title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=495 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Glutathione-mediated changes in productivity, photosynthetic efficiency, osmolytes, and antioxidant capacity of common beans (Phaseolus vulgaris) grown under water deficit link: https://peerj.com/articles/15343 last-modified: 2023-06-22 description: Globally, salinity and drought are severe abiotic stresses that presently threaten vegetable production. This study investigates the potential exogenously-applied glutathione (GSH) to relieve water deficits on Phaseolus vulgaris plants cultivated in saline soil conditions (6.22 dS m−1) by evaluating agronomic, stability index of membrane, water satatus, osmolytes, and antioxidant capacity responses. During two open field growing seasons (2017 and 2018), foliar spraying of glutathione (GSH) at 0.5 (GSH1) or 1.0 (GSH1) mM and three irrigation rates (I100 = 100%, I80 = 80% and I60 = 60% of the crop evapotranspiration) were applied to common bean plants. Water deficits significantly decreased common bean growth, green pods yield, integrity of the membranes, plant water status, SPAD chlorophyll index, and photosynthetic capacity (Fv/Fm, PI), while not improving the irrigation use efficiency (IUE) compared to full irrigation. Foliar-applied GSH markedly lessened drought-induced damages to bean plants, by enhancing the above variables. The integrative I80 + GSH1 or GSH2 and I60 + GSH1 or GSH2 elevated the IUE and exceeded the full irrigation without GSH application (I100) treatment by 38% and 37%, and 33% and 28%, respectively. Drought stress increased proline and total soluble sugars content while decreased the total free amino acids content. However, GSH-supplemented drought-stressed plants mediated further increases in all analyzed osmolytes contents. Exogenous GSH enhanced the common bean antioxidative machinery, being promoted the glutathione and ascorbic acid content as well as up-regulated the activity of superoxide dismutase, catalase, ascorbate peroxidase, and glutathione peroxidase. These findings demonstrate the efficacy of exogenous GSH in alleviating water deficit in bean plants cultivated in salty soil. creator: Taia A. Abd El Mageed creator: Wael Semida creator: Khoulood A. Hemida creator: Mohammed A.H. Gyushi creator: Mostafa M. Rady creator: Abdelsattar Abdelkhalik creator: Othmane Merah creator: Marian Brestic creator: Heba I. Mohamed creator: Ayman El Sabagh creator: Magdi T. Abdelhamid uri: https://doi.org/10.7717/peerj.15343 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Abd El Mageed et al. title: Early pain in females is linked to late pathological features in murine experimental osteoarthritis link: https://peerj.com/articles/15482 last-modified: 2023-06-22 description: BackgroundOsteoarthritis (OA) is a progressive joint disease and a major cause of chronic pain in adults. The prevalence of OA is higher in female patients, who tend to have worse OA outcomes, partially due to pain. The association between joint pain and OA pathology is often inconclusive. Preclinical research studies have largely overlooked sex as a potential determinant in joint pain during OA. This study aimed to investigate the role of sex in joint pain in the collagenase-induced OA (CiOA) model and its link with joint pathology.MethodsMultiple aspects of pain were evaluated during identically executed experiments of CiOA in male and female C57BL/6J mice. Cartilage damage, osteophyte formation, synovial thickness, and cellularity were assessed by histology on day 56. The association between pain and pathology was investigated, disaggregated by sex.ResultsDifferences in pain behavior between sexes were found in the majority of the evaluated pain methods. Females displayed lower weight bearing ability in the affected leg compared to males during the early phase of the disease, however, the pathology at the end stage was comparable between sexes. In the second cohort, males displayed increased mechanical sensitivity in the affected joint compared to females but also showed more cartilage damage at the end stage of the model. Within this cohort, gait analysis showed varied results. Males used the affected paw less often and displayed dynamic weight-bearing compensation in the early phase of the model. These differences were not observed in females. Other evaluated parameters displayed comparable gait behavior between males and females. A detailed analysis of individual mice revealed that seven out of 10 pain measurements highly correlated with OA histopathology in females (Pearson r range: 0.642–0.934), whereas in males this measurement was only two (Pearson r range: 0.645–0.748).ConclusionOur data show that sex is a determinant in the link between pain-related behavior with OA features. Therefore, to accurately interpret pain data it is crucial to segregate data analysis by sex to draw the correct mechanistic conclusion. creator: Natália Valdrighi creator: Arjen B. Blom creator: Henk M. van Beuningen creator: Elly L. Vitters creator: Monique M. Helsen creator: Birgitte Walgreen creator: Peter L.E.M. van Lent creator: Marije I. Koenders creator: Peter M. van der Kraan creator: Fons A.J. van de Loo creator: Esmeralda N. Blaney Davidson uri: https://doi.org/10.7717/peerj.15482 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Valdrighi et al. title: Estimating average wind speed in Thailand using confidence intervals for common mean of several Weibull distributions link: https://peerj.com/articles/15513 last-modified: 2023-06-22 description: The Weibull distribution has been used to analyze data from many fields, including engineering, survival and lifetime analysis, and weather forecasting, particularly wind speed data. It is useful to measure the central tendency of wind speed data in specific locations using statistical parameters for instance the mean to accurately forecast the severity of future catastrophic events. In particular, the common mean of several independent wind speed samples collected from different locations is a useful statistic. To explore wind speed data from several areas in Surat Thani province, a large province in southern Thailand, we constructed estimates of the confidence interval for the common mean of several Weibull distributions using the Bayesian equitailed confidence interval and the highest posterior density interval using the gamma prior. Their performances are compared with those of the generalized confidence interval and the adjusted method of variance estimates recovery based on their coverage probabilities and expected lengths. The results demonstrate that when the common mean is small and the sample size is large, the Bayesian highest posterior density interval performed the best since its coverage probabilities were higher than the nominal confidence level and it provided the shortest expected lengths. Moreover, the generalized confidence interval performed well in some scenarios whereas adjusted method of variance estimates recovery did not. The approaches were used to estimate the common mean of real wind speed datasets from several areas in Surat Thani province, Thailand, fitted to Weibull distributions. These results support the simulation results in that the Bayesian methods performed the best. Hence, the Bayesian highest posterior density interval is the most appropriate method for establishing the confidence interval for the common mean of several Weibull distributions. creator: Manussaya La-ongkaew creator: Sa-Aat Niwitpong creator: Suparat Niwitpong uri: https://doi.org/10.7717/peerj.15513 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 La-ongkaew et al. title: Estimation of genetic variation in yield, its contributing characters and capsaicin content of Capsicum chinense Jacq. (ghost pepper) germplasm from Northeast India link: https://peerj.com/articles/15521 last-modified: 2023-06-22 description: Capsicum chinense Jacq. (ghost pepper), a naturally occurring chili species of Northeast India is known throughout the world for its high pungency and a pleasant aroma. The economic importance is due to the high capsaicinoid levels, the main source for pharmaceutical industries. The present study focused on identifying important traits necessary for increasing the yield and pungency of ghost pepper and to determine the parameters for the selection of superior genotypes. A total of 120 genotypes with more than 1.2% capsaicin content (>1,92,000 Scoville Heat Unit, w/w on dry weight basis) collected from different northeast Indian regions were subjected to variability, divergence and correlation studies. Levene’s homogeneity test of variance studied for three environments did not show significant deviation and so homogeneity of variance was reasonably met for analysis of variance study. Genotypic and phenotypic coefficient of variation was highest for fruit yield per plant (33.702, 36.200, respectively), followed by number of fruits per plant (29.583, 33.014, respectively) and capsaicin content (25.283, 26.362, respectively). The trait number of fruits per plant had maximum direct contribution to fruit yield per plant and the trait fruit yield per plant towards capsaicin content in the correlation study. High heritability with high genetic advance, which is the most favored selection criteria was observed for fruit yield per plant, number of fruits per plant, capsaicin content, fruit length and fruit girth. The genetic divergence study partitioned the genotypes into 20 clusters, where fruit yield per plant contributed maximum towards total divergence. Principal components analysis (PCA) studied to determine the largest contributor of variation showed 73.48% of the total variability, of which the PC1 and PC2 contributed 34.59% and 16.81% respectively. creator: Joyashree Baruah creator: Sunita Munda creator: Neelav Sarma creator: Twahira Begum creator: Sudin Kumar Pandey creator: Sanjoy Kumar Chanda creator: G. Narahari Sastry creator: Mohan Lal uri: https://doi.org/10.7717/peerj.15521 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Baruah et al. title: Comparative analysis of flavonoids, polyphenols and volatiles in roots, stems and leaves of five mangroves link: https://peerj.com/articles/15529 last-modified: 2023-06-22 description: Mangrove plants contain a variety of secondary metabolites, including flavonoids, polyphenols, and volatiles, which are important for their survival and adaptation to the coastal environment, as well as for producing bioactive compounds. To reveal differences in these compounds among five mangrove species’ leaf, root, and stem, the total contents of flavonoids and polyphenols, types and contents of volatiles were determined, analyzed and compared. The results showed that Avicennia marina leaves contained the highest levels of flavonoids and phenolics. In mangrove parts, flavonoids are usually higher than phenolic compounds. A total of 532 compounds were detected by a gas chromatography-mass spectrometry (GC-MS) method in the leaf, root, and stem parts of five mangrove species. These were grouped into 18 classes, including alcohols, aldehydes, alkaloids, alkanes, etc. The number of volatile compounds in A. ilicifolius (176) and B. gymnorrhiza (172) was lower than in the other three species. The number of volatile compounds and their relative contents differed among all three parts of five mangrove species, where the mangrove species factor had a greater impact than the part factor. A total of 71 common compounds occurring in more than two species or parts were analyzed by a PLS-DA model. One-way ANOVA revealed 18 differential compounds among mangrove species and nine differential compounds among parts. Principal component analysis and hierarchical clustering analysis showed that both unique and common compounds significantly differed in composition and concentration between species and parts. In general, A. ilicifolius and B. gymnorrhiza differed significantly from the other species in terms of compound content, while the leaves differed significantly from the other parts. VIP screening and pathway enrichment analysis were performed on 17 common compounds closely related to mangrove species or parts. These compounds were mainly involved in terpenoid pathways such as C10 isoprenoids and C15 isoprenoids and fatty alcohols. The correlation analysis showed that the content of flavonoids/phenolics, the number of compounds, and the content of some common compounds in mangroves were correlated with their salt and waterlogging tolerance levels. These findings will help in the development of genetic varieties and medicinal utilization of mangrove plants. creator: Zhihua Wu creator: Xiuhua Shang creator: Guo Liu creator: Yaojian Xie uri: https://doi.org/10.7717/peerj.15529 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Wu et al. title: Silencing of TRAF5 enhances necroptosis in hepatocellular carcinoma by inhibiting LTBR-mediated NF-κB signaling link: https://peerj.com/articles/15551 last-modified: 2023-06-22 description: BackgroundHepatocellular carcinoma (HCC) is a common malignancy with poor prognosis and high mortality. This study aimed to explore the oncogenic mechanisms of TRAF5 in HCC and provide a novel therapeutic strategy for HCC.MethodsHuman HCC cell lines (HepG2, HuH7, SMMC-LM3, and Hep3B), normal adult liver epithelial cells (THLE-2), and human embryonic kidney cells (HEK293T) were utilized. Cell transfection was performed for functional investigation. qRT-PCR and western blotting were used to detect mRNA expression of TRAF5, LTBR, and NF-κB and protein expression of TRAF5, p-RIP1(S166)/RIP1, p-MLKL(S345)/MLKL, LTBR, and p-NF-κB/NF-κB. Cell viability, proliferation, migration, and invasion were evaluated using CCK-8, colony formation, wound healing, and Transwell assays. Cell survival, necrosis, and apoptosis were assessed using flow cytometry and Hoechst 33342/PI double staining. Co-immunoprecipitation and immunofluorescence were performed to determine the interaction between TRAF5 and LTBR. A xenograft model was established to validate the role of TRAF5 in HCC.ResultsTRAF5 knockdown inhibited HCC cell viability, colony formation, migration, invasion, and survival but enhanced necroptosis. Additionally, TRAF5 is correlated with LTBR and TRAF5 silencing down-regulated LTBR in HCC cells. LTBR knockdown inhibited HCC cell viability, while LTBR overexpression eliminated the effects of TRAF5 deficiency on inhibiting HCC cell proliferation, migration, invasion, and survival. LTBR overexpression abolished the promotive function of TRAF5 knockdown on cell necroptosis. LTBR overexpression undid the suppressive effect of TRAF5 knockdown on NF-κB signaling in HCC cells. Moreover, TRAF5 knockdown suppressed xenograft tumor growth, inhibited cell proliferation, and promoted tumor cell apoptosis.ConclusionsTRAF5 deficiency facilitates necroptosis in HCC by suppressing LTBR-mediated NF-κB signaling. creator: Guolin Wu creator: Fangping Wu creator: Yang Qing Zhou creator: Wenwen Lu creator: Feng Lin Hu creator: Xiaofen Fan uri: https://doi.org/10.7717/peerj.15551 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Wu et al. title: Comparison of the clinical value of MRI and plasma markers for cognitive impairment in patients aged ≥75 years: a retrospective study link: https://peerj.com/articles/15581 last-modified: 2023-06-22 description: BackgroundDementia has become the main cause of disability in older adults aged ≥75 years. Cerebral small vessel disease (CSVD) is involved in cognitive impairment (CI) and dementia and is a cause of vascular CI (VCI), which is manageable and its onset and progression can be delayed. Simple and effective markers will be beneficial to the early detection and intervention of CI. The aim of this study is to investigate the clinical application value of plasma amyloid β1-42 (Aβ42), phosphorylated tau 181 (p-tau181) and conventional structural magnetic resonance imaging (MRI) parameters for cognitive impairment (CI) in patients aged ≥75 years.MethodsWe retrospectively selected patients who visited the Affiliated Hospital of Xuzhou Medical University and were clinically diagnosed with or without cognitive dysfunction between May 2018 and November 2021. Plasma indicators (Aβ42 and p-tau181) and conventional structural MRI parameters were collected and analyzed. Multivariate logistic regression and receiver operator characteristic (ROC) curve were used to evaluate the diagnostic value.ResultsOne hundred and eighty-four subjects were included, including 54 cases in CI group and 130 cases in noncognitive impairment (NCI) groups, respectively. Univariate logistic regression analysis revealed that the percentages of Aβ42+, P-tau 181+, and Aβ42+/P-tau181+ showed no significant difference between the groups of CI and NCI (all P > 0.05). Multivariate logistic regression analysis showed that moderate/severe periventricular WMH (PVWMH) (OR 2.857, (1.365–5.983), P = 0.005), lateral ventricle body index (LVBI) (OR 0.413, (0.243–0.700), P = 0.001), and cortical atrophy (OR 1.304, (1.079−1.575), P = 0.006) were factors associated with CI. The combined model including PVWMH, LVBI, and cortical atrophy to detect CI and NCI showed an area under the ROC curve (AUROC) is 0.782, with the sensitivity and specificity 68.5% and 78.5%, respectively.ConclusionFor individuals ≥75 years, plasma Aβ42 and P-tau181 might not be associated with cognitive impairment, and MRI parameters, including PVWMH, LVBI and cortical atrophy, are related to CI. The cognitive statuses of people over 75 years old were used as the endpoint event in this study. Therefore, it can be considered that these MRI markers might have more important clinical significance for early assessment and dynamic observation, but more studies are still needed to verify this hypothesis. creator: Wei Wang creator: Lin Shi creator: Hong Ma creator: Shiguang Zhu creator: Yaqiong Ge creator: Kai Xu uri: https://doi.org/10.7717/peerj.15581 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Wang et al. title: Investigating the sequence landscape in the Drosophila initiator core promoter element using an enhanced MARZ algorithm link: https://peerj.com/articles/15597 last-modified: 2023-06-22 description: The core promoter elements are important DNA sequences for the regulation of RNA polymerase II transcription in eukaryotic cells. Despite the broad evolutionary conservation of these elements, there is extensive variation in the nucleotide composition of the actual sequences. In this study, we aim to improve our understanding of the complexity of this sequence variation in the TATA box and initiator core promoter elements in Drosophila melanogaster. Using computational approaches, including an enhanced version of our previously developed MARZ algorithm that utilizes gapped nucleotide matrices, several sequence landscape features are uncovered, including an interdependency between the nucleotides in position 2 and 5 in the initiator. Incorporating this information in an expanded MARZ algorithm improves predictive performance for the identification of the initiator element. Overall our results demonstrate the need to carefully consider detailed sequence composition features in core promoter elements in order to make more robust and accurate bioinformatic predictions. creator: Jacqueline M. Dresch creator: Regan D. Conrad creator: Daniel Klonaros creator: Robert A. Drewell uri: https://doi.org/10.7717/peerj.15597 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Dresch et al. title: Concordance of microbial and visual health indicators of white-band disease in nursery reared Caribbean coral Acropora cervicornis link: https://peerj.com/articles/15170 last-modified: 2023-06-21 description: BackgroundCoral diseases are one of the leading causes of declines in coral populations. In the Caribbean, white band disease (WBD) has led to a substantial loss of Acropora corals. Although the etiologies of this disease have not been well described, characterizing the coral microbiome during the transition from a healthy to diseased state is critical for understanding disease progression. Coral nurseries provide unique opportunities to further understand the microbial changes associated with diseased and healthy corals, because corals are monitored over time. We characterized the microbiomes before and during an outbreak of WBD in Acropora cervicornis reared in an ocean nursery in Little Cayman, CI. We asked (1) do healthy corals show the same microbiome over time (before and during a disease outbreak) and (2) are there disease signatures on both lesioned and apparently healthy tissues on diseased coral colonies?MethodsMicrobial mucus-tissue slurries were collected from healthy coral colonies in 2017 (before the disease) and 2019 (during the disease onset). Diseased colonies were sampled at two separate locations on an individual coral colony: at the interface of Disease and ∼10 cm away on Apparently Healthy coral tissue. We sequenced the V4 region of the 16S rRNA gene to characterize bacterial and archaeal community composition in nursery-reared A. cervicornis. We assessed alpha diversity, beta diversity, and compositional differences to determine differences in microbial assemblages across health states (2019) and healthy corals between years (2017 and 2019).ResultsMicrobial communities from healthy A. cervicornis from 2017 (before disease) and 2019 (after disease) did not differ significantly. Additionally, microbial communities from Apparently Healthy samples on an otherwise diseased coral colony were more similar to Healthy colonies than to the diseased portion on the same colony for both alpha diversity and community composition. Microbial communities from Diseased tissues had significantly higher alpha diversity than both Healthy and Apparently Healthy tissues but showed no significant difference in beta-diversity dispersion. Our results show that at the population scale, Healthy and Apparently Healthy coral tissues are distinct from microbial communities associated with Diseased tissues. Furthermore, our results suggest stability in Little Cayman nursery coral microbiomes over time. We show healthy Caymanian nursery corals had a stable microbiome over a two-year period, an important benchmark for evaluating coral health via their microbiome. creator: Monica D. Schul creator: Dagny-Elise Anastasious creator: Lindsay J. Spiers creator: Julie L. Meyer creator: Thomas K. Frazer creator: Anya L. Brown uri: https://doi.org/10.7717/peerj.15170 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Schul et al. title: Microbial community in buckwheat rhizosphere with different nitrogen application rates link: https://peerj.com/articles/15514 last-modified: 2023-06-21 description: Microorganism plays a pivotal role in regulating sustainable development of agriculture. The excessive application of nitrogen fertilizer is considered to affect the microbial structure in many agricultural systems. The present study aimed to assess the impacts of nitrogen application rate on microbial diversity, community and functionality in rhizosphere of Tartary buckwheat in short-time. The nitrogen fertilizer was applied at rates of 90 kg (N90), 120 kg (N120) and 150 kg (N150) urea per hectare, respectively. The soil properties were measured chemical analysis and displayed no difference among treatments. Metagenome analysis results showed that the microbial diversity was not affected, but the microbial community and functionality were affected by the nitrogen application rate. According to the Linear discriminant analysis effect size (LEfSe) analysis, 15 taxa were significantly enriched in the N120 and N150 groups, no taxon was enriched in the N90 group. Kyoto Encyclopaedia of Genes and Genomes (KEGG) annotation results revealed that the genes related to butanoate and beta alanine metabolism were significantly enriched in the N90 group, the genes related to thiamine metabolism, lipopolysaccharide biosynthesis and biofilm formation were significantly enriched in the N120 group, and the genes related to neurodegenerative disease was significantly enriched in the N150 group. In conclusion, short-time nitrogen fertilizer application shifted the microbial community structure and functionality. creator: Dongsheng Wang creator: Haike Ren uri: https://doi.org/10.7717/peerj.15514 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Wang et al.