title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=320 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Caffeoylquinic acid profiling: comparative analysis in yerba mate, Indian camphorweed, and stevia extracts with emphasis on the influence of brewing conditions and cold storage in yerba mate infusion link: https://peerj.com/articles/17250 last-modified: 2024-05-06 description: Herbal infusions exhibit diverse pharmacological effects, such as antioxidant, anti-inflammatory, anticancer, antihypertensive, and antineurodegenerative activities, which can be attributed to the high content of phenolic compounds (e.g., caffeoylquinic acids (CQAs)). In this study, we used ultraperformance liquid chromatography to determine the content of CQAs in the methanolic extracts of model herbs, namely, yerba mate (Ilex paraguariensis), stevia (Stevia rebaudiana), and Indian camphorweed (Pluchea indica (L.) Less.). The results revealed that yerba mate had the highest total CQA content (108.05 ± 1.12 mg/g of dry weight). Furthermore, we evaluated the effect of brewing conditions and storage at 4 °C under dark and light conditions on the antioxidant property and total phenolic and CQA contents of a yerba mate infusion. The analysis of the yerba mate infusions prepared with different steeping times, dried leaf weights, and water temperatures revealed that the amount of extracted CQAs was maximized (∼175 mg/150 mL) when 6 g of dried leaves were steeped in hot water for 10 min. A total of 10-day refrigerated storage resulted in no significant changes in the antioxidant activity and total phenolic and CQA contents of an infusion kept in a brown container (dark). However, the antioxidant properties and total phenolic and CQA contents were negatively affected when kept in a clear container, suggesting the detrimental effect of light exposure. Our study provides practical recommendations for improving the preparation and storage of herbal infusions, thus catering to the needs of consumers, food scientists, and commercial producers. Moreover, it is the first study of the influence of light exposure on the content of crucial quality attributes within plant-based beverages. creator: Gholamreza Khaksar creator: Nantachaporn Chaichana creator: Kitipong Assatarakul creator: Supaart Sirikantaramas uri: https://doi.org/10.7717/peerj.17250 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Khaksar et al. title: XA21-mediated resistance to Xanthomonas oryzae pv. oryzae is dose dependent link: https://peerj.com/articles/17323 last-modified: 2024-05-06 description: The rice receptor kinase XA21 confers broad-spectrum resistance to Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of rice bacterial blight disease. To investigate the relationship between the expression level of XA21 and resulting resistance, we generated independent HA-XA21 transgenic rice lines accumulating the XA21 immune receptor fused with an HA epitope tag. Whole-genome sequence analysis identified the T-DNA insertion sites in sixteen independent T0 events. Through quantification of the HA-XA21 protein and assessment of the resistance to Xoo strain PXO99 in six independent transgenic lines, we observed that XA21-mediated resistance is dose dependent. In contrast, based on the four agronomic traits quantified in these experiments, yield is unlikely to be affected by the expression level of HA-XA21. These findings extend our knowledge of XA21-mediated defense and contribute to the growing number of well-defined genomic landing pads in the rice genome that can be targeted for gene insertion without compromising yield. creator: Nan Zhang creator: Xiaoou Dong creator: Rashmi Jain creator: Deling Ruan creator: Artur Teixeira de Araujo Junior creator: Yan Li creator: Anna Lipzen creator: Joel Martin creator: Kerrie Barry creator: Pamela C. Ronald uri: https://doi.org/10.7717/peerj.17323 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhang et al. title: Synergistic effect of seaweed extract and boric acid and/or calcium chloride on productivity and physico-chemical properties of Valencia orange link: https://peerj.com/articles/17378 last-modified: 2024-05-06 description: Many citrus species and cultivars are grown successfully in tropical and subtropical countries, as well as in arid and semi-arid regions with low levels of organic matter and low cation exchange, resulting in lower nutrient uptake by the plant. The essential nutrients needed for citrus flowering and fruit set are limited in winter due to a reduction in transpiration rate, negatively effecting vegetative growth, flowering, yield, and fruit quality. The present investigation was carried out to assess the nutritional status, fruit yield parameters, and fruit quality of Valencia orange trees after foliar spraying of seaweed extract (SW) combined with calcium chloride and boric acid and their combinations in the 2020/2021 and 2021/2022 seasons. The treatments were arranged in a split-plot design (three levels spraying seaweed extract × four levels spraying calcium chloride and boric acid and their combinations × four replicates × one tree/replicate). The results indicated that all of the characteristics measured, including leaf chlorophyll, leaf mineral contents, fruit yield parameters, fruit physical properties, and fruit chemical properties, were significantly affected by the foliar spraying of seaweed extract (SW) combined with calcium chloride and boric acid and their combinations. Although all treatments increased the productivity and the physical and chemical properties of Valencia orange fruits compared to the control, a treatment of 10 g/L SW combined with 0.5 g/L boric acid and 1 g/L calcium chloride produced superior results. This ratio of SW, boric acid, and calcium chloride is therefore recommended to enhance productivity and improve the physico-chemical properties of Valencia orange for greater fruit yield. creator: Abdullah Alebidi creator: Mahmoud Abdel-Sattar uri: https://doi.org/10.7717/peerj.17378 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Alebidi and Abdel-Sattar title: Whole-genome analysis of Escherichia coli isolated from wild Amur tiger (Panthera tigris altaica) and North China leopard (Panthera pardus japonensis) link: https://peerj.com/articles/17381 last-modified: 2024-05-06 description: BackgroundEscherichia coli is an important intestinal flora, of which pathogenic E. coli is capable of causing many enteric and extra-intestinal diseases. Antibiotics are essential for the treatment of bacterial infections caused by pathogenic E. coli; however, with the widespread use of antibiotics, drug resistance in E. coli has become particularly serious, posing a global threat to human, animal, and environmental health. While the drug resistance and pathogenicity of E. coli carried by tigers and leopards in captivity have been studied intensively in recent years, there is an extreme lack of information on E. coli in these top predators in the wild environment.MethodsWhole genome sequencing data of 32 E. coli strains collected from the feces of wild Amur tiger (Panthera tigris altaica, n = 24) and North China leopard (Panthera pardus japonensis, n = 8) were analyzed in this article. The multi-locus sequence types, serotypes, virulence and resistance genotypes, plasmid replicon types, and core genomic SNPs phylogeny of these isolates were studied. Additionally, antimicrobial susceptibility testing (AST) was performed on these E. coli isolates.ResultsAmong the E. coli isolates studied, 18 different sequence types were identified, with ST939 (21.9%), ST10 (15.6%), and ST3246 (9.4%) being the most prevalent. A total of 111 virulence genes were detected, averaging about 54 virulence genes per sample. They contribute to invasion, adherence, immune evasion, efflux pump, toxin, motility, stress adaption, and other virulence-related functions of E. coli. Sixty-eight AMR genes and point mutations were identified. Among the detected resistance genes, those belonging to the efflux pump family were the most abundant. Thirty-two E. coli isolates showed the highest rate of resistance to tetracycline (14/32; 43.8%), followed by imipenem (4/32; 12.5%), ciprofloxacin (3/32; 9.4%), doxycycline (2/32; 6.3%), and norfloxacin (1/32; 3.1%).ConclusionsOur results suggest that E. coli isolates carried by wild Amur tigers and North China leopards have potential pathogenicity and drug resistance. creator: Hongjia Li creator: Tianming Lan creator: Hao Zhai creator: Mengchao Zhou creator: Denghui Chen creator: Yaxian Lu creator: Lei Han creator: Jinpu Wei creator: Shaochun Zhou creator: Haitao Xu creator: Lihong Tian creator: Guangshun Jiang creator: Zhijun Hou uri: https://doi.org/10.7717/peerj.17381 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al. title: A comparison of five methods to maximize RNA and DNA isolation yield from adipose tissue link: https://peerj.com/articles/17071 last-modified: 2024-05-03 description: Adipose tissue in the human body occurs in various forms with different functions. It is an energy store, a complex endocrine organ, and a source of cells used in medicine. Many molecular analyses require the isolation of nucleic acids, which can cause some difficulties connected with the large amount of lipids in adipocytes. Ribonucleic acid isolation is particularly challenging due to its low stability and easy degradation by ribonucleases. The study aimed to compare and evaluate five RNA and DNA isolation methods from adipose tissue. The tested material was subcutaneous porcine adipose tissue subjected to different homogenization methods and RNA or DNA purification. A mortar and liquid nitrogen or ceramic beads were used for homogenization. The organic extraction (TriPure Reagent), spin columns with silica-membrane (RNeasy Mini Kit or High Pure PCR Template Preparation Kit), and the automatic MagNA Pure system were used for the purification. Five combinations were compared for RNA and DNA isolation. Obtained samples were evaluated for quantity and quality. The methods were compared in terms of yield (according to tissue mass), purity (A260/280 and A260/230), and nucleic acid degradation (RNA Integrity Number, RIN; DNA Integrity Number, DIN). The results were analyzed statistically. The average RNA yield was highest in method I, which used homogenization with ceramic beads and organic extraction. Low RNA concentration didn’t allow us to measure degradation for all samples in method III (homogenization with ceramic beads and spin-column purification). The highest RNA quality was achieved with method IV using homogenization in liquid nitrogen and spin column purification, which makes it the most effective for RNA isolation from adipose tissue. Required values of DNA yield, purity, and integrity were achieved only with spin column-based methods (III and IV). The most effective method for DNA isolation from adipose tissue is method III, using spin-columns without additional homogenization. creator: Pawel Dabrowski creator: Marta Rasmus creator: Arkadiusz Jundzill creator: Tomasz Drewa creator: Marta Pokrywczynska uri: https://doi.org/10.7717/peerj.17071 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Dabrowski et al. title: Are incremental exercise relationships between rating of perceived exertion and oxygen uptake or heart rate reserve valid during steady-state exercises? link: https://peerj.com/articles/17158 last-modified: 2024-05-03 description: BackgroundRating of perceived exertion (RPE) is considered a valid method for prescribing prolonged aerobic steady-state exercise (SSE) intensity due to its association with physiological indicators of exercise intensity, such as oxygen uptake (V̇O2) or heart rate (HR). However, these associations between psychological and physiological indicators of exercise intensity were found during graded exercise tests (GXT) but are currently used to prescribe SSE intensity even though the transferability and validity of the relationships found during GXT to SSE were not investigated. The present study aims to verify whether (a) RPE-HR or RPE-V̇O2 relations found during GXTs are valid during SSEs, and (b) the duration and intensity of SSE affect these relations.MethodsEight healthy and physically active males (age 22.6 ± 1.2 years) were enrolled. On the first visit, pre-exercise (during 20 min standing) and maximal (during a GXT) HR and V̇O2 values were measured. Then, on separate days, participants performed 4 SSEs on the treadmill by running at 60% and 80% of the HR reserve (HRR) for 15 and 45 min (random order). Individual linear regressions between GXTs’ RPE (dependent variable) and HRR and V̇O2 reserve (V̇O2R) values (computed as the difference between maximal and pre-exercise values) were used to predict the RPE associated with %HRR (RPEHRR) and %V̇O2R (RPEV̇O2R) during the SSEs. For each relation (RPE-%HRR and RPE-%V̇O2R), a three-way factorial repeated measures ANOVA (α = 0.05) was used to assess if RPE (dependent variable) was affected by exercise modality (i.e., RPE recorded during SSE [RPESSE] or GXT-predicted), duration (i.e., 15 or 45 min), and intensity (i.e., 60% or 80% of HRR).ResultsThe differences between RPESSE and GXT-predicted RPE, which were assessed by evaluating the effect of modality and its interactions with SSE intensity and duration, showed no significant differences between RPESSE and RPEHRR. However, when RPESSE was compared with RPEV̇O2R, although modality or its interactions with intensity were not significant, there was a significant (p = 0.020) interaction effect of modality and duration yielding a dissociation between changes of RPESSE and RPEV̇O2R over time. Indeed, RPESSE did not change significantly (p = 0.054) from SSE of 15 min (12.1 ± 2.0) to SSE of 45 min (13.5 ± 2.1), with a mean change of 1.4 ± 1.8, whereas RPEV̇O2R decreased significantly (p = 0.022) from SSE of 15 min (13.7 ± 3.2) to SSE of 45 min (12.4 ± 2.8), with a mean change of −1.3 ± 1.5.ConclusionThe transferability of the individual relationships between RPE and physiological parameters found during GXT to SSE should not be assumed as shown by the results of this study. Therefore, future studies modelling how the exercise prescription method used (e.g., RPE, HR, or V̇O2) and SSE characteristics (e.g., exercise intensity, duration, or modality) affect the relationships between RPE and physiological parameters are warranted. creator: Carlo Ferri Marini creator: Lorenzo Micheli creator: Tommaso Grossi creator: Ario Federici creator: Giovanni Piccoli creator: Luca Zoffoli creator: Luca Correale creator: Stefano Dell’Anna creator: Carlo Alberto Naldini creator: Francesco Lucertini creator: Matteo Vandoni uri: https://doi.org/10.7717/peerj.17158 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Ferri Marini et al. title: A new species of Languidipes Hubbard (Ephemeroptera, Polymitarcyidae) from Borneo link: https://peerj.com/articles/17327 last-modified: 2024-05-03 description: The genus Languidipes is currently represented by three species distributed in southeastern Asia, India, and Sri Lanka. Languidipes corporaali is the most widely distributed species, and both, male and female imagos, as well as nymphs, are known. In contrast, the other species, L. taprobanes and L. lithophagus, are only known from nymphs. Here, we describe a new species, Languidipes janae sp nov, based on male imagos collected from Borneo, Indonesia. This new species is characterized by the presence of ommation on mesonotum, and penis almost completely divided, with sub-quadrate base and a small outer projection basal to the long and slender distal arms. This constitutes the first record of the genus for Borneo. A cladistic analysis of the subfamily Asthenopodinae supports its taxonomic status. creator: Guillermo Eduardo Hankel creator: Carlos Molineri uri: https://doi.org/10.7717/peerj.17327 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Hankel and Molineri title: Significance of NKX2-1 as a biomarker for clinical prognosis, immune infiltration, and drug therapy in lung squamous cell carcinoma link: https://peerj.com/articles/17338 last-modified: 2024-05-01 description: BackgroundThis study was performed to determine the biological processes in which NKX2-1 is involved and thus its role in the development of lung squamous cell carcinoma (LUSC) toward improving the prognosis and treatment of LUSC.MethodsRaw RNA sequencing (RNA-seq) data of LUSC from The Cancer Genome Atlas (TCGA) were used in bioinformatics analysis to characterize NKX2-1 expression levels in tumor and normal tissues. Survival analysis of Kaplan–Meier curve, the time-dependent receiver operating characteristic (ROC) curve, and a nomogram were used to analyze the prognosis value of NKX2-1 for LUSC in terms of overall survival (OS) and progression-free survival (PFS). Then, differentially expressed genes (DEGs) were identified, and Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), and Gene Set Enrichment Analysis (GSEA) were used to clarify the biological mechanisms potentially involved in the development of LUSC. Moreover, the correlation between the NKX2-1 expression level and tumor mutation burden (TMB), tumor microenvironment (TME), and immune cell infiltration revealed that NKX2-1 participates in the development of LUSC. Finally, we studied the effects of NKX2-1 on drug therapy. To validate the protein and gene expression levels of NKX2-1 in LUSC, we employed immunohistochemistry(IHC) datasets, The Gene Expression Omnibus (GEO) database, and qRT-PCR analysis.ResultsNKX2-1 expression levels were significantly lower in LUSC than in normal lung tissue. It significantly differed in gender, stage and N classification. The survival analysis revealed that high expression of NKX2-1 had shorter OS and PFS in LUSC. The multivariate Cox regression hazard model showed the NKX2-1 expression as an independent prognostic factor. Then, the nomogram predicted LUSC prognosis. There are 51 upregulated DEGs and 49 downregulated DEGs in the NKX2-1 high-level groups. GO, KEGG and GSEA analysis revealed that DEGs were enriched in cell cycle and DNA replication.The TME results show that NKX2-1 expression was positively associated with mast cells resting, neutrophils, monocytes, T cells CD4 memory resting, and M2 macrophages but negatively associated with M1 macrophages. The TMB correlated negatively with NKX2-1 expression. The pharmacotherapy had great sensitivity in the NKX2-1 low-level group, the immunotherapy is no significant difference in the NKX2-1 low-level and high-level groups. The analysis of GEO data demonstrated concurrence with TCGA results. IHC revealed NKX2-1 protein expression in tumor tissues of both LUAD and LUSC. Meanwhile qRT-PCR analysis indicated a significantly lower NKX2-1 expression level in LUSC compared to LUAD. These qRT-PCR findings were consistent with co-expression analysis of NKX2-1.ConclusionWe conclude that NKX2-1 is a potential biomarker for prognosis and treatment LUSC. A new insights of NKX2-1 in LUSC is still needed further research. creator: Huiyue Lin creator: Juyong Wang creator: Qing Shi creator: Minmin Wu uri: https://doi.org/10.7717/peerj.17338 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Lin et al. title: The Chronic Time Pressure Inventory: further assessment of factorial structure and validity link: https://peerj.com/articles/17373 last-modified: 2024-05-01 description: BackgroundChronic time pressure represents a prevalent concern within modern society, and effective measurement is crucial for research advancement. The Chronic Time Pressure Inventory (CTPI) has thus far demonstrated adequate psychometric properties. However, only two studies have examined the measure and evidence of its validity is limited. Accordingly, the current investigation, via two independent studies, assessed the factorial composition and validity (convergent/discriminant) of the CTPI.MethodsStudy 1 (N = 398) examined competing factorial models and validity in relation to the Big Five personality traits (Extraversion, Agreeableness, Conscientiousness, Neuroticism, Openness). Study 2 (N = 358) replicated the analysis of factor structure and assessed validity in comparison with five time perspectives (Past Negative, Present Fatalistic, Future, Past Positive, Present Hedonistic). Participants across both studies completed standardized self-report measures capturing the variables.ResultsComparison of confirmatory factor analysis (CFA) and exploratory structural equation modelling (ESEM) factor solutions indicated that an ESEM bifactor model provided the strongest data-model fit. This included a general chronic time pressure component alongside specific subfactors of Feeling Harried and Cognitive Awareness of Time Shortage. All scale items reflected the general factor; however, some items loaded weakly on the intended specific factor. The CTPI is thus a robust indicator of chronic time pressure but needs refinement as a measure of the specific factors. Convergent/discriminant validity analyses inferred that the CTPI captured chronic time pressure as a related, but distinct, construct to perceived stress, and evidenced a relationship with theoretically associated constructs (Big Five personality traits and time perspective). Overall, the CTPI is a sound measure of chronic time pressure and has the potential to further cohesive research efforts on the contribution of this construct to various life domains. creator: Andrew Denovan creator: Neil Dagnall creator: Ken Drinkwater uri: https://doi.org/10.7717/peerj.17373 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Denovan et al. title: The efficacy of single mitochondrial genes at reconciling the complete mitogenome phylogeny—a case study on dwarf chameleons link: https://peerj.com/articles/17076 last-modified: 2024-04-30 description: Although genome-scale data generation is becoming more tractable for phylogenetics, there are large quantities of single gene fragment data in public repositories and such data are still being generated. We therefore investigated whether single mitochondrial genes are suitable proxies for phylogenetic reconstruction as compared to the application of full mitogenomes. With near complete taxon sampling for the southern African dwarf chameleons (Bradypodion), we estimated and compared phylogenies for the complete mitogenome with topologies generated from individual mitochondrial genes and various combinations of these genes. Our results show that the topologies produced by single genes (ND2, ND4, ND5, COI, and COIII) were analogous to the complete mitogenome, suggesting that these genes may be reliable markers for generating mitochondrial phylogenies in lieu of generating entire mitogenomes. In contrast, the short fragment of 16S commonly used in herpetological systematics, produced a topology quite dissimilar to the complete mitogenome and its concatenation with ND2 weakened the resolution of ND2. We therefore recommend the avoidance of this 16S fragment in future phylogenetic work. creator: Devon C. Main creator: Jody M. Taft creator: Anthony J. Geneva creator: Bettine Jansenvan Vuuren creator: Krystal A. Tolley uri: https://doi.org/10.7717/peerj.17076 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Main et al.