title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=184 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Enrichment effects on growth, health, and reproduction in a single clone of the asexual Amazon molly, Poecilia formosa link: https://peerj.com/articles/18734 last-modified: 2024-12-23 description: This study examines the impact of two types of environmental enrichment on the growth of the Amazon molly (Poecilia formosa), a clonal fish species. We investigated the effects of two welfare-related enrichment factors: physical enrichment (presence of a halfpipe PVC and gravel substrate, E) and social enrichment (presence of visible neighbor fish, N). Fish were divided into four treatment groups: (1) both physical and social enrichment (EN), (2) no physical enrichment but social enrichment (nEN), (3) physical enrichment without social enrichment (EnN,), and (4) no enrichment (nEnN). Results showed that individuals, which received both types of enrichment, exhibited faster growth rates and lower early life mortality compared to the other groups, indicating improved health and welfare. However, this initial advantage did not persist into adulthood, suggesting that the benefits of enrichment may be stage specific. These findings highlight the importance of environmental factors in promoting welfare in a particular species, especially during early developmental stages. This study may have implications for early life-stage fish research indicating that some environmental factors may play a role in enhancing growth, reproductive competence, and reduced mortality. Enrichment effects on growth, health, and reproduction in a single clone of the asexual Amazon molly, Poecilia formosa. creator: Debbie Cunningham creator: Tyler Reich creator: Theresa E. Rizzi creator: Chance Powell creator: Ingo Schlupp uri: https://doi.org/10.7717/peerj.18734 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Cunningham et al. title: Association of tyrosine kinase 2 polymorphisms with susceptibility to microscopic polyangiitis in a Guangxi population link: https://peerj.com/articles/18735 last-modified: 2024-12-23 description: BackgroundHeredity and epigenetics affect the pathogenesis of microscopic polyangiitis (MPA). Tyrosine kinase 2 (TYK2) polymorphisms (rs2304256C > A, rs280519A > G, and rs12720270G > A) may be potential protective factors against anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV). Current research suggests that TYK2 is associated with various autoimmune diseases; however, no study has examined the relationship between TYK2 polymorphisms and AAV. This study assessed the effect of TYK2 polymorphisms on susceptibility to MPA.MethodsOverall, 562 Chinese participants (265 patients with MPA and 297 healthy volunteers) were recruited. Polymerase chain reactions combined with high-throughput sequencing were used to analyze polymorphic loci, while logistic regression analysis was used to assess the relationship between polymorphism of the TYK2 gene and MPA susceptibility.ResultsIn males, individuals with the CA genotype (rs2304256) in the overdominant model showed a significantly reduced risk of MPA (odds ratio (OR) = 0.52; 95% confidence interval (CI) [0.29–0.93]; p = 0.025). Regarding rs280519, male carriers of the AG genotype had a significantly lower risk of developing MPA in both the codominant (OR = 0.51; 95% CI [0.28–0.93]; p = 0.039) and overdominant (OR = 0.48; 95% CI [0.27–0.86]; p = 0.013) models. The GA genotype of rs12720270 was associated with low susceptibility to MPA in males (OR = 0.52; 95% CI [0.29–0.93]; p = 0.027).ConclusionsThis study indicates that mutations in the TYK2 gene (rs2304256, rs280519, and rs12720270) may be associated with a reduced risk of MPA in the male Chinese population in Guangxi. The A allele of single nucleotide polymorphism (SNP) rs2304256 may be a protective factor against MPA, while the G alleles of SNPs rs280519 and rs12720270 are protective factors against MPA. creator: Binglan Yang creator: Liepeng Chu creator: Fei Feng creator: Shurong Lu creator: Chao Xue uri: https://doi.org/10.7717/peerj.18735 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Yang et al. title: Malignant solid tumor-related spontaneous intracerebral hemorrhage: a propensity score matching study link: https://peerj.com/articles/18737 last-modified: 2024-12-23 description: BackgroundSpontaneous intracerebral hemorrhage (sICH) is a severe event with high mortality. Recently, evidence has emerged suggesting that malignant solid tumors may increase the risk of sICH through unique cancer-related factors. However, the specific risk factors and clinical characteristics of sICH in patients with malignant solid tumor remain poorly understood.ObjectiveThis study aimed to investigate the clinical characteristics of and identify the risk factors associated with sICH in individuals with malignant solid tumors.MethodsThis retrospective study was carried out in patients with active malignant solid tumors and sICH at the First Affiliated Hospital of Guangxi Medical University between January 2010 and December 2020. Patients were separated into control and malignant solid tumor-related spontaneous intracerebral hemorrhage (MST-sICH) groups. The control group consisted of patients presenting with malignant solid tumors alone who were matched to the MST-sICH group using a 1:1 propensity score matching (PSM) approach. Patient clinical data, laboratory findings, and imaging results were collected. Univariate analysis was carried out to determine the risk factors associated with MST-sICH. In addition, a receiver operator characteristic analysis was performed to identify potential predictors for poor prognosis.ResultsDecreased hemoglobin (HGB) levels, together with increased lymphocyte counts (LYCs), and an increased neutrophil-to-lymphocyte ratio (NLR) were found in the MST-sICH group compared to the control group. The results of the multivariate logistic regression analysis indicated a HGB levels (OR: 0.959, 95% CI [0.928–0.992]), an increased in LYCs (OR: 0.095, 95% CI [0.023–0.392]). Furthermore, there was an increased in NLR levels (OR: 2.137, 95% CI [1.427–3.200]). In the receiver operating characteristic (ROC) curve analysis, the area under the curve (AUC) with HGB, LYCs, and NLR as joint predictors was 0.955 (95% CI [0.901–1.000]), with a sensitivity of 100%, a specificity of 82.6%, and a Youden Index of 0.826.ConclusionDecreased HGB levels, elevated LYCs, and a higher NLR were identified as independent risk factors for sICH in patients with active solid malignancies. These markers could assist clinicians in stratifying high-risk patients, facilitating closer monitoring and informing targeted preventive strategies to mitigate the incidence of sICH in this at-risk population. creator: Shuolin Liang creator: Liuyu Liu creator: Bin Qin creator: Shengri Chen creator: Zhijian Liang uri: https://doi.org/10.7717/peerj.18737 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Liang et al. title: Impact of storage and extraction methods on peat soil microbiomes link: https://peerj.com/articles/18745 last-modified: 2024-12-23 description: Recovered microbial community structure is known to be influenced by sample storage conditions and nucleic acid extraction methods, and the impact varies by sample type. Peat soils store a large portion of soil carbon and their microbiomes mediate climate feedbacks. Here, we tested three storage conditions and five extraction protocols on peat soils from three physicochemically distinct habitats in Stordalen Mire, Sweden, revealing significant methodological impacts on microbial (here, meaning bacteria and archaea) community structure. Initial preservation method impacted alpha but not beta diversity, with in-field storage in LifeGuard buffer yielding roughly two-thirds the richness of in-field flash-freezing or transport from the field on ice (all samples were stored at −80 °C after return from the field). Nucleic acid extraction method impacted both alpha and beta diversity; one method (the PowerSoil Total RNA Isolation kit with DNA Elution Accessory kit) diverged from the others (PowerMax Soil DNA Isolation kit-High Humic Acid Protocol, and three variations of a modified PowerMax Soil DNA/RNA isolation kit), capturing more diverse microbial taxa, with divergent community structures. Although habitat and sample depth still consistently dominated community variation, method-based biases in microbiome recovery for these climatologically-relevant soils are significant, and underscore the importance of methodological consistency for accurate inter-study comparisons, long-term monitoring, and consistent ecological interpretations. creator: Dylan Cronin creator: Yueh-Fen Li creator: Paul Evans creator: Gene W. Tyson creator: Ben J. Woodcroft creator: Virginia I. Rich uri: https://doi.org/10.7717/peerj.18745 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Cronin et al. title: Implications of the SNHG10/miR-665/RASSF5/NF-κB pathway in dihydromyricetin-mediated ischemic stroke protection link: https://peerj.com/articles/18754 last-modified: 2024-12-23 description: Ischemic stroke (IS) remains a leading cause of disability and mortality worldwide, and inflammation and oxidative stress play significant roles in its pathogenesis. This study investigates the effects of dihydromyricetin (DHM) on IS using RT-qPCR and western blot with SH-SY5Y cells, focusing on its effects on the small nucleolar RNA host gene 10 (SNHG10)/microRNA (miR)-665/Ras association domain family member 5 (RASSF5) axis and nuclear factor-kappa B (NF-κB) signaling. In addition, the effects of the SNHG10/miR-665/RASSF5 axis on SH-SY5Y cell activity, apoptosis, oxidative stress, and inflammatory markers were analyzed using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, flow cytometry, and enzyme-linked immunosorbent assays. Our results showed that, in response to oxygen-glucose deprivation/reperfusion (OGD/R), DHM treatment improved cell viability, reduced apoptosis, and attenuated neuroinflammation and oxidative stress in a dose-dependent manner (p < 0.05). Interestingly, lncRNA SNHG10 was overexpressed during OGD/R and suppressed by DHM. Through bioinformatics analysis and experimental validation, we identified miR-665 as a direct target of SNHG10 and RASSF5 as a direct target of miR-665. The protective effect of DHM against OGD/R injury was partially reversed by SNHG10 overexpression and further enhanced by co-transfection with the miR-665 mimic and si-RASSF5 (p < 0.05). This study identifies a novel mechanism of DHM against IS, which may act via modulation of the SNHG10/miR-665/RASSF5 axis and inactivation of NF-κB signaling, and offers a promising therapeutic target for IS. creator: Qi Zeng creator: Yan Xiao creator: Xueliang Zeng creator: Hai Xiao uri: https://doi.org/10.7717/peerj.18754 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zeng et al. title: Unique dental arrangement in a new species, Groenlandaspis howittensis (Placodermi, Arthrodira) from the Middle Devonian of Mount Howitt, Victoria, Australia. link: https://peerj.com/articles/18759 last-modified: 2024-12-23 description: Well-preserved specimens of a new species of arthrodiran placoderm, Groenlandaspis howittensis sp. nov. (Middle Devonian of Victoria, Australia), reveals previously unknown information on the dermal skeleton, body-shape and dentition of the wide-spread genus Groenlandaspis. The new material includes dual pineal plates, extrascapular plates, and cheek bones showing the presence of cutaneous sensory organs. The anterior supragnathal, usually a paired element in arthrodires, is a fused median bone in G. howittensis sp. nov. It is positioned anterior to the occlusion of the mouth between the lower jaw (infragnathals) and upper jaw (posterior supragnathals) bones, indicating a specialised feeding mechanism and broadening the known diversity of placoderm dental morphologies. G. howittensis sp. nov. differs from all other groenlandaspidids by a less pronounced posterior expansion of the nuchal plate; the shape of the posterior dorsolateral plate and the presence of a short accessory canal on the anterior dorsolateral plate. A new phylogenetic analysis positions Groenlandaspididae in a monophyly with the phlyctaeniid families Arctolepidae and Arctaspididae, however, the specific intrarelationships of groenlandaspidids remain poorly resolved. creator: Austin N. Fitzpatrick creator: Alice M. Clement creator: John A. Long uri: https://doi.org/10.7717/peerj.18759 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Fitzpatrick et al. title: Spatial variations of soil seed banks in Shanghai’s urban wasteland: a gradient analysis of urbanization effects link: https://peerj.com/articles/18764 last-modified: 2024-12-23 description: Urbanization greatly impacts both the diversity of soil seed banks and the spatial dynamics of species. These seed banks serve as a window into the ecological history and potential for recovery in urban wastelands, which are continually evolving due to urbanization. In this study, we selected 24 plots along urban-rural gradients in Shanghai, China. Soil samples were collected from each plot for seed bank germination experiment in both spring and autumn. We tested whether the seed density, species diversity, and composition of soil seed banks in wasteland varied along an urban-rural gradient. The results showed that seed density was higher in autumn than in spring and no significant difference was found along urban-rural gradients. A total of 74 species, belonging to 26 families and 69 genera, was recorded in soil seed banks, in which annuals were the dominant life form and autochory was the dominant dispersal model. The proportion of exotic species was nearly 40%. There is no significant difference along urban-rural gradients for functional composition, species diversity, and species composition, excepting that marginal significant for autumn Shannon-Wiener index and species composition among urban-rural gradients. The relative homogeneity in the seed bank across urban-rural gradients may primarily be due to the young age of the wastelands. creator: Siyi Xia creator: Shumeng Zhang creator: Yichong Cui creator: Zhiwen Gao creator: Kun Song creator: Liangjun Da uri: https://doi.org/10.7717/peerj.18764 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Xia et al. title: A chromosome-scale genome assembly of mungbean (Vigna radiata) link: https://peerj.com/articles/18771 last-modified: 2024-12-23 description: BackgroundMungbean (Vigna radiata) is one of the most socio-economically important leguminous food crops of Asia and a rich source of dietary protein and micronutrients. Understanding its genetic makeup is crucial for genetic improvement and cultivar development.MethodsIn this study, we combined single-tube long-fragment reads (stLFR) sequencing technology with high-throughput chromosome conformation capture (Hi-C) technique to obtain a chromosome-level assembly of V. radiata cultivar ‘KUML4’.ResultsThe final assembly of the V. radiata genome was 468.08 Mb in size, with a scaffold N50 of 40.75 Mb. This assembly comprised 11 pseudomolecules, covering 96.94% of the estimated genome size. The genome contained 253.85 Mb (54.76%) of repetitive sequences and 27,667 protein-coding genes. Our gene prediction recovered 98.3% of the highly conserved orthologs based on Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis. Comparative analyses using sequence data from single-copy orthologous genes indicated that V. radiata diverged from V. mungo approximately 4.17 million years ago. Moreover, gene family analysis revealed that major gene families associated with defense responses were significantly expanded in V. radiata.ConclusionOur chromosome-scale genome assembly of V. radiata cultivar KUML4 will provide a valuable genomic resource, supporting genetic improvement and molecular breeding. This data will also be valuable for future comparative genomics studies among legume species. creator: Supaporn Khanbo creator: Poompat Phadphon creator: Chaiwat Naktang creator: Duangjai Sangsrakru creator: Pitchaporn Waiyamitra creator: Nattapol Narong creator: Chutintorn Yundaeng creator: Sithichoke Tangphatsornruang creator: Kularb Laosatit creator: Prakit Somta creator: Wirulda Pootakham uri: https://doi.org/10.7717/peerj.18771 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Khanbo et al. title: Dosimetric comparison and evaluation of different convergence modes in nasopharyngeal carcinoma using VMAT treatment deliveries link: https://peerj.com/articles/18773 last-modified: 2024-12-23 description: BackgroundThis study investigates the impact of convergence mode (CM) in Eclipse (Varian Medical Systems) on the quality and complexity of volumetric modulated arc therapy (VMAT) plans for nasopharyngeal carcinoma (NPC) patients.MethodsWe retrospectively analyzed data from 21 NPC patients. For each patient, three VMAT plans with different CM settings (Off, On, and Extended) were created using identical optimization objectives. Plan quality was assessed using indices such as the conformity index (CI) and homogeneity index (HI), as well as evaluating target coverage and sparing of organs at risk (OARs). Complexity was measured by metrics including average leaf pair opening (ALPO), modulation complexity scores for VMAT (MCSv), monitor units (MUs), and optimization time. Dosimetric verification was performed based on the gamma pass rate.ResultsDifferent CM settings can generate treatment plans that meet clinical dose objectives for planning target volumes (PTVs) and OARs. The ‘On’ or ‘Extended’ CM settings improved CI and HI for the NPC target volume and reduced OAR doses, especially the mean dose, without compromising target coverage. The ‘Extended’ CM setting produced the most favorable outcomes. ALPO values for CM settings ‘Off’, ‘On’, and ‘Extended’ were 29.1 ± 4.3 mm, 28.6 ± 4.2 mm, and 28.4 ± 4. 2 mm, respectively. MCSv values for these settings were 0.1730 ± 0.0215, 0.1691 ± 0.0204, and 0.1693 ± 0.0208, respectively. MUs were 796.2 ± 110.8 for CM ‘Off’, 798.6 ± 106.1 for CM ‘On’, and 799.7 ± 103.6 for CM ‘Extended’, with no significant differences (p > 0.05). Gamma pass rates for all plans were above 99% (3%/3 and 2%/2 mm), with no significant differences among groups (p > 0.05). The average optimization times for CM settings ‘Off’, ‘On’, and ‘Extended’ were 14.4 ± 3.2, 35.9 ± 8.9, and 145.6 ± 50.3 min, respectively (p < 0.001).ConclusionCM usage can improve the CI and HI of the target volume and decrease the dose to OARs in VMAT plans for NPC patients. This study suggests that CM can be a valuable tool in VMAT planning for nasopharyngeal carcinoma, given adequate planning time. creator: Maoying Lan creator: Rui Wu creator: Guanhua Deng creator: Bo Yang creator: Yongdong Zhuang creator: Wei Yi creator: Wenwei Xu creator: Jiancong Sun uri: https://doi.org/10.7717/peerj.18773 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Lan et al. title: Effects of vegetation restoration in karst areas on soil nitrogen mineralisation link: https://peerj.com/articles/18582 last-modified: 2024-12-20 description: BackgroundNitrogen mineralization plays a critical role in the ecosystem cycle, significantly influencing both the ecosystem function and the nitrogen biogeochemical cycle. Therefore, it is essential to investigate the evolutionary characteristics of soil nitrogen mineralization during the karst vegetation restoration to better understand its importance in the terrestrial nitrogen cycle.MethodsThis study analyzed from various stages of vegetation growth, including a 40-year-old woodland, 20-year-old shrubland, 15-year-old shrubland, 5-year-old grassland, and nearby cropland. The aerobic incubation technique was used for 35 days to evaluate soil N mineralization characteristics and their correlation with soil environmental factors. The study focused on examining the variations in soil N mineralization rate (NMR), N nitrification rate (NR), net nitrification rate (AR), and NH4+-N and NO3--N levels.ResultsNitrate nitrogen, the primary form of inorganic nitrogen, increased by 19.38% in the 0–40 cm soil layer of the 20-year-old shrubland compared to the cultivated land. Soil NH4+-N levels varied during the incubation period, decreasing by the 14th day and rising again by the 21st day. Soil NO3−-N and total inorganic nitrogen levels initially increased, then declined, and eventually stabilized, reaching their highest levels on the 14th day. During vegetation restoration, the soil NR and NMR decreased gradually with increasing incubation time. The 15-year shrub, 20-year shrub, and 40-year woodland showed the potential to increase soil NR and NMR. Furthermore, the 15-year shrub and 20-year shrub also increased soil AR. The Mantel test analysis indicated positive correlations among total nitrogen (TN), total phosphorus (TP), total potassium (TK), silicon (Si), AR, NR, and NMR. While available phosphorus (AP) and NMR demonstrated positive correlations with NR and NMR. Furthermore, TN, TP, TK, and Si were found to be positively correlated with AR, NR, and NMR, whereas AP and NO3--N showed negative correlations with AR, NR, and NMR. It is worth noting that NH4+-N had the greatest effect on AR, while the bulk density (BD) significantly affected the NR. Furthermore, ammonium nitrogen (AN) and soil organic carbon (SOC) were identified as the primary contributors to NMR. This study provides a theoretical basis for comprehending the influence of vegetation restoration on soil nitrogen mineralization and its role in ecosystem restoration. creator: Jianghong Wu creator: Xianghuan Gong creator: Yingge Shu uri: https://doi.org/10.7717/peerj.18582 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Wu et al.