title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=366 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Organic fertilizer type and dose affect growth, morphological and physiological parameters, and mineral nutrition of watermelon seedlings link: https://peerj.com/articles/16902 last-modified: 2024-02-21 description: BackgroundOrganic agriculture has grown rapidly in recent years due to its environmental friendliness, sustainability, and improved farm profitability. Transplants are commonly used for fruits and vegetables to achieve consistent quality, uniformity, and easy field spacing control. The efficacy and optimal amounts of fertilizers for organic transplant production need to be investigated.MethodsThe effects of three organic fertilizers (Sustane 4-6-4, Nature Safe 7-7-7, and Dramatic 2-4-1) and one conventional fertilizer Peters Professional 20-20-20 (Conventional) with four doses (nitrogen (N) content was matched among fertilizers in each level, as 0.14 g/L, 0.28 g/L, 0.56 g/L, and 0.84 g/L N, respectively) on watermelon seedlings were compared in this study.ResultsThe results showed that all organic fertilizer treatments were not significantly different from the Conventional group in terms of watermelon germination. The only exception was the highest dose of Sustane 4-6-4 (0.84 g/L N) which decreased the germination rate and relative emergence index. Generally, growth index, shoot fresh and dry weights, true leaf number, and stem diameter increased as the amount of N increased within each fertilizer type. The best shoot growth was observed in the highest doses of Conventional and Dramatic 2-4-1 treatments (0.84 g/L N). However, Dramatic 2-4-1 treatments resulted in the lowest root growth when compared to other fertilizers at the same N dose. The second highest fertilization dose (0.56 g/L N) of Sustane 4-6-4 had the best root growth according to root fresh weight, root volume, root area, total root length, as well as the numbers of root tip and crossing when compared to other treatments. For seedlings, a well-developed root system can ensure a good seedling establishment and high survival rate under stressful field conditions after transplanting. Thus, Sustane 4-6-4 at 14 g/L (0.56 g/L N) is recommended to produce high-quality organic watermelon seedlings among the treatments applied in this study. creator: Qianwen Zhang creator: Joseph Masabni creator: Genhua Niu uri: https://doi.org/10.7717/peerj.16902 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhang et al. title: Repair protocols for indirect monolithic restorations: a literature review link: https://peerj.com/articles/16942 last-modified: 2024-02-21 description: Despite the advancements in indirect monolithic restorations, technical complications may occur during function. To overcome this issues, intraoral repair using resin composite is a practical and low-cost procedure, being able to increase the restoration’s longevity. This review aimed to evaluate the need for repair and suggest a standardized repair protocol to the main indirect restorative materials. For this, studies were surveyed from PubMed with no language or date restriction, to investigate the scientific evidence of indirect monolithic restoration repair with direct resin composite. A classification to guide clinical decisions was made based on the FDI World Dental Federation criteria about defective indirect restorations considering esthetic and functional standards, along with the patient’s view, to decide when polishing, repairing or replacing a defective restoration. Based on 38 surveyed studies, different resin composite intraoral repair protocols, that included mechanical and chemical aspects, were defined depending on the substrate considering resin-based, glass-ceramic or zirconia restorations. The presented criteria and protocols were developed to guide the clinician’s decision-making process regarding defective indirect monolithic restorations, prolonging longevity and increasing clinical success. creator: Lucas Saldanha da Rosa creator: Rafaela Oliveira Pilecco creator: Pablo Machado Soares creator: Marília Pivetta Rippe creator: Gabriel Kalil Rocha Pereira creator: Luiz Felipe Valandro creator: Cornelis Johannes Kleverlaan creator: Albert J. Feilzer creator: João Paulo Mendes Tribst uri: https://doi.org/10.7717/peerj.16942 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 da Rosa et al. title: Biological and growth parameters of Plotosus lineatus in the Mediterranean Sea link: https://peerj.com/articles/16945 last-modified: 2024-02-21 description: This study examined the age distribution and growth characteristics of the striped eel catfish (Plotosus lineatus), which is an invasive alien species in the eastern Mediterranean. A total of 1,011 samples were collected from Iskenderun Bay (Turkey), with lengths ranging from 5.1 to 16.8 cm, predominantly comprising females (1:1.92). Age 3 represented the majority in the population (52.03%). The value of the scaling exponent “b” of the length-weight relationship was less than “3” for both sexes (females: 2.28; males: 2.26; combined: 2.27). The results for the von Bertalanffy growth parameters were observed for the combined sexes as, L∞ = 24.9934 cm, k = 0.1718 year−1, and t₀ = −1.7707 years. The striped eel catfish populations in Iskenderun Bay exhibited negative allometric growth patterns and were predominantly composed of adult individuals. This study presents the dataset on the length-weight correlations, age-growth characteristics, and von Bertalanffy growth parameters of Plotosus lineatus in the Mediterranean Sea, thereby significantly contributing to comprehending the stock dynamics. It is anticipated that this study will make a significant contribution to the management of P. lineatus stocks, given its invasive nature. creator: Servet Ahmet Doğdu creator: Cemal Turan uri: https://doi.org/10.7717/peerj.16945 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Doğdu and Turan title: MX1 and UBE2L6 are potential metaflammation gene targets in both diabetes and atherosclerosis link: https://peerj.com/articles/16975 last-modified: 2024-02-21 description: BackgroundThe coexistence of diabetes mellitus (DM) and atherosclerosis (AS) is widespread, although the explicit metabolism and metabolism-associated molecular patterns (MAMPs) responsible for the correlation are still unclear.MethodsTwenty-four genetically wild-type male Ba-Ma mini pigs were randomly divided into five groups distinguished by different combinations of 90 mg/kg streptozotocin (STZ) intravenous injection and high-cholesterol/lipid (HC) or high-lipid (HL) diet feeding for 9 months in total. Pigs in the STZ+HC and STZ+HL groups were injected with STZ first and then fed the HC or HL diet for 9 months. In contrast, pigs in the HC+STZ and HL+STZ groups were fed the HC or HL diet for 9 months and injected with STZ at 3 months. The controls were only fed a regular diet for 9 months. The blood glucose and abdominal aortic plaque observed through oil red O staining were used as evaluation indicators for successful modelling of DM and AS. A microarray gene expression analysis of all subjects was performed.ResultsAtherosclerotic lesions were observed only in the HC+STZ and STZ+HC groups. A total of 103 differentially expressed genes (DEGs) were identified as common between them. The most significantly enriched pathways of 103 common DEGs were influenza A, hepatitis C, and measles. The global and internal protein–protein interaction (PPI) networks of the 103 common DEGs consisted of 648 and 14 nodes, respectively. The top 10 hub proteins, namely, ISG15, IRG6, IRF7, IFIT3, MX1, UBE2L6, DDX58, IFIT2, USP18, and IFI44L, drive aspects of DM and AS. MX1 and UBE2L6 were the intersection of internal and global PPI networks. The expression of MX1 and UBE2L6 was 507.22 ± 342.56 and 96.99 ± 49.92 in the HC+STZ group, respectively, which was significantly higher than others and may be linked to the severity of hyperglycaemia-related atherosclerosis. Further PPI network analysis of calcium/micronutrients, including MX1 and UBE2L6, consisted of 58 and 18 nodes, respectively. The most significantly enriched KEGG pathways were glutathione metabolism, pyrimidine metabolism, purine metabolism, and metabolic pathways.ConclusionsThe global and internal PPI network of the 103 common DEGs consisted of 648 and 14 nodes, respectively. The intersection of the nodes of internal and global PPI networks was MX1 and UBE2L6, suggesting their key role in the comorbidity mechanism of DM and AS. This inference was partly verified by the overexpression of MX1 and UBE2L6 in the HC+STZ group but not others. Further calcium- and micronutrient-related enriched KEGG pathway analysis supported that MX1 and UBE2L6 may affect the inflammatory response through micronutrient metabolic pathways, conceptually named metaflammation. Collectively, MX1 and UBE2L6 may be potential common biomarkers for DM and AS that may reveal metaflammatory aspects of the pathological process, although proper validation is still needed to determine their contribution to the detailed mechanism. creator: Guisheng Wang creator: Rongrong Hua creator: Xiaoxia Chen creator: Xucheng He creator: Yao Dingming creator: Hua Chen creator: Buhuan Zhang creator: Yuru Dong creator: Muqing Liu creator: Jiaxiong Liu creator: Ting Liu creator: Jingwei Zhao creator: Yu Qiong Zhao creator: Li Qiao uri: https://doi.org/10.7717/peerj.16975 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Wang et al. title: Exotic and native plants play equally important roles in supporting and structuring plant-hummingbird networks within urban green spaces link: https://peerj.com/articles/16996 last-modified: 2024-02-21 description: BackgroundUrban gardens, despite their transformed nature, serve as invaluable microcosms for a quantitative examination of floral resource provision to urban pollinators, considering the plant’s origin. Thus, knowledge has increased, emphasizing the importance of these green areas for hosting and conserving pollinator communities. However, there is a significant knowledge gap concerning the changing availability of these native and exotic floral resources over time and their impact on structuring interaction networks with specific pollinators.MethodsOver a year-long period, monthly surveys were conducted to record both native and exotic plant species visited by hummingbirds in an urban garden at Tlaxcala, Mexico. Flower visits were recorded, and the total flowers on each plant visited were tallied. Additionally, all observed hummingbirds were recorded during the transect walks, regardless of plant visits, to determine hummingbird abundance. The interactions were summarized using matrices, and network descriptors like connectance, specializacion, nestedness, and modularity were computed. Plant and hummingbird species in the core and periphery of the network were also identified. Lastly, simulations were performed to assess the network’s resilience to the extinction of highly connected native and exotic plant species, including those previously situated in the network’s core.ResultsWe recorded 4,674 interactions between 28 plant species, and eight hummingbird species. The majority of plants showed an ornithophilic syndrome, with 20 species considered exotic. Despite asynchronous flowering, there was overlap observed across different plant species throughout the year. Exotic plants like Jacaranda mimosifolia and Nicotiana glauca produced more flowers annually than native species. The abundance of hummingbirds varied throughout the study, with Saucerottia berillyna being the most abundant species. The plant-hummingbird network displayed high connectance, indicating generalization in their interaction. Significant nestedness was observed, mainly influenced by exotic plant species. The core of the network was enriched with exotic plants, while Basilinna leucotis and Cynanthus latirostris played central roles among hummingbirds. Network resilience to species extinction remained generally high.ConclusionsOur findings provide valuable insights into the dynamics and structure of plant-hummingbird interactions in urban gardens, emphasizing the influence of exotic plant species and the network’s resilience to perturbations. Understanding and managing the impact of exotic plants on such networks is crucial for the conservation and sustainable functioning of urban ecosystems. creator: Monserrat Sánchez Sánchez creator: Carlos Lara uri: https://doi.org/10.7717/peerj.16996 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Sánchez Sánchez and Lara title: Distribution of rhizosphere fungi of Kobresia humilis on the Qinghai-Tibet Plateau link: https://peerj.com/articles/16620 last-modified: 2024-02-20 description: Kobresia humilis is a major species in the alpine meadow communities of the Qinghai-Tibet Plateau (QTP); it plays a crucial role in maintaining the ecological balance of these meadows. Nevertheless, little is known about the rhizosphere fungi associated with K. humilis on the Qinghai Tibet Plateau. In this study, we used Illumina Miseq to investigate the fungal diversity, community structure, and ecological types in the root and rhizosphere soil of K. humilis across eight areas on the QTP and analyzed the correlation between rhizosphere fungi of K. humilis and environmental factors. A total of 19,423 and 25,101 operational taxonomic units (OTUs) were obtained from the roots and rhizosphere soil of K. humilis. These were classified into seven phyla, 25 classes, 68 orders, 138 families, and 316 genera in the roots, and nine phyla, 31 classes, 76 orders, 152 families, and 407 genera in the rhizosphere soil. There were 435 and 415 core OTUs identified in root and rhizosphere soil, respectively, which were categorized into 68 and 59 genera, respectively, with 25 shared genera. Among them, the genera with a relative abundance >1% included Mortierella, Microscypha, Floccularia, Cistella, Gibberella, and Pilidium. Compared with the rhizosphere soil, the roots showed five differing fungal community characteristics, as well as differences in ecological type, and in the main influencing environmental factors. First, the diversity, abundance, and total number of OTUs in the rhizosphere soil of K. humilis were higher than for the endophytic fungi in the roots by 11.85%, 9.85%, and 22.62%, respectively. The composition and diversity of fungal communities also differed between the eight areas. Second, although saprotroph-symbiotrophs were the main ecological types in both roots and rhizosphere soil; there were 62.62% fewer pathotrophs in roots compared to the rhizosphere soil. Thirdly, at the higher altitude sites (3,900–4,410 m), the proportion of pathotroph fungi in K. humilis was found to be lower than at the lower altitude sites (3,200–3,690 m). Fourthly, metacommunity-scale network analysis showed that during the long-term evolutionary process, ZK (EICZK = 1) and HY (EICHY = 1) were critical sites for development of the fungal community structure in the roots and rhizosphere soil of K. humilis, respectively. Fifthly, canonical correspondence analysis (CCA) showed that key driving factors in relation to the fungal community were longitude (R2 = 0.5410) for the root community and pH (R2 = 0.5226) for the rhizosphere soil community. In summary, these results show that K. humilis fungal communities are significantly different in the root and rhizosphere soil and at the eight areas investigated, indicating that roots select for specific microorganisms in the soil. This is the first time that the fungal distribution of K. humilis on the QTP in relation to long-term evolutionary processes has been investigated. These findings are critical for determining the effects of environmental variables on K. humilis fungal communities and could be valuable when developing guidance for ecological restoration and sustainable utilization of the biological resources of the QTP. creator: Jing Guo creator: Zhanling Xie creator: Qing Meng creator: Hongyan Xu creator: Qingqing Peng creator: Bao Wang creator: Deyu Dong creator: Jiabao Yang creator: Shunbin Jia uri: https://doi.org/10.7717/peerj.16620 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Guo et al. title: Activity of biogenic silver nanoparticles in planktonic and biofilm-associated Corynebacterium pseudotuberculosis link: https://peerj.com/articles/16751 last-modified: 2024-02-20 description: Corynebacterium pseudotuberculosis is a gram-positive bacterium and is the etiologic agent of caseous lymphadenitis (CL) in small ruminants. This disease is characterized by the development of encapsulated granulomas in visceral and superficial lymph nodes, and its clinical treatment is refractory to antibiotic therapy. An important virulence factor of the Corynebacterium genus is the ability to produce biofilm; however, little is known about the characteristics of the biofilm produced by C. pseudotuberculosis and its resistance to antimicrobials. Silver nanoparticles (AgNPs) are considered as promising antimicrobial agents, and are known to have several advantages, such as a broad-spectrum activity, low resistance induction potential, and antibiofilm activity. Therefore, we evaluate herein the activity of AgNPs in C. pseudotuberculosis, through the determination of minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), antibiofilm activity, and visualization of AgNP-treated and AgNP-untreated biofilm through scanning electron microscopy. The AgNPs were able to completely inhibit bacterial growth and inactivate C. pseudotuberculosis at concentrations ranging from 0.08 to 0.312 mg/mL. The AgNPs reduced the formation of biofilm in reference strains and clinical isolates of C. pseudotuberculosis, with interference values greater than 80% at a concentration of 4 mg/mL, controlling the change between the planktonic and biofilm-associated forms, and preventing fixation and colonization. Scanning electron microscopy images showed a significant disruptive activity of AgNP on the consolidated biofilms. The results of this study demonstrate the potential of AgNPs as an effective therapeutic agent against CL. creator: Laerte Marlon Santos creator: Daniela Méria Rodrigues creator: Bianca Vilas Boas Alves creator: Mauricio Alcântara Kalil creator: Vasco Azevedo creator: Debmalya Barh creator: Roberto Meyer creator: Nelson Duran creator: Ljubica Tasic creator: Ricardo Wagner Portela uri: https://doi.org/10.7717/peerj.16751 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Santos et al. title: A novel peroxisome-related gene signature predicts clinical prognosis and is associated with immune microenvironment in low-grade glioma link: https://peerj.com/articles/16874 last-modified: 2024-02-20 description: Low-grade glioma (LGG), a common primary tumor, mainly originates from astrocytes and oligodendrocytes. Increasing evidence has shown that peroxisomes function in the regulation of tumorigenesis and development of cancer. However, the prognostic value of peroxisome-related genes (PRGs) in LGG has not been reported. Therefore, it is necessary to construct a prognostic risk model for LGG patients based on the expression profiles of peroxisome-related genes. Our study mainly concentrated on developing a peroxisome-related gene signature for overall survival (OS) prediction in LGG patients. First, according to these peroxisome-related genes, all LGG patients from The Cancer Genome Atlas (TCGA) database could be divided into two subtypes. Univariate Cox regression analysis was used to find prognostic peroxisome-related genes in TCGA_LGG dataset, and least absolute shrinkage and selection operator Cox regression analysis was employed to establish a 14-gene signature. The risk score based on the signature was positively associated with unfavorable prognosis. Then, multivariate Cox regression incorporating additional clinical characteristics showed that the 14-gene signature was an independent predictor of LGG. Time-dependent ROC curves revealed good performance of this prognostic signature in LGG patients. The performance about predicting OS of LGG was validated using the GSE107850 dataset derived from the Gene Expression Omnibus (GEO) database. Furethermore, we constructed a nomogram model based on the gene signature and age, which showed a better prognostic power. Gene ontology (GO) and Kyoto Encylopedia of Genes and Genomes (KEGG) analyses showed that neuroactive ligand-receptor interaction and phagosome were enriched and that the immune status was decreased in the high-risk group. Finally, cell counting kit-8 (CCK8) were used to detect cell proliferation of U251 and A172 cells. Inhibition of ATAD1 (ATPase family AAA domain-containing 1) and ACBD5 (Acyl-CoA binding-domain-containing-5) expression led to significant inhibition of U251 and A172 cell proliferation. Flow cytometry detection showed that ATAD1 and ACBD5 could induce apoptosis of U251 and A172 cells. Therefore, through bioinformatics methods and cell experiments, our study developed a new peroxisome-related gene signature that migh t help improve personalized OS prediction in LGG patients. creator: Dandan Gao creator: Qiangyi Zhou creator: Dianqi Hou creator: Xiaoqing Zhang creator: Yiqin Ge creator: Qingwei Zhu creator: Jian Yin creator: Xiangqian Qi creator: Yaohua Liu creator: Meiqing Lou creator: Li Zhou creator: Yunke Bi uri: https://doi.org/10.7717/peerj.16874 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Gao et al. title: The pomegranate-derived peptide Pug-4 alleviates nontypeable Haemophilus influenzae-induced inflammation by suppressing NF-kB signaling and NLRP3 inflammasome activation link: https://peerj.com/articles/16938 last-modified: 2024-02-20 description: The respiratory pathogen nontypeable Haemophilus influenzae (NTHi) is the most common cause of exacerbation of chronic obstructive pulmonary disease (COPD), of which an excessive inflammatory response is a hallmark. With the limited success of current medicines there is an urgent need for the development of novel therapeutics that are both safe and effective. In this study, we explored the regulatory potential of pomegranate-derived peptides Pug-1, Pug-2, Pug-3, and Pug-4 on NTHi-induced inflammation. Our results clearly showed that to varying degrees the Pug peptides inhibited NTHi-induced production of IL-1β, a pivotal cytokine in COPD, and showed that these effects were not related to cytotoxicity. Pug-4 peptide exhibited the most potent inhibitory activity. This was demonstrated in all studied cell types including murine (RAW264.7) and human (differentiated THP-1) macrophages as well as human lung epithelial cells (A549). Substantial reduction by Pug-4 of TNF-α, NO and PGE2 in NTHi-infected A549 cells was also observed. In addition, Pug-4 strongly inhibited the expression of nuclear-NF-κB p65 protein and the NF-κB target genes (determined by IL-1β, TNF-α, iNOS and COX-2 mRNA expression) in NTHi-infected A549 cells. Pug-4 suppressed the expression of NLRP3 and pro-IL-1β proteins and inhibited NTHi-mediated cleavage of caspase-1 and mature IL-1β. These results demonstrated that Pug-4 inhibited NTHi-induced inflammation through the NF-κB signaling and NLRP3 inflammasome activation. Our findings herein highlight the significant anti-inflammatory activity of Pug-4, a newly identified peptide from pomegranate, against NTHi-induced inflammation. We therefore strongly suggest the potential of the Pug-4 peptide as an anti-inflammatory medicine candidate for treatment of NTHi-mediated inflammation. creator: Pornpimon Jantaruk creator: Sittiruk Roytrakul creator: Anchalee Sistayanarain creator: Duangkamol Kunthalert uri: https://doi.org/10.7717/peerj.16938 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Jantaruk et al. title: Oral bacteriophages: metagenomic clues to interpret microbiomes link: https://peerj.com/articles/16947 last-modified: 2024-02-20 description: Bacteriophages are bacterial viruses that are distributed throughout the environment. Lytic phages and prophages in saliva, oral mucosa, and dental plaque interact with the oral microbiota and can change biofilm formation. The interactions between phages and bacteria can be considered a portion of oral metagenomics. The metagenomic profile of the oral microbiome indicates various bacteria. Indeed, there are various phages against these bacteria in the oral cavity. However, some other phages, like phages against Absconditabacteria, Chlamydiae, or Chloroflexi, have not been identified in the oral cavity. This review gives an overview of oral bacteriophage and used for metagenomics. Metagenomics of these phages deals with multi-drug-resistant bacterial plaques (biofilms) in oral cavities and oral infection. Hence, dentists and pharmacologists should know this metagenomic profile to cope with predental and dental infectious diseases. creator: Maryam Banar creator: Dinesh Rokaya creator: Reza Azizian creator: Zohaib Khurshid creator: Morteza Banakar uri: https://doi.org/10.7717/peerj.16947 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Banar et al.