparative analysis of the complete plastid genomes of Mangifera species and gene transfer between plastid and mitochondrial genomes link: https://peerj.com/articles/10774 last-modified: 2021-02-10 description: Mango is an important commercial fruit crop belonging to the genus Mangifera. In this study, we reported and compared four newly sequenced plastid genomes of the genus Mangifera, which showed high similarities in overall size (157,780–157,853 bp), genome structure, gene order, and gene content. Three mutation hotspots (trnG-psbZ, psbD-trnT, and ycf4-cemA) were identified as candidate DNA barcodes for Mangifera. These three DNA barcode candidate sequences have high species identification ability. We also identified 12 large fragments that were transferred from the plastid genome to the mitochondrial genome, and found that the similarity was more than 99%. The total size of the transferred fragment was 35,652 bp, accounting for 22.6% of the plastid genome. Fifteen intact chloroplast genes, four tRNAs and numerous partial genes and intergenic spacer regions were identified. There are many of these genes transferred from mitochondria to the chloroplast in other species genomes. Phylogenetic analysis based on whole plastid genome data provided a high support value, and the interspecies relationships within Mangifera were resolved well. creator: Yingfeng Niu creator: Chengwen Gao creator: Jin Liu uri: https://doi.org/10.7717/peerj.10774 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Niu et al. title: Somatic determinants of changes in selected body posture parameters in younger school-age children link: https://peerj.com/articles/10821 last-modified: 2021-02-10 description: BackgroundThe aim of this study was to describe changes in selected parameters of body posture in children between 5 and 9 years old with diversified somatic structures.MethodsThe study was carried out in 2015 and then repeated in 2018 among 67 participants who had previously been observed to have scoliotic posture. Basic body weight and height measurements were taken, which were then used to calculate the body mass index. Posture tests were conducted using the photogrammetric method.ResultsGirls and boys were not significantly different in body dimensions. With age, the number of overweight boys and children with normal growth-weight proportions increased. Temporary differences in posture variables indicating abnormalities were small.ConclusionsThere were no significant differences in somatic parameters between the girls and the boys. Those children with a slender body structure had the most abnormalities in the coronal plane. On the other hand, changes in spinal position in the sagittal plane were more frequent in overweight children. Relations were noted between the compensation index in the sagittal plane and deviation of the trunk inclination, the maximum deviation of the line of the spinous processes, and the angle of the shoulder line in the coronal plane and body mass index values were noted. creator: Marta Kinga Labecka creator: Krystyna Górniak creator: Małgorzata Lichota uri: https://doi.org/10.7717/peerj.10821 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Labecka et al. title: Marine amphipods as a new live prey for ornamental aquaculture: exploring the potential of Parhyale hawaiensis and Elasmopus pectenicrus link: https://peerj.com/articles/10840 last-modified: 2021-02-10 description: Marine amphipods are gaining attention in aquaculture as a natural live food alternative to traditional preys such as brine shrimps (Artemia spp.). The use of Artemia is convenient for the culture of many marine species, but often problematic for some others, such as seahorses and other marine ornamental species. Unlike Artemia, marine amphipods are consumed by fish in their natural environment and show biochemical profiles that better match the nutritional requirements of marine fish, particularly of polyunsaturated fatty acids (PUFA), including eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids. Despite their potentially easy culture, there are no established culture techniques and a deeper knowledge on the reproductive biology, nutritional profiles and culture methodologies is still needed to potentiate the optimization of mass production. The present study assessed, for the first time, the aquaculture potential of Parhyale hawaiensis and Elasmopus pectenicrus, two cosmopolitan marine gammarids (as per traditional schemes of classification) that naturally proliferate in the wild and in aquaculture facilities. For that purpose, aspects of the population and reproductive biology of the species were characterized and then a series of laboratory-scale experiments were conducted to determine amphipod productivity, the time needed to reach sexual maturity by hatchlings (generation time), cannibalism degree, the effects of sex ratio on fecundity and the effects of diet (shrimp diet, plant-based diet and commercial fish diet) on fecundity and juvenile growth. P. hawaiensis, unlike E. pectenicrus, was easily maintained and propagated in laboratory conditions. P. hawaiensis showed a higher total length (9.3 ± 1.3 mm), wet weight (14.4 ± 6.2 mg), dry weight (10.5 ± 4.4 mg), females/males sex ratio (2.24), fecundity (12.8 ± 5.7 embryos per female), and gross energy content (16.71 ± 0.67 kJ g-1) compared to E. pectenicrus (7.9 ± 1.2 mm total length; 8.4 ± 4.3 mg wet weight; 5.7 ± 3.2 mg dry weight; 1.34 females/males sex ratio; 6.5 ± 3.9 embryos per female; 12.86 ± 0.82 kJ g−1 gross energy content). P. hawaiensis juvenile growth showed a small, but significant, reduction by the use of a plant-based diet compared to a commercial shrimp and fish diet; however, fecundity was not affected, supporting the possible use of inexpensive diets to mass produce amphipods as live or frozen food. Possible limitations of P. hawaiensis could be their quite long generation times (50.9 ± 5.8 days) and relatively low fecundity levels (12.8 ± 5.7 embryos per female). With an observed productivity rate of 0.36 ± 0.08 juveniles per amphipod couple per day, P. hawaiensis could become a specialty feed for species that cannot easily transition to a formulated diet such as seahorses and other highly priced marine ornamental species. creator: Jorge Arturo Vargas-Abúndez creator: Humberto Ivan López-Vázquez creator: Maite Mascaró creator: Gemma Leticia Martínez-Moreno creator: Nuno Simões uri: https://doi.org/10.7717/peerj.10840 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Vargas-Abúndez et al.