title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=686
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: The influence of penguin activity on soil diatom assemblages on King George Island, Antarctica with the description of a new Luticola species
link: https://peerj.com/articles/13624
last-modified: 2022-07-04
description: BackgroundIce-free areas in the Antarctic region are strongly limited. The presence of marine mammals and birds in those areas influence soil properties and vegetation composition. Studies on the terrestrial diatom flora in soils influenced by sea birds in the Maritime Antarctic region are scarce.MethodsSamples were collected from two transects on the western shore of the Admiralty Bay region. Light and scanning electron microscopic observations and statistical analyses were conducted to consider the impact of penguin rookeries on soil diatom assemblages.ResultsThe disturbance associated with the presence of penguin rookeries clearly influences the soil diatom diversity. Assemblages from areas with the highest nutrient input were characterized by a much lower diversity with only few species dominating the flora. One of recorded taxa could not be assigned to any of the known species. Therefore, based on the combination of morphological features analyzed using light and scanning electron microscopes and comparison with similar taxa in the Antarctic region and worldwide, the species is described hereby as new to science–Luticola kaweckae sp.nov. The new species is characteristic for soil habitats with strong penguin influence.
creator: Natalia Kochman-Kędziora
creator: Teresa Noga
creator: Maria Olech
creator: Bart Van de Vijver
uri: https://doi.org/10.7717/peerj.13624
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Kochman-Kędziora et al.

title: Comparative actualistic study hints at origins of alleged Miocene coprolites of Poland
link: https://peerj.com/articles/13652
last-modified: 2022-07-04
description: 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.
creator: Tomasz Brachaniec
creator: Dorota Środek
creator: Dawid Surmik
creator: Robert Niedźwiedzki
creator: Georgios L. Georgalis
creator: Bartosz J. Płachno
creator: Piotr Duda
creator: Alexander Lukeneder
creator: Przemysław Gorzelak
creator: Mariusz A. Salamon
uri: https://doi.org/10.7717/peerj.13652
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Brachaniec et al.

title: Curcumin effect on Acanthamoeba triangularis encystation under nutrient starvation
link: https://peerj.com/articles/13657
last-modified: 2022-07-04
description: BackgroundCurcumin 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.MethodsIn 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.ResultsA. 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.ConclusionCurcumin 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.
creator: Rachasak Boonhok
creator: Suthinee Sangkanu
creator: Suganya Phumjan
creator: Ramita Jongboonjua
creator: Nawarat Sangnopparat
creator: Pattamaporn Kwankaew
creator: Aman Tedasen
creator: Chooi Ling Lim
creator: Maria de Lourdes Pereira
creator: Mohammed Rahmatullah
creator: Polrat Wilairatana
creator: Christophe Wiart
creator: Karma G. Dolma
creator: Alok K. Paul
creator: Madhu Gupta
creator: Veeranoot Nissapatorn
uri: https://doi.org/10.7717/peerj.13657
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Boonhok et al.

title: Metabolome and transcriptome profiling reveal regulatory network and mechanism of flavonoid biosynthesis during color formation of Dioscorea cirrhosa L.
link: https://peerj.com/articles/13659
last-modified: 2022-07-04
description: 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.
creator: Lin Yan
creator: Haijun Yang
creator: Qiang Ye
creator: Zhihua Huang
creator: Hongying Zhou
creator: Dafang Cui
uri: https://doi.org/10.7717/peerj.13659
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Yan et al.

title: 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
link: https://peerj.com/articles/13662
last-modified: 2022-07-04
description: 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.
creator: Abigail Gazzard
creator: Philip J. Baker
uri: https://doi.org/10.7717/peerj.13662
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Gazzard and Baker

title: A complete season with attendance restrictions confirms the relevant contribution of spectators to home advantage and referee bias in association football
link: https://peerj.com/articles/13681
last-modified: 2022-07-04
description: BackgroundDue 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.MethodsThe 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.ResultsThe 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.DiscussionThese 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.
creator: Fabrizio Sors
creator: Michele Grassi
creator: Tiziano Agostini
creator: Mauro Murgia
uri: https://doi.org/10.7717/peerj.13681
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Sors et al.

title: Effect of icaritin on autophagy-related protein expression in TDP-43-transfected SH-SY5Y cells
link: https://peerj.com/articles/13703
last-modified: 2022-07-04
description: ObjectiveTo 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.MethodsA 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.ResultsAfter 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.ConclusionICT 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.
creator: Yanjun Zhou
creator: Nanqu Huang
creator: Yuanyuan Li
creator: Zhisheng Ba
creator: Yong Luo
uri: https://doi.org/10.7717/peerj.13703
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Zhou et al.

title: Newly described nesting sites of the green sea turtle (Chelonia mydas) and the hawksbill sea turtle (Eretmochelys imbricata) in the central Red Sea
link: https://peerj.com/articles/13408
last-modified: 2022-07-01
description: BackgroundThere 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.MethodsIn 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.ResultsSea 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.
creator: Kirsty Scott
creator: Lyndsey K. Tanabe
creator: Jeffrey D. Miller
creator: Michael L. Berumen
uri: https://doi.org/10.7717/peerj.13408
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Scott et al.

title: 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
link: https://peerj.com/articles/13514
last-modified: 2022-07-01
description: BackgroundThe 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.MethodsThis 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.ResultsBetween-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).ConclusionsAlthough 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.
creator: Filipe Manuel Clemente
creator: Yusuf Soylu
creator: Ersan Arslan
creator: Bulent Kilit
creator: Joel Garrett
creator: Daniel van den Hoek
creator: Georgian Badicu
creator: Ana Filipa Silva
uri: https://doi.org/10.7717/peerj.13514
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Clemente et al.

title: Dopamine receptor activation elicits a possible stress-related coping behavior in a wild-caught songbird
link: https://peerj.com/articles/13520
last-modified: 2022-07-01
description: 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.
creator: Melanie R. Florkowski
creator: Jessica L. Yorzinski
uri: https://doi.org/10.7717/peerj.13520
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Florkowski and Yorzinski