title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=595 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Future stem cell analysis: progress and challenges towards state-of-the art approaches in automated cells analysis link: https://peerj.com/articles/14513 last-modified: 2022-12-21 description: Background and AimsA microscopic image has been used in cell analysis for cell type identification and classification, cell counting and cell size measurement. Most previous research works are tedious, including detailed understanding and time-consuming. The scientists and researchers are seeking modern and automatic cell analysis approaches in line with the current in-demand technology.ObjectivesThis article provides a brief overview of a general cell and specific stem cell analysis approaches from the history of cell discovery up to the state-of-the-art approaches.MethodologyA content description of the literature study has been surveyed from specific manuscript databases using three review methods: manuscript identification, screening, and inclusion. This review methodology is based on Prism guidelines in searching for originality and novelty in studies concerning cell analysis.ResultsBy analysing generic cell and specific stem cell analysis approaches, current technology offers tremendous potential in assisting medical experts in performing cell analysis using a method that is less laborious, cost-effective, and reduces error rates.ConclusionThis review uncovers potential research gaps concerning generic cell and specific stem cell analysis. Thus, it could be a reference for developing automated cells analysis approaches using current technology such as artificial intelligence and deep learning. creator: Nurul Syahira Mohamad Zamani creator: Wan Mimi Diyana Wan Zaki creator: Zariyantey Abd Hamid creator: Aqilah Baseri Huddin uri: https://doi.org/10.7717/peerj.14513 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Mohamad Zamani et al. title: OPA1 supports mitochondrial dynamics and immune evasion to CD8+ T cell in lung adenocarcinoma link: https://peerj.com/articles/14543 last-modified: 2022-12-21 description: BackgroundMitochondrial fusion and fission were identified to play key roles during multiple biology process. Thus, we aim to investigate the roles of OPA1 in mitochondria fusion and immune evasion of non-small cell lung cancer cells.MethodsThe transcriptional activation of genes related to mitochondrial dynamics was determined by using multi-omics data in lung adenocarcinoma (LUAD). We elucidated the molecular mechanism and roles of OPA1 promoting lung cancer through single-cell sequencing and molecular biological experiments.ResultsHere, we found that copy number amplification of OPA1 and MFN1 were co-occurring and synergistically activated in tumor epithelial cells in lung cancer tissues. Both of OPA1 and MFN1 were highly expressed in LUAD tumor tissues and OPA1 high expression was associated with poor prognosis. In terms of mechanism, the damaged mitochondria activated the apoptotic signaling pathways, inducing cell cycle arrest and cell apoptosis. More interestingly, OPA1 deficiency damaged mitochondrial dynamics and further blocked the respiratory function to increase the sensitivity of tumor epithelial to CD8+ T cells in non-small cell lung cancer.ConclusionsOur study demonstrated the high co-occurrence of copy number amplification and co-expression of OPA1 and MFN1 in LUAD tissue, and further revealed the contribution of OPA1 in maintaining the mitochondria respiratory function and the ability of immune evasion to CD8+ T cells of LUAD. creator: Ying Wang creator: Yadong Li creator: Xuanwei Jiang creator: Yayun Gu creator: Hui Zheng creator: Xiaoxuan Wang creator: Haotian Zhang creator: Jixiang Wu creator: Yang Cheng uri: https://doi.org/10.7717/peerj.14543 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wang et al. title: The diversity, evolution, and development of setal morphologies in bumble bees (Hymenoptera: Apidae: Bombus spp.) link: https://peerj.com/articles/14555 last-modified: 2022-12-21 description: Bumble bees are characterized by their thick setal pile that imparts aposematic color patterns often used for species-level identification. Like all bees, the single-celled setae of bumble bees are branched, an innovation thought important for pollen collection. To date no studies have quantified the types of setal morphologies and their distribution on these bees, information that can facilitate understanding of their adaptive ecological function. This study defines several major setal morphotypes in the common eastern bumble bee Bombus impatiens Cresson, revealing these setal types differ by location across the body. The positions of these types of setae are similar across individuals, castes, and sexes within species. We analyzed the distribution of the two most common setal types (plumose and spinulate) across the body dorsum of half of the described bumble bee species. This revealed consistently high density of plumose (long-branched) setae across bumble bees on the head and mesosoma, but considerable variation in the amount of metasomal plumosity. Variation on the metasoma shows strong phylogenetic signal at subgeneric and smaller group levels, making it a useful trait for species delimitation research, and plumosity has increased from early Bombus ancestors. The distribution of these setal types suggests these setae may serve several functions, including pollen-collecting and thermoregulatory roles, and probable mechanosensory functions. This study further examines how and when setae of the pile develop, evidence for mechanosensory function, and the timing of pigmentation as a foundation for future genetic and developmental research in these bees. creator: Heather M. Hines creator: Shelby Kerrin Kilpatrick creator: István Mikó creator: Daniel Snellings creator: Margarita M. López-Uribe creator: Li Tian uri: https://doi.org/10.7717/peerj.14555 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Hines et al. title: Evaluation of primers for the detection of deadwood-inhabiting archaea via amplicon sequencing link: https://peerj.com/articles/14567 last-modified: 2022-12-21 description: Archaea have been reported from deadwood of a few different tree species in temperate and boreal forest ecosystems in the past. However, while one of their functions is well linked to methane production any additional contribution to wood decomposition is not understood and underexplored which may be also attributed to lacking investigations on their diversity in this substrate. With this current work, we aim at encouraging further investigations by providing aid in primer choice for DNA metabarcoding using Illumina amplicon sequencing. We tested 16S primer pairs on genomic DNA extracted from woody tissue of four temperate deciduous tree species. Three primer pairs were specific to archaea and one prokaryotic primer pair theoretically amplifies both, bacterial and archaeal DNA. Methanobacteriales and Methanomassiliicoccales have been consistently identified as dominant orders across all datasets but significant variability in ASV richness was observed using different primer combinations. Nitrososphaerales have only been identified when using archaea-specific primer sets. In addition, the most commonly applied primer combination targeting prokaryotes in general yielded the lowest relative proportion of archaeal sequences per sample, which underlines the fact, that using target specific primers unraveled a yet unknown diversity of archaea in deadwood. Hence, archaea seem to be an important group of the deadwood-inhabiting community and further research is needed to explore their role during the decomposition process. creator: Julia Moll creator: Björn Hoppe uri: https://doi.org/10.7717/peerj.14567 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Moll and Hoppe title: Physiological changes and gene responses during Ganoderma lucidum growth with selenium supplementation link: https://peerj.com/articles/14488 last-modified: 2022-12-20 description: Ganoderma lucidum basidiomycota is highly appreciated for its health and nutrition value. In the present study, Ganoderma lucidum was cultivated as selenium transformation carrier, and the physiological changes and gene responses by selenium supplementation were revealed through high-throughput RNA-Seq technology. As a result, selenium supplementation increased the stipe length and the cap size, but decreased the cap thickness of G. lucidum. Mineral salt supplementation could greatly promote the formation of triterpene acids and selenium in G. lucidum. The highest yield was gained in the treatment with selenium content of 200 µg/g. Subsequently, the tissues of G. lucidum at budding and mature stages in this treatment group were sampled for transcriptome analysis and compared to those of a control group without selenium supplementation. A total of 16,113 expressed genes were obtained from the transcriptome of G. lucidum, and GO-annotated unigenes were mainly involved in molecular functions and KEGG-annotated ones were highly expressed in ribosomal pathway. Furthermore, genes involved in carbon metabolism pathway were most promoted by selenium at budding stage of G. lucidum, while gene expression was the highest in the pathway of amino acid biosynthesis at mature stage of G. lucidum. Specially, selenium-related genes in G. lucidum, such as GL23172-G, GL29881-G and GL28298-G, played a regulatory role in oxidoreductase, antioxidant activity and tryptophan synthesis. The results provide a theoretical basis for further study of selenium-enriched mushrooms and aid to development of Se-enriched foodstuff and health products made from fungi. creator: Bo Zhang creator: Wei Tan creator: Jie Zhou creator: Lei Ye creator: Dinghong Jia creator: Xiaolin Li uri: https://doi.org/10.7717/peerj.14488 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhang et al. title: Influence of long-term participation in amateur sports on physical posture of teenagers link: https://peerj.com/articles/14520 last-modified: 2022-12-20 description: AimThe aim of this cross-sectional study was to explore the influence of long-term participating in amateur sports on body posture of school students.MethodsA survey on sport participation was conducted on 1,658 volunteer students aged from 6 to 17 years in two primary schools and one meddle school in Tianjin city. The PA200LE body posture evaluation system and a SpineScanSH-115 electronic spine measuring instrument were used to assess the participants’ body posture. According to the survey results and against the inclusion and exclusion criteria, 1,124 eligible participants were divided into seven sport participation groups and seven age-matched control groups for statistical comparisons.ResultsCompared with the age-matched controls, the natural standing thoracic kyphosis angle of the swimming group (35.0 ± 9.5 VS 31.2 ± 8.5; t =  − 2.560; p = 0.011) and the football group (34.6 ± 7.2 VS 31.9 ± 7.5; t =  − 2.754; p = 0.006) were found to be significantly larger; the natural standing lumbar lordosis angle (−23.0 ± 11.0 VS −27.0 ± 11.1; t = 0.344; p = 0.024) and the upright sitting lumbar lordosis angle (−11.7 ± 8.4 VS −15.2 ± 12.3; t = 5.738; p = 0.030) of the swimming group was significantly smaller; the upright sitting thoracic kyphosis angle of the running group (25.1 ± 9.3 VS 22.6 ± 9.9; t =  − 1.970; p = 0.050) was significantly larger; the upright sitting thoracic kyphosis angle (23.9 ± 8.9 VS 27.0 ± 7.6; t = 2.096; p = 0.038), the learning position thoracic kyphosis angle (31.0 ± 8.6 VS 37.1 ± 8.9; t = 3.076; p = 0.003), the shoulder level (−1.3 ± 2.1 VS 0.0 ± 2.5; t = 2.389; p = 0.019) and waist level (−1.2 ± 1.7 VS −0.3 ± 1.7; t = 2.511; p = 0.013) of the table tennis group were significantly smaller.ConclusionsThe results showed that long-term participation in recreational sports training had an impact on the physical posture of adolescents. creator: Yongchao Huang creator: Meiling Zhai creator: Shi Zhou creator: Yahong Jin creator: Li Wen creator: Yuqi Zhao creator: Xu Han uri: https://doi.org/10.7717/peerj.14520 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Huang et al. title: The effect of conventional and sustainable agricultural management practices on carbon and water fluxes in a Mexican semi-arid region link: https://peerj.com/articles/14542 last-modified: 2022-12-20 description: BackgroundAgriculture is essential for food security. However, conventional agriculture alters the water and carbon cycle and soil properties. We investigated the effect of conventional management (CM) and sustainable management (SM) on the carbon and water cycle in crops of nopal (Np) and wheat (Wh).MethodsA micrometeorological eddy covariance tower was installed to measure water use through evapotranspiration (ET) and the net exchange of CO2 during the crop’s development. Gross primary productivity (GPP), water use efficiency (WUE), and soil properties were obtained.ResultsThe results showed that both agricultural managements influenced the carbon flux of the ecosystem, with a lower GPP and Reco in the nopal field (1.85 and 0.99 mmol C m−2 s−1, respectively), compared to the wheat field (6.34 and 1.8 mmol C m−2 s−1, respectively). It was mainly attributed to the metabolic plant differences, phenological stages, and wheat biomass developed during the winter. On the other hand, the accumulated ET in the SM-Wh plots was lower than SM-Np. Therefore, the crops subjected to sustainable practices use water more efficiently with 1.42 and 1.03 g C m−3 H2O for nopal and wheat, respectively. In regard to soil properties, it was observed that tillage alters microbial activity affecting organic matter and carbon. It can be concluded that the differences in agricultural management for both crops altered the carbon and water cycle and soil quality. In addition, implementing good agricultural practices allows more efficient use of water by the plant, higher retention of water in the soil, and less ET. creator: Gabriela Guillen-Cruz creator: Roberto Torres-Arreola creator: Zulia Sanchez-Mejia creator: Dulce Flores-Renteria uri: https://doi.org/10.7717/peerj.14542 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Guillen-Cruz et al. title: Knockdown of hsa_circ_0008922 inhibits the progression of glioma link: https://peerj.com/articles/14552 last-modified: 2022-12-20 description: BackgroundA glioma is a tumor originating from glial cells in the central nervous system. Although significant progress has been made in diagnosis and treatment, most high-grade glioma patients are prone to recurrence. Therefore, molecular targeted therapy may become a new direction for adjuvant therapy in glioma. In recent years, many studies have revealed that circular RNA (circRNA) may play an important role in the occurrence and development of many tumors including gliomas. Our previous study found that the expression of hsa_circ_0008922 was up-regulated in glioma tissues upon RNA sequencing. The biological mechanism of circ_0008922 is still unreported in gliomas. Therefore, in this study, we preliminarily outlined the expression of hsa_circ_0008922 in glioma and explored its biological functions.MethodsThe expression of hsa_circ_0008922 in forty glioma tissues and four glioma cell lines (A172, U251, SF763 and U87) was detected by quantitative real-time polymerase chain reaction (qRT-PCR). The correlation between hsa_circ_0008922 expression and clinicopathological features of glioma patients was evaluated by Fisher’s exact test. To understand the potential function of hsa_circ_0008922 in glioma, we constructed small interfering RNA (siRNA) to hsa_circ_0008922 to downregulate its expression in glioma cell lines A172 and U251. With these hsa_circ_0008922 downregulated cells, a series of assays were carried out as follows. Cell proliferation was detected by CCK8 assay, migration and invasion were determined by wound healing assay and transwell assay, respectively. Colony formation ability was evaluated by plate clonogenic assay. Moreover, flow cytometry combined with Western blot was performed to analyze apoptosis status and the expression of apoptotic related proteins (caspase 3 and caspase 9). Finally, the possible biological pathways and potential miRNA targets of hsa_circ_0008922 were predicted by bioinformatics.ResultsWe found that the expression of hsa_circ_0008922 in glioma tissues was 3.4 times higher than that in normal tissues. The expression of has_circ_0008922 was correlated with WHO tumor grade. After down-regulating the expression of hsa_circ_0008922, malignant biological behavior of glioma cells was inhibited, such as cell proliferation, colony formation, migration, and invasion. At the same time, it also induced apoptosis of glioma cells. Predicted analysis by bioinformatics demonstrated that hsa_circ_0008922 may be involved in tumor-related pathways by acting as a molecular sponge for multiple miRNAs (hsa-let-7e-5p, hsa-miR-506-5p, hsa-let-7b-5p, hsa-let-7c-5p and hsa-let-7a-5p). Finally, we integrated our observation to build a circRNA-miRNA-mRNA predictive network. creator: Chunhong Xue creator: Chang Liu creator: Xiang Yun creator: Xiaoqiong Zou creator: Xin Li creator: Ping Wang creator: Feng Li creator: Yingying Ge creator: Qingmei Zhang creator: Xiaoxun Xie creator: Xisheng Li creator: Bin Luo uri: https://doi.org/10.7717/peerj.14552 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Xue et al. title: Effects of calcium on cell wall metabolism enzymes and expression of related genes associated with peel creasing in Citrus fruits link: https://peerj.com/articles/14574 last-modified: 2022-12-20 description: Fruit peel creasing is a serious pre-harvest physiological disorder in citrus, influencing fruit quality, storage, and yield. Four- and eight-year-old ‘Hongjiang’ oranges grafted onto Canton lemon rootstocks were treated with calcium and calcium inhibitors, respectively, to study the effects of different treatments on fruit creasing rate, mechanical properties of the peel, cell wall metabolism enzyme activities, and the expression of related genes. Foliar application of 0.5% calcium nitrate significantly reduced the fruit creasing rate, while treatment with EGTA and LaCl3, inhibitors of calcium uptake, increased the fruit creasing rate; But the effect of calcium nitrate treatment on changing the mechanical properties of pericarp and inhibiting the activity of hydrolase (PG, Cx and PE) was not very significant. Furthermore, it was observed that the expression levels of genes (PG, Cx, and PE) encoding cell wall-degrading enzymes were significantly lower in the normal fruit peel than in the creased fruit peel. Meanwhile, the expression levels of PG, Cx, and PE were higher in the peel of shaded fruit than in the peel of exposed fruit. During the high incidence period of fruit creasing, calcium nitrate treatment down-regulated the expression of PG, Cx, and PE, while EGTA treatment up-regulated the expression of these genes. In conclusion, foliar spraying of calcium nitrate at the fruit rapid enlargement stage can increase the Ca content in the peel of ‘Hongjiang’ orange and significantly suppress the expression of cell wall degrading enzymes genes (PG, PE and Cx) in ‘Hongjiang’ orange peel during the high occurrence period of fruit creasing, resulting in reducing the occurrence of fruit creasing and cracking. creator: Bin Huai creator: Yunli Wu creator: Chunhui Liang creator: Panfeng Tu creator: Tingting Mei creator: Anquan Guan creator: Qing Yao creator: Juan Li creator: Jiezhong Chen uri: https://doi.org/10.7717/peerj.14574 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Huai et al. title: Opening the black box of bird-window collisions: passive video recordings in a residential backyard link: https://peerj.com/articles/14604 last-modified: 2022-12-20 description: Collisions with windows on buildings are a major source of bird mortality. The current understanding of daytime collisions is limited by a lack of empirical data on how collisions occur in the real world because most data are collected by recording evidence of mortality rather than pre-collision behaviour. Based on published literature suggesting a causal relationship between bird collision risk and the appearance of reflections on glass, the fact that reflections vary in appearance depending on viewing angle, and general principles of object collision kinematics, we hypothesized that the risk and lethality of window collisions may be related to the angle and velocity of birds’ flight. We deployed a home security camera system to passively record interactions between common North American bird species and residential windows in a backyard setting over spring, summer and fall seasons over 2 years. We captured 38 events including 29 collisions and nine near-misses in which birds approached the glass but avoided impact. Only two of the collisions resulted in immediate fatality, while 23 birds flew away immediately following impact. Birds approached the glass at variable flight speeds and from a wide range of angles, suggesting that the dynamic appearance of reflections on glass at different times of day may play a causal role in collision risk. Birds that approached the window at higher velocity were more likely to be immediately killed or stunned. Most collisions were not detected by the building occupants and, given that most birds flew away immediately, carcass surveys would only document a small fraction of window collisions. We discuss the implications of characterizing pre-collision behaviour for designing effective collision prevention methods. creator: Brendon Samuels creator: Brock Fenton creator: Esteban Fernández-Juricic creator: Scott A. MacDougall-Shackleton uri: https://doi.org/10.7717/peerj.14604 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Samuels et al.