Comparative actualistic study hints at origins of alleged Miocene coprolites of Poland
Excrement-shaped ferruginous masses have been recovered from the Miocene of Turów mine in south-western Poland. These siderite masses have been the subject of much controversy, having been interpreted either as being coprolites, cololithes or pseudofossils created by mechanical deformation of plastic sediment. Here we present the results of mineralogical, geochemical, petrographic and microtomographical analyses. Our data indicate that these masses consist of siderite and iron oxide rather than phosphate, and rarely contain recognizable food residues, which may suggest abiotic origins of these structures. On the other hand, evidence in support of a fecal origin include: (i) the presence of two distinct morphotypes differing in size and shape, (ii) the presence of rare hair-like structures or coalified inclusions and (iii) the presence of rare fine striations on the surface. Importantly, comparative actualistic study of recent vertebrate feces shows overall resemblance of the first morphotype (sausage-shaped with rare coalified debris) to excrements of testudinoid turtles (Testudinoidea), whose shell fragment was found in the investigated locality. The second morphotype (rounded to oval-shaped with hair-like structures), in turn, is similar to the feces of some snakes (Serpentes), the remains of which were noted in the Miocene of the neighborhood areas. Other potential producers (such as lizards and crocodiles) and even abiotic origins cannot be fully excluded but are less likely.
Brachaniec et al. (2022) Comparative actualistic study hints at origins of alleged Miocene coprolites of Poland. PeerJ 10:e13652 https://doi.org/10.7717/peerj.13652
Curcumin effect on Acanthamoeba triangularis encystation under nutrient starvation
Background Curcumin is an active compound derived from turmeric, Curcuma longa, and is known for its benefits to human health. The amoebicidal activity of curcumin against Acanthamoeba triangularis was recently discovered. However, a physiological change of intracellular pathways related to A. triangularis encystation mechanism, including autophagy in the surviving amoeba after curcumin treatment, has never been reported. This study aims to investigate the effect of curcumin on the survival of A. triangularis under nutrient starvation and nutrient-rich condition, as well as to evaluate the A. triangularis encystation and a physiological change of Acanthamoeba autophagy at the mRNA level. Methods In this study, A. triangularis amoebas were treated with a sublethal dose of curcumin under nutrient starvation and nutrient-rich condition and the surviving amoebas was investigated. Cysts formation and vacuolization were examined by microscopy and transcriptional expression of autophagy-related genes and other encystation-related genes were evaluated by real-time PCR. Results A. triangularis cysts were formed under nutrient starvation. However, in the presence of the autophagy inhibitor, 3-methyladenine (3-MA), the percentage of cysts was significantly reduced. Interestingly, in the presence of curcumin, most of the parasites remained in the trophozoite stage in both the starvation and nutrient-rich condition. In vacuolization analysis, the percentage of amoebas with enlarged vacuole was increased upon starvation. However, the percentage was significantly declined in the presence of curcumin and 3-MA. Molecular analysis of A. triangularis autophagy-related (ATG) genes showed that the mRNA expression of the ATG genes, ATG3, ATG8b, ATG12, ATG16, under the starvation with curcumin was at a basal level along the treatment. The results were similar to those of the curcumin-treated amoebas under a nutrient-rich condition, except AcATG16 which increased later. On the other hand, mRNA expression of encystation-related genes, cellulose synthase and serine proteinase, remained unchanged during the first 18 h, but significantly increased at 24 h post treatment. Conclusion Curcumin inhibits cyst formation in surviving trophozoites, which may result from its effect on mRNA expression of key Acanthamoeba ATG-related genes. However, further investigation into the mechanism of curcumin in A. triangularis trophozoites arrest and its association with autophagy or other encystation-related pathways is needed to support the future use of curcumin.
Boonhok et al. (2022) Curcumin effect on Acanthamoeba triangularis encystation under nutrient starvation. PeerJ 10:e13657 https://doi.org/10.7717/peerj.13657
Metabolome and transcriptome profiling reveal regulatory network and mechanism of flavonoid biosynthesis during color formation of Dioscorea cirrhosa L.
Dioscorea cirrhosa is a plant that is used as a dye as well as in medicine. Many metabolites with pharmacological activity exist in the tubers of D. cirrhosa. However, little is known about the mechanism regulating biosynthesis in these metabolites. In this study, transcriptome and metabolome profiling were performed in four color tubers. A total of 531 metabolites, including 62 flavonoids, were identified. Epicatechin and proanthocyanin B2 were the key metabolites that exhibited high content levels in the four tubers. These metabolites were divided into nine classes with distinct change patterns. A total of 22,865 differentially expressed genes (DEGs) were identified by transcriptome analysis. Among these DEGs, we identified 67 candidate genes related to the flavonoid biosynthesis pathway and three genes that played pivotal roles in proanthocyanin (PA) synthesis. A weighted gene co-expression network analysis (WGCNA) revealed that the two modules, “MEblue” and “MEblack,” were two key gene sets strongly associated with phenylpropanoid and flavonoid biosynthesis. We also found that the plant hormone signal transduction biological process exhibited activity in the late stage of tuber color formation. Additionally, we identified 37 hub transcript factors related to flavonoid biosynthesis, of which 24 were found to be highly associated with flavonoid pathway genes. In addition to the MYB-bHLH-WD40 (MBW) genes, we found that the plant hormone gene families exhibited high expression levels. This study provides a reference for understanding the synthesis of D. cirrhosa tuber metabolites at the molecular level and provides a foundation for the further development of D. cirrhosa related plant pigments as well as its further use in the pharmaceutical industry.
Yan et al. (2022) Metabolome and transcriptome profiling reveal regulatory network and mechanism of flavonoid biosynthesis during color formation of Dioscorea cirrhosa L.. PeerJ 10:e13659 https://doi.org/10.7717/peerj.13659
What makes a house a home? Nest box use by West European hedgehogs (Erinaceus europaeus) is influenced by nest box placement, resource provisioning and site-based factors
Artificial refuges provided by householders and/or conservation practitioners potentially represent one mechanism for mitigating declines in the availability of natural nest sites used for resting, breeding and hibernating in urban areas. The effectiveness of such refuges for different species is, however, not always known. In this study, we conducted a questionnaire survey of UK householders to identify factors associated with the use of ground-level nest boxes for West European hedgehogs (Erinaceus europaeus), a species of conservation concern. Overall, the percentage of boxes used at least once varied with season and type of use: summer day nesting (35.5–81.3%), breeding (7.2–28.2%), winter day nesting (20.1–66.5%) and hibernation (21.7–58.6%). The length of time the box had been deployed, the availability of artificial food and front garden to back garden access significantly increased the likelihood that a nest box had been used for all four nesting types, whereas other factors related to placement within the garden (e.g., in a sheltered location, on hardstanding such as paving, distance from the house) and resource provisioning (bedding) affected only some nesting behaviours. The factors most strongly associated with nest box use were the provisioning of food and bedding. These data suggest, therefore, that householders can adopt simple practices to increase the likelihood of their nest box being used. However, one significant limitation evident within these data is that, for welfare reasons, householders do not routinely monitor whether their box has been used. Consequently, future studies need to adopt strategies which enable householders to monitor their boxes continuously. Ultimately, such studies should compare the survival rates and reproductive success of hedgehogs within artificial refuges versus more natural nest sites, and whether these are affected by, for example, the impact of nest box design and placement on predation risk and internal microclimate.
Gazzard et al. (2022) What makes a house a home? Nest box use by West European hedgehogs (Erinaceus europaeus) is influenced by nest box placement, resource provisioning and site-based factors. PeerJ 10:e13662 https://doi.org/10.7717/peerj.13662
A complete season with attendance restrictions confirms the relevant contribution of spectators to home advantage and referee bias in association football
Background Due to the unfortunate pandemic situation, the phenomena of home advantage and referee bias in sports have recently received a particular research attention, especially in association football. In this regard, several studies were conducted on the last portion of the 2019–20 season: the majority of them suggests a reduction—but not the elimination—of the two phenomena, with some exceptions in which no reduction was found or, at the other extreme, the phenomena were not observed at all. Methods The continuation of the pandemic made it possible to replicate the previous studies considering the complete 2020–21 season, thus with the important added value of having a fully balanced home/away schedule—and a higher number of matches—in the various leagues. In particular, the sample of the present study consisted of 3,898 matches from the first and second divisions of the UEFA top five ranked countries, that is, England, Spain, Italy, Germany, and France. For the home advantage, the following variables were examined: distribution of matches outcomes and home advantage for points (also for previous seasons from the 2014–15 one); ball possession; total shots; shots on goal; and corner kicks. Instead, for he referee bias, the following variables were examined: fouls; yellow cards; red cards; penalty kicks; and extra time. Chi-square tests were used to compare the distribution of matches outcomes, and t-tests to compare home vs. away data for the other variables in the 2020–21 season; Bayesian and equivalence analyses were also conducted. Results The main results are as follows: (a) the distribution of matches outcomes in the 2020–21 season was significantly different from that of the last five complete seasons with spectators (Chi-square = 37.42, df = 2, p < 0.001), with fewer home victories and more away victories; the resulting values of the home advantage for points were 54.95% for the 2020–21 season, and 59.36% for the previous seasons; (b) for the other home advantage variables, a statistically significant overall advantage for the home team emerged; nevertheless, the strength of the differences between home and away teams was generally small (0.09 < Cohen’s d < 0.17), and the corresponding means can be considered statistically equivalent for all variables but the total shots; (c) no statistically significant differences emerged between home and away teams for any of the referee bias variables. Discussion These findings demonstrate that the absence of spectators significantly reduced the home advantage compared to previous seasons with spectators. A slight home advantage persisted in the 2020–21 season, probably due to other factors, namely, learning and travel, according to the model by Courneya & Carron (1992). Conversely, the referee bias was not observed, suggesting that it mainly derives from the pressure normally exerted by spectators.
Sors et al. (2022) A complete season with attendance restrictions confirms the relevant contribution of spectators to home advantage and referee bias in association football. PeerJ 10:e13681 https://doi.org/10.7717/peerj.13681
Effect of icaritin on autophagy-related protein expression in TDP-43-transfected SH-SY5Y cells
Objective To study the protective effect and mechanism of icaritin (ICT) in a SH-SY5Y cells with virus-loaded TAR DNA-binding domain protein 43(TDP-43) by examining the effect of ICT on the expression of autophagy-related proteins in TDP-43-infected SH-SY5Y cells. Methods A TDP-43-induced neuronal cell injury model was established by transfecting well-growing SH-SY5Y cells with virus loaded with the TDP-43 gene. The changes in cell viability were detected by the CCK-8 method. After successful transfection, the establishment of the model was verified by real-time quantitative PCR (qPCR) and Western blot methods. After the cells were subjected to drug intervention with ICT, the changes in the expression levels of TDP-43, cleaved Caspase-3, LC3 II/I, Beclin-1 and p62 were detected by Western blotting. Results After ICT intervention, it was found that compared with that of the TDP-43 group, the cell viability of the TDP-43+ICT group increased, the expression level of TDP-43 decreased, and the expression levels of the apoptotic protein cleaved Caspase-3, autophagy protein Beclin-1, and LC3-II/I decreased, while the expression level of the autophagy protein p62 increased. Conclusion ICT has a protective effect on the SH-SY5Y cell injury model transfected with TDP-43. This protective effect may be related to reducing the protein expression of TDP-43 and inhibiting autophagy.
Zhou et al. (2022) Effect of icaritin on autophagy-related protein expression in TDP-43-transfected SH-SY5Y cells. PeerJ 10:e13703 https://doi.org/10.7717/peerj.13703
Newly described nesting sites of the green sea turtle (Chelonia mydas) and the hawksbill sea turtle (Eretmochelys imbricata) in the central Red Sea
Background There is relatively little published information about sea turtle nesting distribution and seasonality in the Saudi Arabian Red Sea. Upcoming large-scale developments occurring along the Saudi Arabian Red Sea coast could negatively affect many sea turtle nesting beaches with potential impacts on the survival of local populations. Methods In 2019, two coastal beaches and three near-shore islands were surveyed for turtle nesting in the central Red Sea. We recorded all emergences, examined beach morphology, and collected sand samples to determine grain size, moisture content and colour. Results Sea turtle nesting was found at all surveyed sites, though emergence counts were often low. The limited occurrence of nesting at several previously undocumented sites suggests that nesting activity may be widespread, but sparsely distributed, in the central Red Sea region. In addition, nesting at novel sites appeared to favour the seaward side of islands, a pattern that was not observed in previously documented areas. The substrate of most surveyed sites was composed of calcium carbonate with Ras Baridi as the only exception; it was composed of dark quartz-rich sediment. This study highlights several important sea turtle rookeries while also demonstrating that low levels of nesting occur throughout the region, although inter-annual nesting patterns still need to be determined. Future developments should be steered away from key nesting areas and the seaward bias in marginal rookeries should be taken into account where possible.
Scott et al. (2022) Newly described nesting sites of the green sea turtle (Chelonia mydas) and the hawksbill sea turtle (Eretmochelys imbricata) in the central Red Sea. PeerJ 10:e13408 https://doi.org/10.7717/peerj.13408
Can high-intensity interval training and small-sided games be effective for improving physical fitness after detraining? A parallel study design in youth male soccer players
Background The aim of this study was two-fold: (i) analyze the within-group physical fitness adaptations promoted by a detraining period (4 weeks) followed by an intervention period (4 weeks) using small-sided games (SSGs) or running-based high intensity interval training (HIIT); and (ii) analyze the between-group differences aiming to identify the effectiveness of each training intervention on the physical fitness of youth male soccer players. Methods This study followed a randomized parallel study design. Forty male soccer players (age: 16.4 ± 0.5 years old) were assessed three times: (i) baseline; (ii) after 4 weeks of detraining; and (iii) after a retraining period of 4 weeks. After returning from detraining, players were randomized to an SSG-based training intervention (n = 20) or running-based HIIT (n = 20). Interventions lasted 4 weeks, with a training frequency of three sessions per week. At all timepoints, players were assessed by: (i) anthropometry (height, body mass, fat mass (FM)), countermovement jump (CMJ), standing broad jump (SBJ), triple hop jump (THJ), linear sprint test (5-, 10-, and 20-m), zig-zag test with (ZZwB) and without (ZZwoB) ball, three corner run test (3CRT), Y-balance test and the Yo-Yo intermittent recovery test level 1 (YYIRT). Mixed ANOVA (time * group) was conducted for testing interactions between the three timepoints of repeated measures and the two groups. Effect size (ES) for pairwise comparisons was calculated using Cohen’s. Results Between-group analysis revealed significantly smaller SBJ (t = −2.424, p = 0.020, d = −0.767 small ES) and THT (t = −4.353, p < 0.001, d = −1.376 large ES) in the SSG group after the retraining period. At the same time, SSG presented significantly greater FM after retraining compared to HIIT (t = 3.736, p < 0.001, d = 1.181 large ES). Additionally, SSG had significantly smaller values than HIIT in the ZZwB (t = −3.645, p < 0.001, d = −1.153 large ES), but greater times in the ZZwoB (t = 2.679, p = 0.011, d = 0.847 large ES) and 3CRT (t = 3.126, p = 0.003, d = 0.989 large ES). Conclusions Although SSG and HIIT interventions improved physical fitness outcomes after a period of detraining, they were not able to effectively restore body composition, CMJ, 20-m sprint, ZZwB, and YYIRT compared with the baseline assessments (before detraining). Only HIIT was significantly effective for restoring SBJ, short linear sprin speed, and change-of-direction compared with baseline. HIIT was also significantly better than SSG in improving SBJ and ZZwoB. Although the small sample, the non determination of maturation status and the need to be cautious regarding generalization, HIIT appears to be more beneficial than SSG after a detraining period for recovery of body composition and physical fitness qualities in this specific context of youth soccer players.
Clemente et al. (2022) Can high-intensity interval training and small-sided games be effective for improving physical fitness after detraining? A parallel study design in youth male soccer players. PeerJ 10:e13514 https://doi.org/10.7717/peerj.13514
Dopamine receptor activation elicits a possible stress-related coping behavior in a wild-caught songbird
Animals experience stress throughout their lives and exhibit both physiological and behavioral responses to cope with it. The stress response can become harmful when prolonged and increasing evidence suggests that dopamine plays a critical role in extinguishing the stress response. In particular, activation of the D2 dopamine receptor reduces glucocorticoids and increases coping behavior, i.e., behavioral responses to adverse stimuli that reduce the harmful effects of stress. However, few studies have examined the effects of dopamine on the stress responses of wild species. We therefore tested the hypothesis that activation of the D2 dopamine receptor influences coping-like behavior in a wild-caught species. We recorded behavior of house sparrows (Passer domesticus) before and after they received injections of D2 dopamine agonists, D2 dopamine antagonists, or saline. House sparrows are common in urban environments and understanding how they cope with stress may help us better understand how animals cope with urban stressors. We found that the birds significantly increased biting of inanimate objects after the agonist but there was no change following the antagonist or saline. The biting of inanimate objects may be a mechanism of behavioral coping. This change in biting behavior was not correlated with general movement. This study supports the hypothesis that D2 dopamine receptor activation is involved in the regulation of the stress response in a wild bird.
Florkowski et al. (2022) Dopamine receptor activation elicits a possible stress-related coping behavior in a wild-caught songbird. PeerJ 10:e13520 https://doi.org/10.7717/peerj.13520
Characterization of the complete chloroplast genome sequences of six Dalbergia species and its comparative analysis in the subfamily of Papilionoideae (Fabaceae)
Dalbergia spp. are numerous and widely distributed in pantropical areas in Asia, Africa and America, and most of the species have important economic and ecological value as precious timber. In this study, we determined and characterized six complete chloroplast genomes of Dalbergia species (Dalbergia obtusifolia, D. hupeana, D. mimosoides, D. sissoo, D. hancei, D. balansae), which displayed the typical quadripartite structure of angiosperms. The sizes of the genomes ranged from 155,698 bp (D. hancei) to 156,419 bp (D. obtusifolia). The complete chloroplast genomes of Dalbergia include 37 tRNA genes, eight rRNA genes and 84 protein-coding genes. We analysed the sequence diversity of Dalberigia chloroplast genomes coupled with previous reports. The results showed 12 noncoding regions (rps16-accD, trnR-UCU-trnG-UCC, ndhE-ndhG, trnG-UCC-psbZ, rps8-rpl14, trnP-UGG-psaJ, ndhH-rps15, trnQ-UUG-rps16, trnS-GCU-psbI, rps12-clpP, psbA-trnK-UUU, trnK-UUU-intron), and four coding regions (rps16, ycf1, rps15 and ndhF) showed many nucleotide variations that could be used as potential molecular markers. Based on a site-specific model, we analysed the selective pressure of chloroplast genes in Dalbergia species. Twenty-two genes with positively selected sites were detected, involving the photosynthetic system (ndhC, adhD, ndhF, petB, psaA, psaB, psbB, psbC, psbK and rbcL), self-replication category of genes (rpoA, rpoC2, rps3, rps12 and rps18) and others (accD, ccsA, cemA, clpP, matK, ycf1 and ycf2). Additionally, we identified potential RNA editing sites that were relatively conserved in the genus Dalbergia. Furthermore, the comparative analysis of cp genomes of Dalbergieae species indicated that the boundary of IRs/SSC was highly variable, which resulted in the size variation of cp genomes. Finally, phylogenetic analysis showed an inferred phylogenetic tree of Papilionoideae species with high bootstrap support and suggested that Amorpheae was the sister of the clade Dalbergieae. Moreover, three genera of the Pterocarpus clade showed a nested evolutionary relationship. These complete cp genomes provided valuable information for understanding the genetic variation and phylogenetic relationship of Dalbergia species with their relatives.
Li et al. (2022) Characterization of the complete chloroplast genome sequences of six Dalbergia species and its comparative analysis in the subfamily of Papilionoideae (Fabaceae). PeerJ 10:e13570 https://doi.org/10.7717/peerj.13570