title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=154 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en 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. title: Vegetation–soil–microbiota dynamics across a 50-year reconstructed grassland chronosequence on the Loess Plateau of China link: https://peerj.com/articles/18723 last-modified: 2024-12-20 description: Alfalfa (Medicago sativa L.) establishment is an effective strategy for grassland reconstruction in degraded ecosystems. However, the mechanisms underlying vegetation succession in reconstructed grasslands following alfalfa establishment remain elusive. In this study, we investigated vegetation community, soil quality and rhizosphere microbiota dynamics across a reconstructed grassland chronosequence in the loess region of Northwest China. A space-for-time substitution method was used to evaluate grassland vegetation coverage and alfalfa production performance in nine stands of different ages (1–50 years old). High-throughput sequencing was conducted to characterise rhizosphere microbial communities associated with alfalfa. The plant heights, yields and stem-to-leaf ratios of alfalfa all peaked in the 7-year-old stand and then decreased in older stands, with Stipa bungeana replacing alfalfa as the dominant species in the 50-year-old stand. Soil bulk density and major nutrient contents were highest in the artificial grassland (1–10 years). Soil enzyme activities (e.g., urease and sucrase) were enhanced in the transitional grassland (10–30 years), accompanied by enrichment of potentially beneficial microbial taxa (e.g., Actinobacteria and Mortierella) and functional fungi (e.g., saprotrophs and symbiotrophs) in the rhizosphere. Soil water content, total porosity and rhizosphere microbial diversity reached their maximum levels in the natural grassland (>30 years). The results indicate that alfalfa establishment alters soil structure and nutrient status in the short term, creating an optimal rhizosphere micro-environment. The improved soil conditions and rhizosphere microbiota are favourable for subsequent establishment of native grass species, leading to the formation of a stable semi-natural grasslands. creator: Yuanyuan Ma creator: Yan Shen creator: Ling Jin creator: Yu Tian creator: Hongbin Ma creator: Jian Lan creator: Bingzhe Fu uri: https://doi.org/10.7717/peerj.18723 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ma et al. title: Effect of seedling size on post-planting growth and survival of five Mexican Pinus species and their hybrids link: https://peerj.com/articles/18725 last-modified: 2024-12-20 description: BackgroundSeedling growth and survival depend on seedling quality. However, there is no experimental evidence showing that the seedling dimensions of the abundant, economically important and widely distributed tree species Pinus arizonica, P. durangensis, P. engelmannii, P. leiophylla, and P. teocote and their hybrids effectively improve survival and growth in reforestations and plantations in Mexico. Therefore, the aim was to evaluate the influence of initial morphological parameters of 2,007 nursery seedlings of these species and their hybrids on their growth and survival 44 months after planting in the Sierra Madre Occidental, Mexico.MethodsSpearman’s coefficient (rs) and the unbiased conditional pseudo coefficient of determination (R2c) between each specific predictor and each response variable and their 95% confidence interval (CI95%) were determined using Random Forest, generalized linear model, and bootstrapping. By bootstrapping, the potential environmental heterogeneity inside the trial fields and its impact on the results were also quantified.ResultsAmong the studied species and their hybrids moderate correlations were observed between the nursery seedling dimensions and the plant dimensions 44 months after planting. However, only weak significant correlations were found between survival rate (SR) and height (H) (rs = 0.10) and between SR and robustness index (HRCD) both before planting (rs = 0.06). Also, weak significant R2c values of the seedlings RCD, H and HRCD were detected with respect to the corresponding RCD, H and SR 44 months after planting, respectively. Furthermore, the predictor variable “seed provenance” (with 23 provenances) significantly explained the variation in the post-planting RCD, H and SR of the seedlings, with R2c values ranging from 0.10 to 0.15. The low width of the CI95% shows that the environmental conditions in the trial fields were quite homogeneous.DiscussionThe results also show that the inclusion of “confounding” variables in the statistical analysis of the study was crucial. Important factors to explain this low association could be the strong damage observed caused by pocket gopher, the typically low winter-spring precipitation in both field trials and adaptation factors. The study findings provide preliminary insights and information aimed at helping to design more appropriate standards for nurseries. creator: José Alberto Ponce-Figueroa creator: Pablo Antúnez creator: José Ciro Hernández-Díaz creator: José Ángel Prieto-Ruíz creator: Artemio Carrillo-Parra creator: Pablito Marcelo López-Serrano creator: Christian Wehenkel uri: https://doi.org/10.7717/peerj.18725 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ponce-Figueroa et al. title: The movement and distribution of pregnant spotted ragged-tooth sharks, Carcharias taurus, in the iSimangaliso Wetland Park, South Africa link: https://peerj.com/articles/18736 last-modified: 2024-12-20 description: The spotted ragged-tooth shark, Carcharias taurus, is widely distributed in subtropical continental coastal seas. In South Africa, it is commonly found along the entire south and east coasts, including the iSimangaliso Wetland Park (IWP) in the far north, which is the largest Marine Protected Area on the South African coast. Pregnant females occur there for much of the year, with the largest aggregations in summer. It is here we used remote underwater photography (RUP), supplemented with in-situ surveys to photo-identify individuals, using unique spot patterns. Three known aggregation sites (Raggie Reef, Quarter-Mile Reef and Mushroom Rocks) were monitored over a 5-year period between 2018 and 2023. We photo-identified 574 individuals (569 females and five males) and registered 1,200 sightings, using images of the right flank. The identification of new individuals persisted throughout the study, with the discovery curve showing no signs of reaching an asymptote. A total of 97% (n = 550) of females observed were noticeably pregnant. Individuals were consistently identified across all sample years and at all three reefs, exhibiting movements among the three monitored sites. The reproductive cycle is generally regarded as 2 years, but some females appeared to have a 2-year rest between pregnancies. Raggie Reef, which lies in the sanctuary zone, emerged as the reef with the highest index of popularity, as individuals were present almost constantly (90% of the sampling days). The findings of this study confirm the crucial role that the IWP plays in the conservation of a species that is globally Critically Endangered. creator: Sara C. Cerqueira creator: Jennifer Margaret Olbers creator: Grant Smith creator: Michelle Carpenter creator: Mário J. Pereira creator: Geremy Cliff uri: https://doi.org/10.7717/peerj.18736 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Cerqueira et al. title: Visual codon: a user-friendly Python program for viewing and optimizing gene GC content link: https://peerj.com/articles/18755 last-modified: 2024-12-20 description: Due to the codon bias of different species, codon optimization is usually carried out in the process of heterologous protein expression. At present, there are a variety of codon optimization tools. However, the optimized sequences may still have high or low points of local guanine and cytosine (GC) content, which is not conducive to the primer design of gene subcloning, and also makes it difficult to perform the experiment of synthesizing the whole gene with DNA fragments by polymerase chain reaction (PCR) reaction. In this study, we present a stand-alone software written in Python, with which users can manually check and adjust the GC content of sequence-optimized genes. The software takes the codon frequency of Escherichia coli as default and can work with other species as well. It provides a Graphical User Interface (GUI) interface, which allows users to change codons and intuitively see the effect of codon changes on local GC content. Our program brings convenience for the optimization of gene GC content and the subsequent gene cloning experiments. creator: Shiming Lin creator: Fei Xu creator: Bifang Huang creator: Li-li Zhao creator: Danni Pan creator: Shiqiang Lin uri: https://doi.org/10.7717/peerj.18755 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Lin et al. title: Correlation and mediation analysis between plasmapheresis donation behavior and bone mineral density and bone metabolism biomarkers: a cross-sectional study based on plasmapheresis donors at high risk of osteoporosis in China link: https://peerj.com/articles/18589 last-modified: 2024-12-19 description: BackgroundAs a group of more than 3.67 million people, the bone health of Chinese plasmapheresis donors, which the main population is also a risk group of osteoporosis (OP), has raised concerns. Therefore, this article investigates the relationship between bone mineral density (BMD), bone metabolism indicators, and plasmapheresis donation behavior among some high-risk plasmapheresis donors for OP in China, and further explores the mediating factors through reasonable statistical methods.MethodsRecruiting long-term and highly active plasmapheresis donors and new donors to measure the total calcium, albumin (ALB), 25-hydroxy vitamin D (25OHD), parathyroid hormone (PTH), type I procollagen amino-terminal peptide (P1NP), and type I collagen carboxy-terminal peptide (β-CTX) and serum ferritin (SF). Then, multiple linear regression was used to adjust confounding factors. Using restrictive cubic splines to explore the nonlinear relationship. Using the Bootstrap method, investigate whether SF has a mediating effect between plasmapheresis donation behavior and bone metabolism biomakers. Finally, analyze the differences in BMD between the two.ResultsCompared to new donors, repeat donors have a lower 25OHD, β-CTX and SF levels, while P1NP and PTH levels are high, with statistical differences. The Bootstrap analysis results show that SF level is a partial mediating factor between plasmapheresis donation behavior and bone metabolism biomakers, with a mediating effect ratio of 21.8%. There was no significant difference in the BMD between the two.ConclusionLong-term and frequently plasmapheresis donation does not affect the bone mass of even elderly donors at high risk for osteoporosis under the existing collection standards and anticoagulant use in China. However, as a self-regulation way, it does increase the osteogenic activity of the body. creator: Wan Li creator: Jia Liu creator: Changqing Li creator: Hui Yang creator: Yating Yang creator: Zhiwei Li creator: Shouqiang Yang creator: Yuan He creator: Guanglin Xiao creator: Ya Wang creator: Yongjun Chen uri: https://doi.org/10.7717/peerj.18589 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Li et al. title: Updated range distribution of the non-native Asian green mussel Perna viridis (Linnaeus, 1758) at Guanabara Bay, Rio de Janeiro, Brazil link: https://peerj.com/articles/18649 last-modified: 2024-12-19 description: Guanabara Bay, located at Rio de Janeiro, Brazil, is a highly urbanized and polluted estuary that houses different port areas, shipyards, and marinas of intense maritime traffic. This infrastructure is widely associated with the introduction and spread of non-native sessile species. A rapid assessment of non-native benthic sessile species conducted in the bay in late 2022 across 19 sites identified a total of 83 taxa, both native and non-native, classified into the following main groups: one Cyanophyta, 13 Macroalgae, 14 Porifera, 11 Cnidaria, six Bryozoa, five Annelida, 10 Mollusca, six Crustacea, 10 Echinodermata, and seven Ascidiacea. Our findings revealed the proliferation of the Asian green mussel (Perna viridis Linnaeus, 1758), a species noted for its exceptional ability to achieve extremely high biomass levels globally. In Brazil, the bivalve was first reported less than 6 years ago in 2018 at Guanabara Bay, on a mariculture farm at Arraial do Cabo (200 km away) in 2023 and more recently in the south (Paranaguá Bay), besides two coastal islands outside Guanabara Bay on natural rocky shores. The present survey recorded P. viridis at 17 sites, including natural substrata, co-occurring with native species. No Tubastraea spp. were observed in Guanabara Bay. Controlling and mitigating the consequences of bioinvasion events can be challenging, but biosafety protocols should be adopted in the near feature to minimize the risks and impacts caused by species dispersal. creator: Luciana V. R. de Messano creator: José E. A. Gonçalves creator: Alexandre D. Kassuga creator: Alexandre R. da Silva creator: Bruno P. Masi creator: Héctor F. Messano creator: Denny Fardin creator: Ricardo Coutinho uri: https://doi.org/10.7717/peerj.18649 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 de Messano et al.