title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=689 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en 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 title: Characterization of the complete chloroplast genome sequences of six Dalbergia species and its comparative analysis in the subfamily of Papilionoideae (Fabaceae) link: https://peerj.com/articles/13570 last-modified: 2022-07-01 description: 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. creator: Changhong Li creator: Yu Liu creator: Furong Lin creator: Yongqi Zheng creator: Ping Huang uri: https://doi.org/10.7717/peerj.13570 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Li et al. title: Genome-wide identification and functional analysis of class III peroxidases in Gossypium hirsutum link: https://peerj.com/articles/13635 last-modified: 2022-07-01 description: Class III peroxidase (PRX) genes play essential roles in various processes, such as auxin catabolism, removal of H2O2, crosslinking cell wall components, and response to biotic and abiotic stresses. In this study, we identified 166, 78 and 89 PRX genes from G. hirsutum, G. arboretum and G. raimondii, respectively. These PRX genes were classified into seven subfamilies based on phylogenetic tree analysis and the classification of PRX genes in Arabidopsis. Segmental duplication and purifying selection were the major factors driving the evolution of GhPRXs. GO and KEGG enrichment analysis revealed that GhPRX genes were mainly associated with responding to oxidative stresses, peroxidase activities and phenylpropanoid biosynthesis pathways. Transcriptome data analysis showed that GhPRX genes expression were significantly different in microspore development between the sterility line-JinA and the maintainer line MB177. We confirmed the up-regulation of GhPRX107 and down-regulation of GhPRX128 in the sterile line compared to its maintainer line using qRT-PCR, suggesting their roles in pollen fertility. In addition, silencing GhPRX107 in cotton showed a significant decrease of the reactive oxygen species (ROS) levels of microsporocyte stage anthers compared to control. Overexpressing GhPRX107 in Arabidopsis significantly increased the ROS levels of anthers compared to wild type. In conclusion, we identified GhPRX107 as a determinant of ROS levels in anther. This work sets a foundation for PRX studies in pollen development. creator: Yi Chen creator: Jiajia Feng creator: Yunfang Qu creator: Jinlong Zhang creator: Li Zhang creator: Dong Liang creator: Yujie Yang creator: Jinling Huang uri: https://doi.org/10.7717/peerj.13635 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Chen et al. title: Recent advances in methods for in situ root phenotyping link: https://peerj.com/articles/13638 last-modified: 2022-07-01 description: Roots assist plants in absorbing water and nutrients from soil. Thus, they are vital to the survival of nearly all land plants, considering that plants cannot move to seek optimal environmental conditions. Crop species with optimal root system are essential for future food security and key to improving agricultural productivity and sustainability. Root systems can be improved and bred to acquire soil resources efficiently and effectively. This can also reduce adverse environmental impacts by decreasing the need for fertilization and fresh water. Therefore, there is a need to improve and breed crop cultivars with favorable root system. However, the lack of high-throughput root phenotyping tools for characterizing root traits in situ is a barrier to breeding for root system improvement. In recent years, many breakthroughs in the measurement and analysis of roots in a root system have been made. Here, we describe the major advances in root image acquisition and analysis technologies and summarize the advantages and disadvantages of each method. Furthermore, we look forward to the future development direction and trend of root phenotyping methods. This review aims to aid researchers in choosing a more appropriate method for improving the root system. creator: Anchang Li creator: Lingxiao Zhu creator: Wenjun Xu creator: Liantao Liu creator: Guifa Teng uri: https://doi.org/10.7717/peerj.13638 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Li et al. title: Genetic diversity of enterotoxigenic Bacillus cereus strains in coriander in southwestern Mexico link: https://peerj.com/articles/13667 last-modified: 2022-07-01 description: BackgroundCoriander, like other leafy green vegetables, is available all year round and is commonly consumed raw in Mexico as in other countries in the preparation of street or homemade food. Bacillus cereus (B. cereus) is a microorganism that can reach coriander because it is usually found in the soil and in some regions the vegetables are irrigated with polluted water. Therefore, the aim of this study was to determinate the presence of B. cereus in coriander used for human consumption in southwestern Mexico and determine the toxigenic profile, biofilm production, genes associated with the production of biofilms, sporulation rates, enzymatic profile, psychotropic properties, and genetic diversity of B. cereus.MethodsFresh coriander samples were collected from several vegetable retailers in different markets, microbiological analysis was performed. Molecular identification, genes related to the production of biofilm, and toxin gene profiling of B. cereus isolates were determined by PCR. The biofilm formation was measured by performing a crystal violet assay. The genetic diversity of B. cereus strains was determined by PCR of repetitive elements using oligonucleotide (GTG) 5.ResultsWe found a frequency of B. cereus in vegetables was 20% (13/65). In this study, no strains with genes for the HBL toxin were found. In the case of genes related to biofilms, the frequency was low for sipW [5.8%, (1/17)] and tasA [11.7%, (2/17)]. B. cereus strains produce a low amount of biofilm with sporulation rates around 80%. As for genetic diversity, we observed that strains isolated from the same market, but different vegetable retailers are grouped into clusters. In the coriander marketed in southwestern Mexico, were found B. cereus strains with genes associated with the production of diarrheal toxins. Together, these results show actual information about the state of art of B. cereus strains circulating in the southwestern of Mexico. creator: Daniel Alexander Castulo-Arcos creator: Roberto Adame-Gómez creator: Natividad Castro-Alarcón creator: Aketzalli Galán-Luciano creator: María Cristina Santiago Dionisio creator: Marco A. Leyva-Vázquez creator: Jose-Humberto Perez-Olais creator: Jeiry Toribio-Jiménez creator: Arturo Ramirez-Peralta uri: https://doi.org/10.7717/peerj.13667 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Castulo-Arcos et al. title: Manipulation of light quality is an effective tool to regulate photosynthetic capacity and fruit antioxidant properties of Solanum lycopersicum L. cv. ‘Microtom’ in a controlled environment link: https://peerj.com/articles/13677 last-modified: 2022-07-01 description: Light quality plays an essential role in setting plant structural and functional traits, including antioxidant compounds. This paper aimed to assess how manipulating the light spectrum during growth may regulate the photosynthetic activity and fruit bioactive compound synthesis in Solanum lycopersicum L. cv. ‘Microtom’ to improve plant physiological performance and fruit nutritional value. Plants were cultivated under three light quality regimes: red-green-blue LEDs (RGB), red-blue LEDs (RB) and white fluorescent lamps (FL), from sowing to fruit ripening. Leaf functional traits, photosynthetic efficiency, Rubisco and D1 protein expression, and antioxidant production in fruits were analyzed. Compared to FL, RGB and RB regimes reduced height and increased leaf number and specific leaf area, enhancing plant dwarf growth. The RGB regime improved photosynthesis and stomatal conductance despite lower biomass, favoring Rubisco synthesis and carboxylation rate than RB and FL regimes. The RB light produced plants with fewer flowers and fruits with a lower ascorbic acid amount but the highest polyphenol content, antioxidant capacity and SOD and CAT activities. Our data indicate that the high percentage of the green wavelength in the RGB regime promoted photosynthesis and reduced plant reproductive capacity compared to FL and RB. Conversely, the RB regime was the best in favoring the production of health-promoting compounds in tomato berries. creator: Ermenegilda Vitale creator: Violeta Velikova creator: Tsonko Tsonev creator: Giulia Costanzo creator: Roberta Paradiso creator: Carmen Arena uri: https://doi.org/10.7717/peerj.13677 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Vitale et al. title: Spatial distribution of soil nutrients and evaluation of cultivated land in Xuwen county link: https://peerj.com/articles/13239 last-modified: 2022-06-30 description: It is of great significance to promote the quantitative research of soil science and the implementation of precision agriculture. On this basis, taking Xuwen County as the research object, this paper comprehensively analyzed the soil characteristics of cultivated land in Xuwen County and clarify the soil nutrient content and spatial distribution characteristics of cultivated land in Xuwen County, this paper comprehensively applied the methods of geostatistics, geographic information system (GIS) and fuzzy mathematics, and referred to the cultivated land quality grade standard (GB/T 33469-2016), to analyze the soil characteristics and evaluate the soil fertility of this region. The results show that the optimal interpolation model of soil pH and available phosphorus (AP) is a Gaussian model, and the optimal interpolation model of soil organic matter (SOM), available nitrogen (AN) and available potassium (AK) is a J-Bessel model. In addition, the spatial correlation of AK is weak, whereas pH, SOM, AN and AP show moderate spatial correlation. The proportion of excellent, good, average, medium and poor comprehensive fertility index are 26.00%, 32.67%, 19.33%, 19.00% and 3.00%, respectively. The overall level of soil fertility in Xuwen County is above the average, and the fertility quality presents an obvious trend of high in the South and low in the North. Areas that above average fertility are mainly distributed in Maichen Town, Qujie Town, Nanshan Town and Chengbei Town. The results can provide theoretical basis for improving the utilization rate of chemical fertilizer, fine management of cultivated land and ecological environment in this region, which can help in decision-making of precision fertilization. creator: Chao Zheng creator: Xiaofei Yang creator: Zhiqiang Liu creator: Kexing Liu creator: Yongxiang Huang uri: https://doi.org/10.7717/peerj.13239 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zheng et al.