Molecular identification of critically endangered European eels (Anguilla anguilla) in US retail outlets
The European eel (Anguilla anguilla) has declined by over 90% since the early 1980s and has been listed as critically endangered. Yet, despite strict export bans from the European Union, the European eel is still sold illegally in many countries. Efforts to monitor the trade of European eels have been primarily concentrated in Asian markets where concerningly high rates of European eel have been reported. Comparably fewer studies have assessed the identities of eel samples from the United States (US), despite the obvious implications for eel conservation. To address this knowledge gap, we purchased 137 eel products (134 freshwater eels and three saltwater eels) from grocers, sushi bars, and restaurants in nine states across the US from 2019 to 2021. Seven samples (5.2%) labeled as freshwater eels (or “unagi”) were identified as European eels using a combination of mitochondrial (cytochrome b) and nuclear (18S rRNA) restriction digestion assays, a fast and inexpensive molecular tool for seafood identification that can identify hybrids between European eels (A. anguilla) and American eels (A. rostrata). No hybrids between European and American eels were found and all seven samples identified with restriction digestion as European eels were confirmed by sequencing of cytochrome b and 18S rRNA. Frequency of European eels in US markets did not significantly correlate with state or retail type. Although illegal eel exports are likely reaching US consumers, the frequency of European eel samples in this study of the US market is much lower than found in other non-European countries.
Ely et al. (2023) Molecular identification of critically endangered European eels (Anguilla anguilla) in US retail outlets. PeerJ 11:e14531 https://doi.org/10.7717/peerj.14531
Remote sensing technology for rapid extraction of burned areas and ecosystem environmental assessment
Forest fires are one of the significant disturbances in forest ecosystems. It is essential to extract burned areas rapidly and accurately to formulate forest restoration strategies and plan restoration plans. In this work, we constructed decision trees and used a combination of differential normalized burn ratio (dNBR) index and OTSU threshold method to extract the heavily and mildly burned areas. The applicability of this method was evaluated with three fires in Muli County, Sichuan, China, and we concluded that the extraction accuracy of this method could reach 97.69% and 96.37% for small area forest fires, while the extraction accuracy was lower for large area fires, only 89.32%. In addition, the remote sensing environment index (RSEI) was used to evaluate the ecological environment changes. It analyzed the change of the RSEI level through the transition matrix, and all three fires showed that the changes in RSEI were stronger for heavily burned areas than for mildly burned areas, after the forest fire the ecological environment (RSEI) was reduced from good to moderate. These results realized the quantitative evaluation and dynamic evaluation of the ecological environment condition, providing an essential basis for the restoration, decision making and management of the affected forests.
Spatial and Geographic Information Science
Zhang et al. (2023) Remote sensing technology for rapid extraction of burned areas and ecosystem environmental assessment. PeerJ 11:e14557 https://doi.org/10.7717/peerj.14557
Putative source and niche shift pattern of a new alien ant species (Odontomachus troglodytes) in Taiwan
Alien species may pose substantial impacts on biodiversity around the globe through international trade and travel. A niche shift hypothesis was proposed to explain the adaptive change of alien or invasive species in new habitats. However, whether niche shifts occur in alien species likely depends on both characteristics inherent to the species itself and its original distribution. Here we identified a newly exotic trap-jaw ant (Odontomachus troglodytes) in Taiwan by morphological and phylogenetic analyses. The possible distribution range and the niche shift pattern were evaluated using ecological niche modelling. The results indicated that exotic O. troglodytes in the newly distributed area displayed a significant niche shift with low niche overlap and high niche expansion. This study reveals a long-distance invasive event from central Africa to Southeast Asia (more than 10,000 km) and predicts the potential distribution range of this new alien species in Taiwan.
Lin et al. (2023) Putative source and niche shift pattern of a new alien ant species (Odontomachus troglodytes) in Taiwan. PeerJ 11:e14718 https://doi.org/10.7717/peerj.14718
Cross-sectional associations between body mass index, waist circumference, and multimorbidity: Pró-Saúde study
Background This study aimed (1) To investigate the association between the Body Mass Index (BMI) and waist circumference (WC) with multimorbidity (MM), and (2) To identify patterns of MM and investigate the relationship between BMI and WC with specific combinations of MM (patterns of MM). Methods A cross-sectional study was conducted with 2,698 participants of the fourth phase of the Brazilian Longitudinal Study of Adult Health (Pró-Saúde Study). MM was defined by the presence of two or more morbidities. MM patterns were identified by exploratory factor analysis based on tetrachoric correlations. Logistic regression models were used to assess associations (odds ratios (OR) with the respective confidence intervals (CI)). Results Of the total number of participants, 39.5% were overweight and 30.0% were obese; 89.0% (n = 1,468) of women and 77.0% (n = 952) of men were abdominally obese. Indeed, 60.7% (n = 1,635) was identified with MM. For the category four or more morbidities, OR values of 5.98 (95% CI 4.84–7.13) and 7.48 (95% CI 6.14–8.18) were found for each point of increase in BMI, and 6.74 (95% CI 5.48–7.99) and 8.48 (95% CI 7.64–9.29) for each additional centimeter in the WC, for female and male, respectively. Five patterns of MM were identified: respiratory, osteoarticular, cardiometabolic, gastric, and thyroid diseases (56.4% of the total variance). Positive associations were found between BMI and patterns of cardiometabolic, osteoarticular, thyroid and gastric diseases (higher OR of 1.09 [95% CI 1.04–1.14]) and less pronounced between WC and patterns of cardiometabolic and osteoarticular (higher OR of 1.04 [95% CI 1.03–1.04]). Conclusions The results showed that an increase of both BMI and WC was associated with a higher number of morbidities and with patterns of cardiometabolic and osteoarticular diseases.
Stumpf et al. (2023) Cross-sectional associations between body mass index, waist circumference, and multimorbidity: Pró-Saúde study. PeerJ 11:e14744 https://doi.org/10.7717/peerj.14744
Efficacy of Saccharothrix algeriensis NRRL B-24137 to suppress Fusarium oxysporum f.sp. vasinfectum induced wilt disease in cotton
Fusarium cotton wilt is a devastating disease of the cotton crop throughout the world, caused by Fusarium oxysporum f.sp. vasinfectum (FOV). Chemical control has many side effects, so, biological controls have been widely used for the management of Fusarium wilt. This study aimed to investigate the possible use of an actinomycetes Saccharothrix algeriensis (SA) NRRL B-24137 to control FOV. To access in-vitro anti-Fusarium ability of SA NRRL B-24137, dual culture assay, spore germination and seed germination tests were carried out. Following in-vitro investigations, several pot tests in a greenhouse environment were used to evaluate the biological control potential of SA NRRL B-24137 against FOV. Dual culture assay and spore germination revealed that SA NRRL B-24137 showed significant anti-Fusarium activity.During spore germination 87.77% inhibition of spore germination were observed. In pot experiments, SA NRRL B-24137 primed cotton seeds resulted in a 74.0% reduction in disease incidence. In soil there was a significant reduction in FOV spores in the presence of SA NRRL B-24137. Positive correlation was also observed on different concentrations of SA NRRL B-24137 towards FOV reduction. The results of this study showed that SA NRRL B-24137 has the potential to be employed as a biocontrol agent against Fusarium cotton wilt, improving cotton growth characteristics and yield.
Asif et al. (2023) Efficacy of Saccharothrix algeriensis NRRL B-24137 to suppress Fusarium oxysporum f.sp. vasinfectum induced wilt disease in cotton. PeerJ 11:e14754 https://doi.org/10.7717/peerj.14754
Prohexadione calcium enhances rice growth and tillering under NaCl stress
Salt stress affects crop quality and reduces crop yields, and growth regulators enhance salt tolerance of crop plants. In this report, we examined the effects of prohexadione-calcium (Pro-Ca) on improving rice (Oryza sativa L.) growth and tillering under salt stress. We found that NaCl stress inhibited the growth of two rice varieties and increased malondialdehyde (MDA) levels, electrolyte leakage, and the activities of the antioxidant enzymes. Foliar application of Pro-Ca reduced seedling height and increased stem base width and lodging resistance of rice. Further analyses showed that Pro-Ca application reduced MDA content, electrolyte leakage, and membrane damage in rice leaves under NaCl stress. Pro-Ca enhanced the net photosynthetic rate (Pn), stomatal conductance (Gs), and intercellular CO2 concentration (Ci) of rice seedlings, while increasing the activities of superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and ascorbic acid peroxidase (APX) at the tillering stage under salt stress. Overall, Pro-Ca improves salt tolerance of rice seedlings at the tillering stage by enhancing lodging resistance, reducing membrane damages, and enhancing photosynthesis and antioxidant capacities of rice seedlings.
Zhang et al. (2023) Prohexadione calcium enhances rice growth and tillering under NaCl stress. PeerJ 11:e14804 https://doi.org/10.7717/peerj.14804
Influence of resin modified glass ionomer cement incorporating protein-repellent and antimicrobial agents on supragingival microbiome around brackets: an in-vivo split-mouth 3-month study
Objective To explore the influence of resin modified glass ionomer cement (RMGIC) adhesives containing protein-repellent and quaternary ammonium salt agents on supragingival microbiome, enamel and gingival health around brackets. Materials and Methods Ten patients (21.4 ± 3.5 years) about to receive fixed orthodontics were enrolled in this study. Unilateral upper teeth bonded with RMGIC incorporating 2-Methacryloyloxyethyl phosphorylcholine (MPC) and Dimethylaminohexadecyl methacrylate (DMAHDM) were regarded as experimental group (RMD), while contralateral upper teeth bonded with RMGIC were control group (RMGIC), using a split-mouth design. Supragingival plaque was collected from both groups before treatment (T0), and at 1 month (T1) and 3 months (T2) of treatment. High-throughput sequencing was performed targeting v3–v4 of 16S rRNA gene. Streptococcus mutans and Fusobacterium nucleatum quantification was done by qPCR analysis. Bracket failures, enamel decalcification index (EDI), DIAGNODent scores (Dd), plaque index (PI) and gingival index (GI) were monitored at indicated time points. Results Within 3 months, alpha and beta diversity of supragingival plaque had no difference between RMGIC and RMD groups. From T0 to T2, the relative abundance of Streptococcus depleted in RMD but remained steady in RMGIC group. Streptococcus, Prevotella, and Fusobacterium became depleted in RMD, Haemophilus and Capnocytophaga became depleted in RMGIC group but Prevotella enriched. Quantification of Fusbacterium nucleatum and Streptococcus mutans showed significant difference between RMGIC and RMD groups at T2. Teeth bonded with RMD had significant lower plaque index (PI) and DIAGNODent (Dd) score at T2, compared with teeth bonded with RMGIC (p < 0.05). No difference in bracket failure rate was examined between both groups (p > 0.05). Conclusion By incorporating MPC and DMAHDM into RMGIC, the material could affect the supragingival microbial composition, inhibit the progress of plaque accumulation as well as the key pathogens S. mutans and F. nucleatum in the early stage of orthodontic treatment.
Ma et al. (2023) Influence of resin modified glass ionomer cement incorporating protein-repellent and antimicrobial agents on supragingival microbiome around brackets: an in-vivo split-mouth 3-month study. PeerJ 11:e14820 https://doi.org/10.7717/peerj.14820
Construction and validation of a fatty acid metabolism-related gene signature for predicting prognosis and therapeutic response in patients with prostate cancer
Background Reprogramming of fatty acid metabolism is a newly-identified hallmark of malignancy. However, no studies have systematically investigated the fatty acid metabolism related-gene set in prostate cancer (PCa). Methods A cohort of 381 patients with gene expression and clinical data from The Cancer Genome Atlas was used as the training set, while another cohort of 90 patients with PCa from GEO (GSE70769) was used as the validation set. Differentially expressed fatty acid metabolism-related genes were subjected to least absolute shrinkage and selection operator (LASSO)-Cox regression to establish a fatty acid metabolism-related risk score. Associations between the risk score and clinical characteristics, immune cell infiltration, tumor mutation burden (TMB), tumor immune dysfunction and exclusion (TIDE) score, and response to chemotherapy were analyzed. Finally, the expression level of genes included in the model was validated using real-time PCR. Results A prognostic risk model based on five fatty acid metabolism related genes (ALDH1A1, CPT1B, CA2, CROT, and NUDT19) were constructed. Tumors with higher risk score were associated with larger tumor size, lymph node involvement, higher Gleason score, and poorer biochemical recurrence (BCR)-free survival. Furthermore, the high- and low-risk tumors exhibited distinct immune cell infiltration features and immune-related pathway activation. High-risk tumors were associated with favorable response to immunotherapy as indicated by high TMB and low TIDE score, but poor response to bicalutamide and docetaxel chemotherapy. Conclusion This study established a fatty acid metabolism-related gene signature which was predictive of BCR and response to chemotherapy and immunotherapy, providing a novel therapeutic biomarker for PCa.
Zhao et al. (2023) Construction and validation of a fatty acid metabolism-related gene signature for predicting prognosis and therapeutic response in patients with prostate cancer. PeerJ 11:e14854 https://doi.org/10.7717/peerj.14854
Elevated serum FGF21 levels predict heart failure during hospitalization of STEMI patients after emergency percutaneous coronary intervention
Background Fibroblast growth factor 21 (FGF21) has multiple cardioprotective effects including modulation of glucolipid metabolism, anti-inflammation, and anti-oxidative stress, but its association with the heart failure during hospitalization in patients with ST-segment elevation myocardial infarction (STEMI) undergoing emergency percutaneous coronary intervention (PCI) has not been reported. Methods A total of 348 STEMI patients treated with emergency PCI were included from January 2016 to December 2018. Relevant biochemical indicators were measured by central laboratory. Serum FGF21 levels were measured by ELISA. The occurrence of heart failure during hospitalization was recorded. Patients’ cardiac function was assessed by echocardiography. Results Serum FGF21 levels were significantly higher in the STEMI group with heart failure than in the group without heart failure (249.95 ± 25.52 vs. 209.98 ± 36.35, P < 0.001). Serum FGF21 levels showed a strong positive correlation with N-terminal precursor B-type natriuretic peptide (NT-proBNP) in STEMI patients (r = 0.749, P < 0.001). FGF21 was found to be an independent risk factor for the development of heart failure during hospitalization in STEMI patients by binary logistic regression analysis. The area under curve (AUC) for FGF21 to predict the development of heart failure during hospitalization in STEMI patients was 0.816 (95% CI [0.770–0.863]) according to the receiver operating characteristic (ROC) curve analysis. Conclusion Elevated serum FGF21 levels have been shown to be a strong predictor of heart failure during hospitalization in patients with STEMI after emergency PCI.
Gu et al. (2023) Elevated serum FGF21 levels predict heart failure during hospitalization of STEMI patients after emergency percutaneous coronary intervention. PeerJ 11:e14855 https://doi.org/10.7717/peerj.14855
Comparative chloroplast genome analyses of diverse Phoebe (Lauraceae) species endemic to China provide insight into their phylogeographical origin
The genus Phoebe (Lauraceae) includes about 90 evergreen tree species that are an ideal source of timber. Habitat destruction and deforestation have resulted in most of them being endemic to China. The accurate identification of endangered Phoebe species in China is necessary for their conservation. Chloroplast genome sequences can play an important role in species identification. In this study, comparative chloroplast genome analyses were conducted on diverse Phoebe species that are primarily distributed in China. Despite the conserved nature of chloroplast genomes, we detected some highly divergent intergenic regions (petA–psbE, ndhF–rpl32, and psbM–trnD-GUC) as well as three highly divergent genes (rbcL, ycf1, and ycf2) that have potential applications in phylogenetics and evolutionary analysis. The phylogenetic analysis indicated that various Phoebe species in China were divided into three clades. The complete chloroplast genome was better suited for phylogenetic analysis of Phoebe species. In addition, based on the phylogeographical analysis of Phoebe species in China, we inferred that the Phoebe species in China first originated in Yunnan and then spread to other southern areas of the Yangtze River. The results of this research will add to existing case studies on the phylogenetic analysis of Phoebe species and have the potential to contribute to the conservation of Phoebe species that are in danger of extinction.
Shi et al. (2023) Comparative chloroplast genome analyses of diverse Phoebe (Lauraceae) species endemic to China provide insight into their phylogeographical origin. PeerJ 11:e14573 https://doi.org/10.7717/peerj.14573