title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=187 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en 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. title: A new approach for increasing graduate students’ science communication capacity and confidence link: https://peerj.com/articles/18594 last-modified: 2024-12-20 description: There is an increasing demand for emerging scientists to improve their ability to communicate with public audiences, yet little research investigates the effectiveness of science communication training for graduate students. We responded to this need by developing SciWrite@URI—an interdisciplinary model for science graduate students designed around three learning outcomes based on tenets from the field of writing and rhetoric—habitual writing, multiple genres, and frequent review. SciWrite students completed courses and a science communication internship, attended writing workshops, and became tutors at a newly established Graduate Writing Center. After 2 years of training, students more frequently wrote multiple drafts and engaged in peer review, increased their confidence as writers, and decreased their apprehension about writing. We conclude the tenets of the SciWrite program helped students improve as science communicators, and we make suggestions for effective ways graduate departments and training programs might implement and build on our model. creator: Erin R. Harrington creator: Scott R. McWilliams creator: Nancy E. Karraker creator: Caroline Gottschalk Druschke creator: Jenna Morton-Aiken creator: Elaine Finan creator: Ingrid E. Lofgren uri: https://doi.org/10.7717/peerj.18594 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Harrington et al. title: Modeling the effects of water temperature on the population dynamics of Galba viatrix and infection by Fasciola hepatica: a two-year survey in Andean Patagonia, Argentina link: https://peerj.com/articles/18648 last-modified: 2024-12-20 description: BackgroundThe trematode parasite Fasciola hepatica (liver fluke) can infect livestock, wild mammals, and humans, generating serious economic losses worldwide. Aquatic or amphibious snails of the Lymnaeidae family are the intermediate host of this parasite. Both snail population dynamics and parasite development are closely associated with temperature, although most field studies have recorded air temperature rather than water temperature. Our aim was to statistically model the population dynamics of lymnaeid snails and their infection by F. hepatica under natural environmental conditions in Northwest Andean Patagonia.MethodsFor two years, we sampled snails monthly in four bodies of water, while registering water and air temperature hourly, and assessing F. hepatica infection in snails. Hierarchical Bayesian modeling allowed us to estimate the functional relationship between water temperature and population growth, the probability of detecting snails, and infection by F. hepatica.ResultsA total of 1,411 Galba viatrix snails were collected, identified, and analyzed for F. hepatica infection. All sites showed seasonal variation in the number of snails collected and in water temperature as well as sharp variations in snail counts between surveys adjacent in time. The hierarchical model revealed that water temperature acts, at least, at two different time scales: water temperature at the time of sampling determines snail detection probability, whereas the average water temperature between sampling dates affects lymnaeid population growth. We found maximum F. hepatica prevalences in snails of 40% (2/5 and 4/10), followed by 33% (65/197). These are the highest prevalences recorded in G. viatrix populations in Argentina to date. Our modeling evidenced that the positive effects of water temperature on infection probability increases with snail size and prevalence on the previous survey, while previous prevalence strongly enhances the effects of snail size.ConclusionsOur results underscore the high temporal and spatial variability in the population of snails and the prevalence of F. hepatica, as well as the major impact temperature has on detecting snails. Our models provide quantifications of the effects of water temperature on the population growth of G. viatrix, its detection, and infection under natural field conditions. These are crucial steps towards generating mechanistic models of F. hepatica transmission that would facilitate the design and simulation of potential interventions based on treatments and on environmental and livestock management, taking into account the specific characteristics of each region. creator: Paula Soler creator: Juan Manuel Gurevitz creator: Juan Manuel Morales creator: Marcela Larroza uri: https://doi.org/10.7717/peerj.18648 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Soler et al. title: Quorum sensing signals of the grapevine crown gall bacterium, Novosphingobium sp. Rr2-17: use of inducible expression and polymeric resin to sequester acyl-homoserine lactones link: https://peerj.com/articles/18657 last-modified: 2024-12-20 description: BackgroundA grapevine crown gall tumor strain, Novosphingobium sp. strain Rr2-17 was previously reported to accumulate copious amounts of diverse quorum sensing signals during growth. Genome sequencing identified a single luxI homolog in strain Rr2-17, suggesting that it may encode for a AHL synthase with broad substrate range, pending functional validation. The exact identity of the complete suite of AHLs formed by novIspR1 is largely unknown.MethodsThis study validates the function of novIspR1 through inducible expression in Escherichia coli and in the wild-type parental strain Rr2-17. We further enhanced the capture of acyl homoserine lactone (AHL) signals produced by novIspR1 using polymeric resin XAD-16 and separated the AHLs by one- and two-dimensional thin layer chromatography followed by detection using AHL-dependent whole cell biosensor strains. Lastly, the complete number of AHLs produced by novIspR1 in our system was identified by LC-MS/MS analyses.ResultsThe single LuxI homolog of N. sp. Rr2-17, NovIspR1, is able to produce up to eleven different AHL signals, including AHLs: C8-, C10-, C12-, C14-homoserine lactone (HSL) as well as AHLs with OH substitutions at the third carbon and includes 3-OH-C6-, 3-OH-C8-, 3-OH-C10-, 3-OH-C12- and 3-OH-C14-HSL. The most abundant AHL produced was identified as 3-OH-C8-HSL and isopropyl-D-1-thiogalactopyranoside (IPTG) induction of novIspR1 expression in wild type parental Rr2-17 strain increased its concentration by 6.8-fold when compared to the same strain with the vector only control plasmid. Similar increases were identified with the next two most abundant AHLs, 3-OH-C10- and unsubstituted C8-HSL. The presence of 2% w/v of XAD-16 resin in the growth culture bound 99.3 percent of the major AHL (3-OH-C8-HSL) produced by IPTG-induced overexpression of novIspR1 in Rr2-17 strain. This study significantly adds to our understanding of the AHL class of quorum sensing system in a grapevine crown gall tumor associated Novosphingobium sp. Rr2-17 strain. The identity of nine AHL signals produced by this bacterium will provide a framework to identify the specific function(s) of the AHL-mediated quorum-sensing associated genes in this bacterium. creator: Han Ming Gan creator: Lucas Dailey creator: Peter Wengert creator: Nigel Halliday creator: Paul Williams creator: André O. Hudson creator: Michael A. Savka uri: https://doi.org/10.7717/peerj.18657 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Gan et al. title: Exploring the potential role of ENPP2 in polycystic ovary syndrome and endometrial cancer through bioinformatic analysis link: https://peerj.com/articles/18666 last-modified: 2024-12-20 description: BackgroundGrowing evidence indicates a significant correlation between polycystic ovary syndrome (PCOS) and endometrial carcinoma (EC); nevertheless, the fundamental molecular mechanisms involved continue to be unclear.MethodsInitially, differential analysis, the least absolute shrinkage and selection operator (LASSO) regression, and support vector machine-recursive feature elimination (SVM-RFE) algorithms were employed to identify candidate genes associated with ferroptosis in PCOS. Subsequently, the TCGA-UCEC data were utilized to pinpoint the core gene. Then, the expression of ENPP2 in granulosa cells and endometrium of PCOS was validated using real-time PCR (RT-qPCR). Additionally, we investigated the role of ENPP2 in the progression from PCOS to EC through western blotting (WB), colony formation assay, cell scratch assay, transwell assay, and immunofluorescence (IF). Subsequently, ENPP2 gene set enrichment analysis (GSEA) analyses were conducted to identify common pathways involved in PCOS and EC, which were then verified by RT-qPCR. Finally, immune infiltration and the tumor microenvironment (TME) were explored to examine the involvement of ENPP2 in EC progression.ResultsThe datasets TCGA-UCEC (pertaining to EC), GSE34526, GSE137684, and GSE6798 (related to PCOS) were procured and subjected to analysis. The gene ENPP2 has been recognized as the shared element connecting PCOS and EC. Next, we observed a significant downregulation of ENPP2 expression in the granulosa cells in PCOS compared to the normal patients, while an upregulation of ENPP2 expression was observed in the endometrium of hyperandrogenic PCOS patients relative to the normal. In vitro, the WB revealed that 5-dihydrotestosterone (DHT) upregulated ENPP2 expression in Ishikawa and HEC-1-A cells. Additionally, we found that ENPP2 promoted the proliferation, migration, and invasion of Ishikawa and HEC-1-A cells. Subsequently, we discovered that overexpressed ENPP2 may lead to an increase in CYP19A1 (aromatase) and AR mRNA level. IF demonstrated that ENPP2 increased the expression of AR, suggesting a regulatory role for ENPP2 in hormonal response within PCOS and EC. Our findings indicated a significant correlation between ENPP2 expression and the modulation of immune responses. creator: Xumin Zhang creator: Jianrong Liu creator: Chunmei Bai creator: Yang Li creator: Yanxin Fan uri: https://doi.org/10.7717/peerj.18666 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhang et al. title: Antimicrobial resistance pattern of Escherichia coli isolated from imported frozen shrimp in Saudi Arabia link: https://peerj.com/articles/18689 last-modified: 2024-12-20 description: Contamination of seafood products with multi-drug-resistant (MDR) bacteria is considered to be a potential source for the spread of MDR bacteria in communities. However, little is known about the extent of the contamination of seafood, in particular shrimp, with MDR bacteria in Saudi Arabia. In this study, imported frozen shrimp in retail markets were examined for the antimicrobial susceptibility patterns of Escherichia coli. Escherichia coli was isolated from 40 frozen shrimp samples; a total of 25 and 15 shrimp samples were imported from China and Vietnam, respectively. Of the 40 examined frozen shrimp samples, 30 tested positive for E. coli, resulting in an overall isolation rate of 75%, with a total of 180 isolates being identified. The largest number of positive samples for E. coli isolates (n = 140) were found in 22 out of 25 samples from frozen shrimp imported from China. Additionally, eight out of 15 samples from frozen shrimp imported from Vietnam were positive for E. coli, leading to the recovery of 40 isolates. Overall, the susceptibilities among E. coli isolates were observed against 99.4% for amikacin, augmentin and kanamycin, 95% for cefoxitin and 92.7% for ceftazidime and nitrofurantoin. High percentage of the isolates exhibited resistance to cephalothin (174/180, 96.6%), ampicillin (167/180, 92.7%), Cephalexin (163/180. 90.5%), piperacillin (156/180, 86.6%), ceftriaxone (123/180, 68.3%), nalidixic acid (95/180, 52.7%), trimethoprim sulphamethoxazole (90/180, 50%), and tetracycline (88/180, 48.8%). Additionally, the MDR (resistant to ≥3 different class of antimicrobials) rate among E. coli isolates was 94.4% (170/180). A relatively high intermediate resistance of 60% (108/180) was exhibited for aztreonam. Notably, E. coli showed 71 different antibiotic resistance patterns with the multiple antibiotic resistant (MAR) index ranging from 0.04 to 0.66 and 89.4% of E. coli isolates recorded very significant MAR indexes above the range of 0.2. In this study, we recorded highest antimicrobial co-resistance patterns of 162 (90%) isolates between cephalothin and ampicillin, followed by 158 (87.7%) isolates between cephalothin and cephalexin. Furthermore, and interestingly, the segregation of antimicrobial resistance patterns based on the source of country origin of frozen shrimp revealed few inter-country resistant patterns found interconnecting and this influenced 44 (24.4%) isolates overlapping between isolates origin from frozen shrimp imported from China and Vietnam. This study documents the antimicrobial resistance in E. coli isolated from imported frozen shrimp and the presence of MDR E. coli in shrimp consuming communities, which may pose a risk to public health and the transfer of resistant bacteria to the food chain and environment. creator: Ibrahim Alhabib creator: Nasreldin Elhadi uri: https://doi.org/10.7717/peerj.18689 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Alhabib and Elhadi title: Construction and clinical application of a risk model based on N6-methyladenosine regulators for colorectal cancer link: https://peerj.com/articles/18719 last-modified: 2024-12-20 description: BackgroundColorectal cancer (CRC) shows a high incidence in developed countries. This study established a prognosis signature based on N6-methyladenosine (m6A) regulators involved in CRC progression.MethodThe bulk RNA-seq data from the Atlas and Compass of Immune-Colon cancer-Microbiome interactions (AC-ICAM) and GSE33113 CRC datasets were obtained from the cBioportal and GEO databases, and a total of 21 m6A regulators genes were collected from a previous study. The scRNA-seq analysis of the GSE146771 cohort was conducted applying the Seurat and harmony R packages. Consensus clustering based on the expressions of m6A regulators was performed with the ConsensusClusterPlus package. The ggGSEA package was used for the Gene Set Enrichment Analysis (GSEA). The un/multivariate and LASSO Cox analysis were performed applying the “survival” and “glmnet” packages for developing a risk model. The pRRophetic and GSVA packages were utilized to analyze potential drugs for CRC and immune infiltration in different risk groups, followed by the Kaplan–Meier (KM) survival and ROC analysis with the “survival” and “timeROC” packages. In vitro assays included the quantitative polymerase chain reaction (qPCR), wound healing and transwell were performed.ResultsCRC patients in the AC-ICAM cohort were assigned into three molecular subtypes (S1, 2 and 3) based on nine m6A regulator genes. Specifically, the prognostic outcome of the S3 was the most favorable, while that of the S1 was the worst and this subtype was associated with the activation of NF-kB, TNF-α and hypoxia pathways. Three key genes, namely, methyltransferase-like 3 (METTL3), insulinolike Growth Factor2 mRNA-Binding Protein 3 (IGF2BP3) and YTH domain-containing protein 2 (YTHDC2), selected from the 9 m6A regulator genes were combined into a RiskScore, which showed a high classification effectiveness in dividing the patients into high- and low-risk groups. Inhibition of the expression of METTL3A or that of IGF2BP3 suppressed the invasion and migration of CRC cells. Notably, the high-risk patients had higher immune cell infiltration to support the activation of multiple immune responses and exhibited significantly poor prognosis. Meanwhile, a nomogram with practical clinical value was developed based on the RiskScore and other clinical features. Finally, eight potential drugs associated with the RiskScore were identified, and CD4+ cells and Tregs were found to be closely associated with CRC progression.ConclusionThe RiskScore model developed based on m6A regulators played a critical role in CRC development and can be considered as a prognosis predictor for patients with the cancer. The present discoveries will facilitate the diagnosis and clinical management of CRC patients. creator: Hanhan Zhu creator: Yu Yang creator: Zhenfeng Zhou uri: https://doi.org/10.7717/peerj.18719 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhu et al.