title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=308 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: The unexpected effect of the compound microbial agent NP-M2 on microbial community dynamics in a nonylphenol-contaminated soil: the self-stability of soil ecosystem link: https://peerj.com/articles/17424 last-modified: 2024-05-30 description: BackgroundNonylphenol (NP) is widely recognized as a crucial environmental endocrine-disrupting chemical and persistent toxic substance. The remediation of NP-contaminated sites primarily relies on biological degradation. Compound microbial products, as opposed to pure strains, possess a greater variety of metabolic pathways and can thrive in a wider range of environmental conditions. This characteristic is believed to facilitate the synergistic degradation of pollutants. Limited research has been conducted to thoroughly examine the potential compatibility of compound microbial agents with indigenous microflora, their ability to function effectively in practical environments, their capacity to enhance the dissipation of NP, and their potential to improve soil physicochemical and biological characteristics.MethodsIn order to efficiently eliminate NP in contaminated soil in an eco-friendly manner, a simulation study was conducted to investigate the impact of bioaugmentation using the functional compound microbial agent NP-M2 at varying concentrations (50 and 200 mg/L) on the dynamics of the soil microbial community. The treatments were set as follows: sterilized soil with 50 mg/kg NP (CK50) or 200 mg/kg NP (CK200); non-sterilized soil with 50 mg/kg NP (TU50) or 200 mg/kg NP (TU200); non-sterilized soil with the compound microbial agent NP-M2 at 50 mg/kg NP (J50) or 200 mg/kg NP (J200). Full-length 16S rRNA analysis was performed using the PacBio Sequel II platform.ResultsBoth the indigenous microbes (TU50 and TU200 treatments) and the application of NP-M2 (J50 and J200 treatments) exhibited rapid NP removal, with removal rates ranging from 93% to 99%. The application of NP-M2 further accelerated the degradation rate of NP for a subtle lag period. Although the different treatments had minimal impacts on the soil bacterial α-diversity, they significantly altered the β-diversity and composition of the bacterial community. The dominant phyla were Proteobacteria (35.54%–44.14%), Acidobacteria (13.55%–17.07%), Planctomycetes (10.78%–11.42%), Bacteroidetes (5.60%–10.74%), and Actinobacteria (6.44%–8.68%). The core species were Luteitalea_pratensis, Pyrinomonas_methylaliphatogenes, Fimbriiglobus_ruber, Longimicrobium_terrae, and Massilia_sp003590855. The bacterial community structure and taxon distribution in polluted soils were significantly influenced by the activities of soil catalase, sucrase, and polyphenol oxidase, which were identified as the major environmental factors. Notably, the concentration of NP and, to a lesser extent, the compound microbial agent NP-M2 were found to cause major shifts in the bacterial community. This study highlights the importance of conducting bioremediation experiments in conjunction with microbiome assessment to better understand the impact of bioaugmentation/biostimulation on the potential functions of complex microbial communities present in contaminated soils, which is essential for bioremediation success. creator: Zhaoliang Chen creator: Juanqin Zhang creator: Weiguang Lv creator: Hanlin Zhang creator: Shuangxi Li creator: Haiyun Zhang creator: Yue Shen creator: Chunnu Geng creator: Naling Bai uri: https://doi.org/10.7717/peerj.17424 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Chen et al. title: Sucrose rinse modulates the salivary behavior of carbonic anhydrase VI and its buffering capacity: a longitudinal study in 4 to 6.5-year-old children link: https://peerj.com/articles/17429 last-modified: 2024-05-30 description: BackgroundCarbonic anhydrase VI (CA VI) is crucial in regulating oral pH and predicting susceptibility to dental caries. The hypothesis posits that caries activity may alter the CA VI function, diminishing its capacity to regulate pH effectively and potentially exacerbating cariogenic challenges. This 1-year cohort study sought to investigate the enzymatic activity of salivary CA VI and buffering capacity following a 20% sucrose rinse in 4 to 6.5-year-old children.MethodThis research involved 46 volunteers categorized into three groups based on their caries status after follow-up: caries-free (CFee), arrested caries (CArrested), and caries active (CActive). Children underwent visible biofilm examination and saliva collection for salivary flow rate, buffering capacity, and CA VI analyses before and after a 20% sucrose rinse.ResultsA reduction in the buffering capacity was observed after sucrose rinse in all groups. The CA VI activity decreased significantly in CFee and CArrested groups after sucrose rinse, although it did not change in the CActive group. An improvement in the buffering capacity and salivary flow rate was found at follow-up when compared with the baseline. After 1-year follow-up, buffering capacity and salivary flow rate increased in all groups, whilst the CA VI activity reduced only in CFree and CArrested children.ConclusionSucrose rinse universally reduces the salivary buffering capacity, while caries activity may disrupt CA VI activity response during a cariogenic challenge. After a year, increased salivary flow enhances buffering capacity but not CA VI activity in caries-active children. creator: Thayse Rodrigues de Souza creator: Bruna Raquel Zancope creator: Emerson Tavares de Sousa creator: Thais Manzano Parisotto creator: Marcelo Rocha Marques creator: Marinês Nobre dos Santos uri: https://doi.org/10.7717/peerj.17429 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Souza et al. title: Crizotinib inhibits the metabolism of tramadol by non-competitive suppressing the activities of CYP2D1 and CYP3A2 link: https://peerj.com/articles/17446 last-modified: 2024-05-30 description: ObjectivesTo investigate the interaction between tramadol and representative tyrosine kinase inhibitors, and to study the inhibition mode of drug-interaction.MethodsLiver microsomal catalyzing assay was developed. Sprague-Dawley rats were administrated tramadol with or without selected tyrosine kinase inhibitors. Samples were prepared and ultra-performance liquid chromatography–tandem mass spectrometry (UPLC-MS/MS) was used for analysis. Besides, liver, kidney, and small intestine were collected and morphology was examined by hematoxyline-eosin (H&E) staining. Meanwhile, liver microsomes were prepared and carbon monoxide differential ultraviolet radiation (UV) spectrophotometric quantification was performed.ResultsAmong the screened inhibitors, crizotinib takes the highest potency in suppressing the metabolism of tramadol in rat/human liver microsome, following non-competitive inhibitory mechanism. In vivo, when crizotinib was co-administered, the AUC value of tramadol increased compared with the control group. Besides, no obvious pathological changes were observed, including cell morphology, size, arrangement, nuclear morphology with the levels of alanine transaminase (ALT) and aspartate transaminase (AST) increased after multiple administration of crizotinib. Meanwhile, the activities of CYP2D1 and CYP3A2 as well as the total cytochrome P450 abundance were found to be decreased in rat liver of combinational group.ConclusionsCrizotinib can inhibit the metabolism of tramadol. Therefore, this recipe should be vigilant to prevent adverse reactions. creator: Nanyong Gao creator: Xiaoyu Xu creator: Feng Ye creator: Xin-yue Li creator: Chengqi Lin creator: Xiu-wei Shen creator: Jianchang Qian uri: https://doi.org/10.7717/peerj.17446 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Gao et al. title: Analysis of rotational grazing management for sheep in mixed grassland link: https://peerj.com/articles/17453 last-modified: 2024-05-30 description: Sown mixed grassland is rarely used for livestock raising and grazing; however, different forages can provide various nutrients for livestock, which may be beneficial to animal health and welfare. We established a sown mixed grassland and adopted a rotational grazing system, monitored the changes in aboveground biomass and sheep weights during the summer grazing period, measured the nutrients of forage by near-infrared spectroscopy, tested the contents of medium- and long-chain fatty acids by gas chromatography, and explored an efficient sheep fattening system that is suitable for agro-pastoral interlacing areas. The results showed that the maximum forage supply in a single grazing paddock was 4.6 kg DM/d, the highest dry matter intake (DMI) was 1.80 kg DM/ewe/d, the average daily weight gain (ADG) was 193.3 g, the DMI and ADG were significantly correlated (P < 0.05), and the average feed weight gain ratio (F/G) reached 8.02. The average crude protein and metabolizable energy intake by sheep were 286 g/ewe/d and 18.5 MJ/ewe/d respectively, and the n-6/n-3 ratio of polyunsaturated fatty acids in mutton was 2.84. The results indicated that the sheep fattening system had high feed conversion efficiency, could improve the yield and quality of sheep, and could be promoted in suitable regions. creator: Zongyong Tong creator: Xianlin Dai creator: Yu Wang creator: Xianglin Li creator: Feng He creator: Guomei Yin uri: https://doi.org/10.7717/peerj.17453 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Tong et al. title: Genomic insights into CKX genes: key players in cotton fibre development and abiotic stress responses link: https://peerj.com/articles/17462 last-modified: 2024-05-30 description: Cytokinin oxidase/dehydrogenase (CKX), responsible for irreversible cytokinin degradation, also controls plant growth and development and response to abiotic stress. While the CKX gene has been studied in other plants extensively, its function in cotton is still unknown. Therefore, a genome-wide study to identify the CKX gene family in the four cotton species was conducted using transcriptomics, quantitative real-time PCR (qRT-PCR) and bioinformatics. As a result, in G. hirsutum and G. barbadense (the tetraploid cotton species), 87 and 96 CKX genes respectively and 62 genes each in G. arboreum and G. raimondii, were identified. Based on the evolutionary studies, the cotton CKX gene family has been divided into five distinct subfamilies. It was observed that CKX genes in cotton have conserved sequence logos and gene family expansion was due to segmental duplication or whole genome duplication (WGD). Collinearity and multiple synteny studies showed an expansion of gene families during evolution and purifying selection pressure has been exerted. G. hirsutum CKX genes displayed multiple exons/introns, uneven chromosomal distribution, conserved protein motifs, and cis-elements related to growth and stress in their promoter regions. Cis-elements related to resistance, physiological metabolism and hormonal regulation were identified within the promoter regions of the CKX genes. Expression analysis under different stress conditions (cold, heat, drought and salt) revealed different expression patterns in the different tissues. Through virus-induced gene silencing (VIGS), the GhCKX34A gene was found to improve cold resistance by modulating antioxidant-related activity. Since GhCKX29A is highly expressed during fibre development, we hypothesize that the increased expression of GhCKX29A in fibres has significant effects on fibre elongation. Consequently, these results contribute to our understanding of the involvement of GhCKXs in both fibre development and response to abiotic stress. creator: Rasmieh Hamid creator: Feba Jacob creator: Zahra Ghorbanzadeh creator: Mojtaba Khayam Nekouei creator: Mehrshad Zeinalabedini creator: Mohsen Mardi creator: Akram Sadeghi creator: Sushil Kumar creator: Mohammad Reza Ghaffari uri: https://doi.org/10.7717/peerj.17462 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Hamid et al. title: Regulation of dye-decolorizing peroxidase gene expression in Pleurotus ostreatus grown on glycerol as the carbon source link: https://peerj.com/articles/17467 last-modified: 2024-05-30 description: Dye-decolorizing peroxidases (DyPs) (E.C. 1.11.1.19) are heme peroxidases that catalyze oxygen transfer reactions similarly to oxygenases. DyPs utilize hydrogen peroxide (H2O2) both as an electron acceptor co-substrate and as an electron donor when oxidized to their respective radicals. The production of both DyPs and lignin-modifying enzymes (LMEs) is regulated by the carbon source, although less readily metabolizable carbon sources do improve LME production. The present study analyzed the effect of glycerol on Pleurotus ostreatus growth, total DyP activity, and the expression of three Pleos-dyp genes (Pleos-dyp1, Pleos-dyp2 and Pleos-dyp4), via real-time RT-qPCR, monitoring the time course of P. ostreatus cultures supplemented with either glycerol or glucose and Acetyl Yellow G (AYG) dye. The results obtained indicate that glycerol negatively affects P. ostreatus growth, giving a biomass production of 5.31 and 5.62 g/L with respective growth rates (micra; m) of 0.027 and 0.023 h−1 for fermentations in the absence and presence of AYG dye. In contrast, respective biomass production levels of 7.09 and 7.20 g/L and growth rates (μ) of 0.033 and 0.047 h−1 were observed in equivalent control fermentations conducted with glucose in the absence and presence of AYG dye. Higher DyP activity levels, 4,043 and 4,902 IU/L, were obtained for fermentations conducted on glycerol, equivalent to 2.6-fold and 3.16-fold higher than the activity observed when glucose is used as the carbon source. The differential regulation of the DyP-encoding genes in P. ostreatus were explored, evaluating the carbon source, the growth phase, and the influence of the dye. The global analysis of the expression patterns throughout the fermentation showed the up- and down- regulation of the three Pleos-dyp genes evaluated. The highest induction observed for the control media was that found for the Pleos-dyp1 gene, which is equivalent to an 11.1-fold increase in relative expression (log2) during the stationary phase of the culture (360 h), and for the glucose/AYG media was Pleos-dyp-4 with 8.28-fold increase after 168 h. In addition, glycerol preferentially induced the Pleos-dyp1 and Pleos-dyp2 genes, leading to respective 11.61 and 4.28-fold increases after 144 h. After 360 and 504 h of culture, 12.86 and 4.02-fold increases were observed in the induction levels presented by Pleos-dyp1 and Pleos-dyp2, respectively, in the presence of AYG. When transcription levels were referred to those found in the control media, adding AYG led to up-regulation of the three dyp genes throughout the fermentation. Contrary to the fermentation with glycerol, where up- and down-regulation was observed. The present study is the first report describing the effect of a less-metabolizable carbon source, such as glycerol, on the differential expression of DyP-encoding genes and their corresponding activity. creator: Jorge Cuamatzi-Flores creator: Soley Nava-Galicia creator: Edgardo Ulises Esquivel-Naranjo creator: Agustin Lopez Munguia creator: Analilia Arroyo-Becerra creator: Miguel Angel Villalobos-López creator: Martha Bibbins-Martínez uri: https://doi.org/10.7717/peerj.17467 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Cuamatzi-Flores et al. title: Exogenous silicon induces aluminum tolerance in white clover (Trifolium repens) by reducing aluminum uptake and enhancing organic acid secretion link: https://peerj.com/articles/17472 last-modified: 2024-05-30 description: Excessive aluminum (Al) in acidic soils is a primary factor that hinders plant growth. The objective of the present study was to investigate the effect and physiological mechanism of exogenous silicon (Si) in alleviating aluminum toxicity. Under hydroponic conditions, 4 mM Al significantly impeded the growth of white clover; however, pretreatments with 1 mM Si mitigated this inhibition, as evidenced by notable changes in growth indicators and physiological parameters. Exogenous silicon notably increased both shoot and root length of white clover and significantly decreased electrolyte leakage (EL) and malondialdehyde (MDA) content compared to aluminum treatments. This positive effect was particularly evident in the roots. Further analysis involving hematoxylin staining, scanning electron microscopy (SEM), and examination of organic acids (OAs) demonstrated that silicon relieved the accumulation of bioactive aluminum and ameliorated damage to root tissues in aluminum-stressed plants. Additionally, energy-dispersive X-ray (EDX) analysis revealed that additional silicon was primarily distributed in the root epidermal and cortical layers, effectively reducing the transport of aluminum and maintaining the balance of exchangeable cations absorption. These findings suggest that gradual silicon deposition in root tissues effectively prevents the absorption of biologically active aluminum, thereby reducing the risk of mineral nutrient deficiencies induced by aluminum stress, promoting organic acids exudation, and compartmentalizing aluminum in the outer layer of root tissues. This mechanism helps white clover alleviate the damage caused by aluminum toxicity. creator: Weiqiang Yang creator: Huahao Feng creator: Jianzhen Zhou creator: Tong Jia creator: Tao Tang creator: Han Zhang creator: Yan Peng uri: https://doi.org/10.7717/peerj.17472 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Yang et al. title: Exploring Barbronia species diversity and phylogenetic relationship within Suborder Erpobdelliformes (Clitellata: Annelida) link: https://peerj.com/articles/17480 last-modified: 2024-05-30 description: BackgroundBarbronia, a genus of freshwater macrophagous leeches, belongs to Erpobdelliformes (Salifidae: Clitellata: Annelida), and B. weberi, a well-known leech within this genus, has a worldwide distribution. However, the systematics of Barbronia have not yet been adequately investigated, primarily due to a few molecular markers, and only 20 Barbronia sequences available in the GenBank database. This gap significantly limits our understanding of the Barbronia species identification, as well as the phylogenetic placement of the genus Barbronia within Salifidae.MethodsNext-generation sequencing (NGS) was used to simultaneously capture the entire mitochondrial genome and the full-length 18S/28S rDNA sequences. The species boundary of Barbronia species was estimated using bGMYC and bPTP methods, based on all available Barbronia COI sequences. Uncorrected COI p-distance was calculated in MEGA. A molecular data matrix consisting of four loci (COI, 12S, 18S, and 28S rDNA) for outgroups (three Haemopis leeches) and 49 erpobdellid leeches, representing eight genera within the Suborder Erpobdelliformes was aligned using MAFFT and LocARNA. This matrix was used to reconstruct the phylogenetic relationship of Barbronia via Bayesian inference (BI) and the maximum likelihood (ML) method.ResultsThe full lengths of the mitochondrial genome, 18S and 28S rDNAs of B. cf. gwalagwalensis, are 14847 bp, 1876 bp 1876 bp, and 2863 bp, respectively. Both bGMYC and bPTP results based on COI data are generally congruent, suggesting that the previously proposed taxa (B. arcana, B. weberi formosana, and B. wuttkei or Erpobdella wuttkei) are synonyms of B. weberi. The specimens listed in the B. gwalagwalensis group, however, are split into at least two Primary Species Hypotheses (PSHs). The p-distance of the first PSH is less than 1.3% but increased to 4.5% when including the secondary PSH (i.e., B. cf. gwalagwalensis). In comparison, the interspecific p-distance between the B. weberi group and the B. gwalagwalensis group ranged from 6.4% to 8.7%, and the intraspecific p-distance within the B. weberi group is less than 0.8%. Considering the species delimitation results and the sufficient large p-distance, the specimen sampled in China is treated as B. cf. gwalagwalensis. The monophyly of the four Erpobdelliformes families Salifidae, Orobdellidae, Gastrostomobdellidae sensu stricto and Erpobdellidae is well supported in ML and BI analysis based on a data of four markers. Within the Salifidae, a well-supported Barbronia is closely related to a clade containing Odontobdella and Mimobdella, and these three genera are sister to a clade consisted of Salifa and Linta. According to the results of this study, the strategy of simultaneous obtaining both whole mitochondria and nuclear markers from extensively sampled Salifids species using NGS is expected to fathom both the species diversity of B. gwalagwalensis and the evolutionary relationship of Salifidae. creator: Yingkui Liu creator: Xinxin Fu creator: Yu Wang creator: Jing Liu creator: Yong Liu creator: Chong Li creator: Jiajia Dong uri: https://doi.org/10.7717/peerj.17480 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Liu et al. title: Reassessment of pore occlusion in some diatom taxa with re-evaluation of Placoneis Mereschkowsky (Bacillariophyceae: Cymbellales) and description of two new genera link: https://peerj.com/articles/17278 last-modified: 2024-05-29 description: In this article, the history and taxonomy of Placoneis gastrum, the type species of the genus Placoneis, was discussed. We investigated the structure of pore occlusions in Placoneis and related genera. As a result, we propose a new classification for tectulum-like types of pore occlusions. The new classification is congruent with previously-published and newly-constructed phylogenies based on molecular data. Based on the different structures of the pore occlusions, species of Placoneis are transferred to Witkowskia gen. nov. Hence, 168 new combinations are introduced. A new diatom species, with a similar morphology to Placoneis flabellata, was discovered in Bắc Kạn Province, Vietnam. It is described in this article as Chudaevia densistriata sp. nov. Placoneis flabellata is transferred to Chudaevia gen. nov. We also illustrate Placoneis flabellata herein and compare it to Chudaevia densistriata sp. nov. An unknown diatom, similar to Placoneis coloradensis, was discovered in Chukotka, Russia. It is introduced as Placoneis elinae sp. nov. below. Additionally, we discuss the distribution of some species of Witkowskia gen. nov. and Chudaevia gen. nov. creator: Andrei Mironov creator: Anton Glushchenko creator: Yevhen Maltsev creator: Sergey Genkal creator: Irina Kuznetsova creator: John Patrick Kociolek creator: Yan Liu creator: Maxim Kulikovskiy uri: https://doi.org/10.7717/peerj.17278 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Mironov et al. title: Investigating molecular markers linked to acute myocardial infarction and cuproptosis: bioinformatics analysis and validation in the AMI mice model link: https://peerj.com/articles/17280 last-modified: 2024-05-29 description: Cuproptosis-related key genes play a significant role in the pathological processes of acute myocardial infarction (AMI). However, a complete understanding of the molecular mechanisms behind this participation remains elusive. This study was designed to identify genes and immune cells critical to AMI pathogenesis. Based on the GSE48060 dataset (31 AMI patients and 21 healthy persons, GPL570-55999), we identified genes associated with dysregulated cuproptosis and the activation of immune responses between normal subjects and patients with a first myocardial attack. Two molecular clusters associated with cuproptosis were defined in patients with AMI. Immune infiltration analysis showed that there was significant immunity heterogeneity among different clusters. Multiple immune responses were closely associated with Cluster2-specific differentially expressed genes (DEGs). The generalized linear model machine model presented the best discriminative performance with relatively lower residual and root mean square error, and a higher area under the curve (AUC = 0.870). A final two-gene-based generalized linear model was constructed, exhibiting satisfactory performance in two external validation datasets (AUC = 0.719, GSE66360 and AUC = 0.856, GSE123342). Column graph, calibration curve, and decision curve analyses also proved the accuracy of AMI prediction. We also constructed a mouse C57BL/6 model of AMI (3 h, 48 h, and 1 week) and used qRT-PCR and immunofluorescence to detect the expression changes of CBLB and ZNF302. In this study, we present a systematic analysis of the complex relationship between cuproptosis and a first AMI attack, and provide new insights into the diagnosis and treatment of AMI. creator: Bingyu Wang creator: Jianqing Zhou creator: Ning An uri: https://doi.org/10.7717/peerj.17280 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Wang et al.