title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=287 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Changes in the composition of invertebrate assemblages from wave-exposed intertidal mussel stands along the Nova Scotia coast, Canada link: https://peerj.com/articles/17697 last-modified: 2024-07-08 description: Rocky intertidal habitats occur worldwide and are mainly characterized by primary space holders such as seaweeds and sessile invertebrates. Some of these organisms are foundation species, as they can form structurally complex stands that host many small invertebrates. The abundance of primary space holders is known to vary along coastlines driven directly or indirectly by environmental variation. However, it is less clear if the invertebrate assemblages associated to a foundation species may remain relatively unchanged along coastlines, as similar stands of a foundation species can generate similar microclimates. We examined this question using abundance data for invertebrate species found in mussel stands of a similar structure in wave-exposed rocky habitats at mid-intertidal elevations along the Atlantic coast of Nova Scotia (Canada). While the most abundant invertebrate species were found at three locations spanning 315 km of coastline, species composition (a combined measure of species identity and their relative abundance) differed significantly among the locations. One of the species explaining the highest amount of variation among locations (a barnacle) exhibited potential signs of bottom-up regulation involving pelagic food supply, suggesting benthic–pelagic coupling. The abundance of the species that explained the highest amount of variation (an oligochaete) was positively related to the abundance of their predators (mites), further suggesting bottom-up forcing in these communities. Overall, we conclude that species assemblages associated to structurally similar stands of a foundation species can show clear changes in species composition at a regional scale. creator: Ricardo A. Scrosati creator: Julius A. Ellrich uri: https://doi.org/10.7717/peerj.17697 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Scrosati and Ellrich title: Lysyl oxidase-like 1 predicts the prognosis of patients with primary glioblastoma and promotes tumor invasion via EMT pathway link: https://peerj.com/articles/17579 last-modified: 2024-07-05 description: BackgroundLysyl oxidase enzymes (LOXs), as extracellular matrix (ECM) protein regulators, play vital roles in tumor progression by remodeling the tumor microenvironment. However, their roles in glioblastoma (GBM) have not been fully elucidated.MethodsThe genetic alterations and prognostic value of LOXs were investigated via cBioPortal. The correlations between LOXs and biological functions/molecular tumor subtypes were explored in The Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA). After Kaplan‒Meier and Cox survival analyses, a Loxl1-based nomogram and prognostic risk score model (PRSM) were constructed and evaluated by time-dependent receiver operating characteristic curves, calibration curves, and decision curve analyses. Tumor enrichment pathways and immune infiltrates were explored by single-cell RNA sequencing and TIMER. Loxl1-related changes in tumor viability/proliferation and invasion were further validated by CCK-8, western blot, wound healing, and Transwell invasion assays.ResultsGBM patients with altered LOXs had poor survival. Upregulated LOXs were found in IDH1-wildtype and mesenchymal (not Loxl1) GBM subtypes, promoting ECM receptor interactions in GBM. The Loxl1-based nomogram and the PRSM showed high accuracy, reliability, and net clinical benefits. Loxl1 expression was related to tumor invasion and immune infiltration (B cells, neutrophils, and dendritic cells). Loxl1 knockdown suppressed GBM cell proliferation and invasion by inhibiting the EMT pathway (through the downregulation of N-cadherin/Vimentin/Snai1 and the upregulation of E-cadherin).ConclusionThe Loxl1-based nomogram and PRSM were stable and individualized for assessing GBM patient prognosis, and the invasive role of Loxl1 could provide a promising therapeutic strategy. creator: Gui-Qiang Yuan creator: Guoguo Zhang creator: Qianqian Nie creator: Zhong Wang creator: Hong-Zhi Gao creator: Gui-Shan Jin creator: Zong-Qing Zheng uri: https://doi.org/10.7717/peerj.17579 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Yuan et al. title: The antioxidant effects of butylated hydroxytoluene on cryopreserved goat sperm from a proteomic perspective link: https://peerj.com/articles/17580 last-modified: 2024-07-05 description: At present, there are few reports about the proteomics changes provoked by butylated hydroxytoluene (BHT) supplementation on cryopreserved semen in mammals. Thus, we aimed to evaluate the effects of different concentrations of BHT on goat sperm and to investigate the proteomics changes of adding BHT to cryopreserved goat (Capra hircus) sperm. Firstly, semen samples were collected from four goats, and frozen in the basic extenders containing different concentrations of BHT (0.5 mM, 1.0 mM, 2.0 mM) and a control without BHT, respectively. After thawing, the protective effects of dose-dependent replenished BHT to the freezing medium on post-thaw sperm motility, integrities of plasma membrane and acrosome, reactive oxygen species levels were confirmed, with 0.5 mM BHT being the best (B group) as compared to the control (without BHT, C group). Afterwards, TMT-based quantitative proteomic technique was performed to profile proteome of the goat sperm between C group and B group. Parallel reaction monitoring was used to confirm reliability of the data. Overall, 2,476 proteins were identified and quantified via this approach. Comparing the C and B groups directly (C vs. B), there were 17 differentially abundant proteins (DAPs) po-tentially associated with sperm characteristics and functions were identified, wherein three were upregulated and 14 were downregulated, respectively. GO annotation analysis demonstrated the potential involvement of the identified DAPs in metabolic process, multi-organism process, reproduction, reproductive process, and cellular process. KEGG enrichment analysis further indicated their potential roles in renin-angiotensin system and glutathione metabolism pathways. Together, this novel study clearly shows that BHT can effectively improve quality parameters and fertility potential of post-thawed goat sperm at the optimal concentration, and its cryoprotection may be realized through regulation of sperm metabolism and antioxidative capability from the perspective of sperm proteomic modification. creator: Chunyan Li creator: Larbi Allai creator: Jiachong Liang creator: Chunrong Lv creator: Xiaoqi Zhao creator: Xiaojun Ni creator: Guoquan Wu creator: Weidong Deng creator: Bouabid Badaoui creator: Guobo Quan uri: https://doi.org/10.7717/peerj.17580 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Li et al. title: In vitro cytoprotective and in vivo anti-oral mucositis effects of melatonin and its derivatives link: https://peerj.com/articles/17608 last-modified: 2024-07-05 description: According to our preliminary study, melatonin and its N-amide derivatives (N-(2-(1-4-bromobenzoyl-5-methoxy-1H-indol-3-yl)ethyl)acetamide (BBM) and 4-bromo-N-(2-(5-methoxy-1H-indol-3-yl)ethyl)benzamide (EBM)) inhibited the marker of acute inflammation in tests in vitro and in vivo. The anti-inflammatory agent is intended for the prevention and treatment of chemotherapy-induced toxicity. In this study aimed to evaluate the effect of melatonin and its derivatives on mechanisms related to chemotherapy-induced oral mucositis by in vitro ROS and 5-FU-induced human keratinocyte cells as well as in vivo oral mucositis model. In in vitro H2O2-induced HaCaT cells, BBM had the highest level of protection (34.57%) at a concentration 50 µM, followed by EBM (26.41%), and melatonin (7.9%). BBM also protected cells against 5-FU-induced to 37.69–27.25% at 12.5–100 µM while EBM was 36.93–29.33% and melatonin was 22.5–11.39%. In in vivo 5-FU-induced oral mucositis in mice, melatonin, BBM, and EBM gel formulations protected tissue damage from 5-FU similar to the standard compound, benzydamine. Moreover, the weight of mice and food consumption recovered more quickly in the BBM group. These findings suggested that it was possible to develop BBM and EBM as new therapeutic agents for the treatment of oral mucositis. creator: Pramote Mahakunakorn creator: Pimpichaya Sangchart creator: Panyada Panyatip creator: Juthamat Ratha creator: Teerasak Damrongrungruang creator: Aroonsri Priprem creator: Ploenthip Puthongking uri: https://doi.org/10.7717/peerj.17608 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Mahakunakorn et al. title: Exploring main soil drivers of vegetation succession in abandoned croplands of Minqin Oasis, China link: https://peerj.com/articles/17627 last-modified: 2024-07-05 description: BackgroundThe Minqin Oasis, which is located in Wuwei City, Gansu Province, China, faces a very serious land desertification problem, with about 94.5% of its total area desertified. Accordingly, it is crucial to implement ecological restoration policies such as cropland abandonment in this region. In abandoned croplands, abiotic factors such as soil properties may become more important than biotic factors in driving vegetation succession. However, the connections between soil properties and vegetation succession remain unclear. To fill this knowledge gap, this study investigated these connections to explore major factors that affected vegetation succession, which is meaningful to designing management measures to restore these degraded ecosystems.MethodsThis study investigated seven 1–29-year-old abandoned croplands using the “space for time” method in Minqin Oasis. Vegetation succession was classified into different stages using a canonical correlation analysis (CCA) and two-way indicator species analysis (Twinspan). The link between soil properties and vegetation succession was analyzed using CCA. The primary factors shaping community patterns of vegetation succession were chosen by the “Forward selection” in CCA. The responses of dominant species to soil properties were analyzed using generalized additive models (GAMs).ResultsDominant species turnover occurred obviously after cropland abandonment. Vegetation succession can be classified into three stages (i.e., early, intermediate, and late successional stages) with markedly different community composition and diversity. The main drivers of vegetation succession among soil properties were soil salinity and saturated soil water content and they had led to different responses of the dominant species in early and late successional stages. During the development of vegetation succession, community composition became simpler, and species diversity decreased significantly, which was a type of regressive succession. Therefore, measures should be adopted to manage these degraded, abandoned croplands. creator: Li Chang creator: Shuhua Yi creator: Yu Qin creator: Yi Sun creator: Huifang Zhang creator: Jing Hu creator: Kaiming Li creator: Xuemei Yang uri: https://doi.org/10.7717/peerj.17627 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Chang et al. title: Brazilin cream from Caesalpinia sappan inhibit periodontal disease: in vivo study link: https://peerj.com/articles/17642 last-modified: 2024-07-05 description: BackgroundGingivitis is an inflammation of the gums that is the initial cause of the development of periodontal disease by the activity of Nuclear Factor-kappa B (NF-κB), Interleukin-1β (IL-1β), Interleukin-6 (IL-6), p38, and Tumor Necrosis Factor-α (TNF-α). Unaddressed chronic inflammation can lead to persistent disturbances in other parts of the body. Brazilin is a naturally occurring plant chemical that may have antibacterial and anti-inflammatory effects. Treatment based on the natural plant compound, brazilin, is developed in the form of a topical cream for easy application.ObjectiveThe aim is to develop the natural compound brazilin in the form of a topical cream as an anti-inflammatory agent to reduce NF-κB expression through Imunohistochemistry (IHC) methods, and the expression of pro-inflammatory genes IL-1β, IL-6, p38, and TNF-α.MethodsMale Sprague-Dawley rats were induced with gingivitis using P. gingivalis bacteria. The observed groups included rats treated with a single application of brazilin cream and rats treated with two applications of brazilin cream. The treatment was administered for 15 days. On days 3, 6, 9, 12, and 15, anatomical wound observations and wound histology using hematoxylin-eosin and Masson’s Trichrome staining were performed. NF-κB protein expression was analyzed using the IHC method. Gingival inflammation gene expression of NF-κB, IL-1β, IL-6, p38, and TNF-α was measured using q-RTPCR.ResultsSingle and double applications of brazilin cream increased angiogenesis and decreased NF-κB protein expression, in addition to the IL-1β, IL-6, p38, and TNF-α gene expressions.ConclusionIn a rat gingivitis model, Brazilin cream may function as an anti-inflammatory agent in the gingival tissue. creator: Vinna Kurniawati Sugiaman creator: Jeffrey Jeffrey creator: Silvia Naliani creator: Natallia Pranata creator: Shelly Lelyana creator: Wahyu Widowati creator: Rival Ferdiansyah creator: Dhanar Septyawan Hadiprasetyo creator: Vini Ayuni uri: https://doi.org/10.7717/peerj.17642 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Sugiaman et al. title: Elucidating the regulatory role of long non-coding RNAs in drought stress response during seed germination in leaf mustard link: https://peerj.com/articles/17661 last-modified: 2024-07-05 description: Leaf mustard (Brassica juncea L. Czern & Coss), an important vegetable crop, experiences pronounced adversity due to seasonal drought stress, particularly at the seed germination stage. Although there is partial comprehension of drought-responsive genes, the role of long non-coding RNAs (lncRNAs) in adjusting mustard’s drought stress response is largely unexplored. In this study, we showed that the drought-tolerant cultivar ‘Weiliang’ manifested a markedly lower base water potential (−1.073 MPa vs −0.437 MPa) and higher germination percentage (41.2% vs 0%) than the drought-susceptible cultivar ‘Shuidong’ under drought conditions. High throughput RNA sequencing techniques revealed a significant repertoire of lncRNAs from both cultivars during germination under drought stress, resulting in the identification of 2,087 differentially expressed lncRNAs (DELs) and their correspondingly linked 12,433 target genes. It was noted that 84 genes targeted by DEL exhibited enrichment in the photosynthesis pathway. Gene network construction showed that MSTRG.150397, a regulatory lncRNA, was inferred to potentially modulate key photosynthetic genes (Psb27, PetC, PetH, and PsbW), whilst MSTRG.107159 was indicated as an inhibitory regulator of six drought-responsive PIP genes. Further, weighted gene co-expression network analysis (WGCNA) corroborated the involvement of light intensity and stress response genes targeted by the identified DELs. The precision and regulatory impact of lncRNA were verified through qPCR. This study extends our knowledge of the regulatory mechanisms governing drought stress responses in mustard, which will help strategies to augment drought tolerance in this crop. creator: Jinxing Wei creator: Haibo Li creator: Xiaoer Huang creator: Yongguo Zhao creator: Lejun Ouyang creator: Mingken Wei creator: Chun Wang creator: Junxia Wang creator: Guangyuan Lu uri: https://doi.org/10.7717/peerj.17661 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wei et al. title: Comparison of perceived masticatory ability in completely edentulous patients treated with thermoplastic complete denture versus single implant-retained mandibular overdenture: a single-center prospective observational study link: https://peerj.com/articles/17670 last-modified: 2024-07-05 description: BackgroundThis study aimed to compare the perceived masticatory ability (PrMA) in completely edentulous patients (EDPs) with thermoplastic conventional complete dentures (CDs) versus single implant-retained mandibular overdentures.MethodsThe current study was conducted in the outpatient Prosthodontic Clinic, Faculty of Dental Medicine, Al-Azhar University, Cairo, Egypt. PrMA was evaluated in 45 completely edentulous patients (46% males, mean age 50.4 ± 4.7 years). Each patient received a thermoplastic PMMA complete denture (Polyan IC TM Bredent GmbH & Co.KG, Germany). The PrMA was evaluated at one-month and six-month intervals of denture use. An immediate loading single implant was placed into the mid-symphyseal for each patient, and the denture was adjusted. Subsequently, the PrMA was reevaluated after one month and six months. The data were collected and statistically analyzed using the SPSS@V25 to assess the changes in PrMA.ResultsThe PrMA demonstrated improvement after six months of thermoplastic conventional denture use. However, this improvement was not statistically significant (p = 0.405). In addition, the PrMA showed a substantial increase following a single implant placement at one and six months (p < 0.001) of the overdenture use compared to the conventional denture. The PrMA insignificantly improved (p = 0.397) after six months of the single implant retained overdenture use.DiscussionThe study’s findings indicate that using immediate loading single implant-retained mandibular overdentures significantly improved PrMA in completely edentulous patients. creator: Mostafa I. Fayad creator: Ihab I. Mahmoud creator: Ahmed Atef Aly Shon creator: Mohamed Omar Elboraey creator: Ramy M. Bakr creator: Rania Moussa uri: https://doi.org/10.7717/peerj.17670 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Fayad et al. title: Ursolic acid attenuates oligospermia in busulfan-induced mice by promoting motor proteins link: https://peerj.com/articles/17691 last-modified: 2024-07-05 description: BackgroundOligospermia is one of the most common reasons for male infertility which is troubling numerous couples of child-bearing age. This investigation scrutinizes the implications and mechanistic underpinnings of ursolic acid’s effect on busulfan-induced oligospermia in mouse models.MethodsA singular intraperitoneal injection of busulfan at a dosage of 30 mg/kg induced oligospermia. Two weeks subsequent to this induction, mice were subjected to various dosages of ursolic acid (10, 30, and 50 mg/kg body weight, respectively) on a daily basis for four consecutive weeks. Following this treatment period, a meticulous analysis of epididymal sperm parameters, encompassing concentration and motility, was conducted using a computer-assisted sperm analysis system. The histopathology of the mice testes was performed utilizing hematoxylin and eosin staining, and the cytoskeleton regeneration of the testicular tissues was analyzed via immunofluorescent staining. Serum hormone levels, including testosterone, luteinizing hormone, and follicle-stimulating hormone, as well as reactive oxygen species levels (inclusive of reactive oxygen species and malondialdehyde), were gauged employing specific enzyme-linked immunosorbent assay kits. Differentially expressed genes of testicular mRNA between the oligospermia-induced group and the various ursolic acid treatment groups were identified through RNA sequencing analysis.ResultsThe results revealed that a dosage of 50 mg/kg ursolic acid treatment could increase the concentration of epididymal sperm in oligospermia mice, promote the recovery of testicular morphology, regulate hormone levels and ameliorate oxidative damage. The mechanism research results indicated that ursolic acid increased the expression level of genes related to motor proteins in oligospermia mice. creator: Jin Dong creator: Taowen Ye creator: Yanli Dong creator: Jie Hui creator: Xiaorong Wang uri: https://doi.org/10.7717/peerj.17691 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Dong et al. title: Investigating the second whitefly population outbreak within a decade in the cotton growing zone of North India link: https://peerj.com/articles/17476 last-modified: 2024-07-04 description: The whitefly, Bemisia tabaci (Gennadius), is a polyphagous and major pest of cotton worldwide. Both adults and nymphs of B. tabaci affect the crop by causing direct and indirect damage. A severe whitefly outbreak was experienced during 2015 on cotton in North India and this was followed by a profound infestation during 2022. The present research rigorously examined whether the proliferation in the whitefly population was an outbreak or the result of a multi factor resurgence. During 2015, whitefly counts remained above the economic threshold level (ETL) between 28th and 35th Standard Meteorological Week (SMW). However, during 2022 above ETL population was observed in 27th SMW and it persisted until 36th SMW. The peak incidence of the whitefly was noticed during 31st and 29th SMW in 2015 and 2022, respectively. The early pest build up in 2022 and longer persistence (≥10 weeks) over the cotton season resulted in more damage to cotton crop. Additionally, pest survillence across the zone on the farmers’ fields during 2022 revealed 44.4 per cent spots (585 out of 1,317 locations) above ETL while the corresponding locations in 2015 was 57% (620 out of 1,089). Thus, in 2022 infestation was not uniform in the entire zone wherein only few blocks of Punjab, Haryana and Rajasthan states of India experienced severe infestations of the whitefly. This study reports the complex of factors including weather, delayed sowing, use of tank mixtures/ subleathal doses of insecticides, pest resurgence etc. that might have possibly contributed to these upsurges in whitefly on cotton in north India. creator: Rishi Kumar creator: Satish Kumar Sain creator: Satnam Singh creator: Suneet Pandher creator: Roop Singh Meena creator: Anil Jakhar creator: Jasjinder Kaur creator: Mandeep Pathania creator: Debashis Paul creator: Prakash A.H. creator: Prasad Y.G. uri: https://doi.org/10.7717/peerj.17476 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Kumar et al.