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: Identification of iron metabolism-related genes as prognostic indicators for papillary thyroid carcinoma: a retrospective study link: https://peerj.com/articles/15592 last-modified: 2023-06-21 description: BackgroundThe thyroid cancer subtype that occurs more frequently is papillary thyroid carcinoma (PTC). Despite a good surgical outcome, treatment with traditional antitumor therapy does not offer ideal results for patients with radioiodine resistance, recurrence, and metastasis. The evidence for the connection between iron metabolism imbalance and cancer development and oncogenesis is growing. Nevertheless, the iron metabolism impact on PTC prognosis is still indefinite.MethodsHerein, we acquired the medical data and gene expression of individuals with PTC from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) database. Typically, three predictive iron metabolism-related genes (IMRGs) were examined and employed to build a risk score (RS) model via the least absolute shrinkage and selection operator (LASSO) regression, univariate Cox, and differential gene expression analyses. Then we analyzed somatic mutation and immune cell infiltration among RS groups. We also validated the prognostic value of two IMRGs (SFXN3 and TFR2) by verifying their biological function through in vitro experiments.ResultsBased on RS, all patients with PTC were stratified into low- and high-risk groups, where Kaplan-Meier analysis indicated that disease-free survival (DFS) in the high-risk group was much lower than in the low-risk group (P < 0.0001). According to ROC analysis, the RS model successfully predicted the 1-, 3-, and 5-year DFS of individuals with PTC. Additionally, in the TCGA cohort, a nomogram model with RS was developed and exhibited a strong capability to anticipate PTC patients’ DFS. In the high-risk group, the enriched pathological processes and signaling mechanisms were detected utilizing the gene set enrichment analysis (GSEA). Moreover, the high-risk group had a significantly higher level of BRAF mutation frequency, tumor mutation burden, and immune cell infiltration than the low-risk group. In vitro experiments found that silencing SFXN3 or TFR2 significantly reduced cell viability.ConclusionCollectively, our predictive model depended on IMRGs in PTC, which could be potentially utilized to predict the PTC patients’ prognosis, schedule follow-up plans, and provide potential targets against PTC. creator: Tiefeng Jin creator: Luqi Ge creator: Jianqiang Chen creator: Wei Wang creator: Lizhuo Zhang creator: Minghua Ge uri: https://doi.org/10.7717/peerj.15592 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Jin et al. title: Genotypic characteristics of Uropathogenic Escherichia coli isolated from complicated urinary tract infection (cUTI) and asymptomatic bacteriuria—a relational analysis link: https://peerj.com/articles/15305 last-modified: 2023-06-20 description: BackgroundUropathogenic Escherichia coli (UPEC) is the predominant agent causing various categories of complicated urinary tract infections (cUTI). Although existing data reveals that UPEC harboured numerous virulence determinants to aid its survival in the urinary tract, the reason behind the occurrence of differences in the clinical severity of uninary tract infections (UTI) demonstrated by the UPEC infection is poorly understood. Therefore, the present study aims to determine the distribution of virulence determinants and antimicrobial resistance among different phylogroups of UPEC isolated from various clinical categories of cUTI and asymptomatic bacteriuria (ASB) E. coli isolates. The study will also attempt a relational analysis of the genotypic characteristics of cUTI UPEC and ASB E. coli isolates.MethodsA total of 141 UPEC isolates from cUTI and 160 ASB E. coli isolates were obtained from Universiti Malaya Medical Centre (UMMC). Phylogrouping and the occurrence of virulence genes were investigated using polymerase chain reaction (PCR). Antimicrobial susceptibility of the isolates to different classes of antibiotics was determined using the Kirby Bauer Disc Diffusion method.ResultsThe cUTI isolates were distributed differentially among both Extraintestinal Pathogenic E. coli (ExPEC) and non-ExPEC phylogroups. Phylogroup B2 isolates were observed to possess the highest average aggregative virulence score (7.17), a probable representation of the capability to cause severe disease. Approximately 50% of the cUTI isolates tested in this study were multidrug resistant against common antibiotics used to treat UTI. Analysis of the occurrence of virulence genes among different cUTI categories demonstrated that UPEC isolates of pyelonephritis and urosepsis were highly virulent and had the highest average aggregative virulence scores of 7.80 and 6.89 respectively, compared to other clinical categories. Relational analysis of the occurrence of phylogroups and virulence determinants of UPEC and ASB E. coli isolates showed that 46.1% of UPEC and 34.3% of ASB E. coli from both categories were distributed in phylogroup B2 and had the highest average aggregative virulence score of 7.17 and 5.37, respectively. The data suggest that UPEC isolates which carry virulence genes from all four virulence genes groups studied (adhesions, iron uptake systems, toxins and capsule synthesis) and isolates from phylogroup B2 specifically could predispose to severe UTI involving the upper urinary tract. Therefore, specific analysis of the genotypic characteristics of UPEC could be further explored by incorporating the combination of virulence genes as a prognostic marker for predicting disease severity, in an attempt to propose a more evidence driven treatment decision-making for all UTI patients. This will go a long way in enhancing favourable therapeutic outcomes and reducing the antimicrobial resistance burden among UTI patients. creator: Lalitha Maniam creator: Kumutha Malar Vellasamy creator: Teng Aik Ong creator: Cindy Shuan Ju Teh creator: Kartini Abdul Jabar creator: Vanitha Mariappan creator: Vallikkannu Narayanan creator: Jamuna Vadivelu creator: Vinod Pallath uri: https://doi.org/10.7717/peerj.15305 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Maniam et al. title: Spatial and temporal population genetic analysis of Semaprochilodus insignis (Prochilodontidae), an overexploited fish from the Amazon basin link: https://peerj.com/articles/15503 last-modified: 2023-06-20 description: BackgroundSemaprochilodus insignis is a migratory fish of commercial and subsistence importance to communities in the Amazon. Despite the high intensity of exploitation, recent studies have not been carried out to assess the genetic status of its stocks.MethodsThis study is the first to estimate genetic diversity and to test the existence of spatial and temporal structuring of S. insignis through sequencing of the mtDNA control region (n = 241) and eight microsatellite loci (n = 180) of individuals sampled at 11 sites distributed in the Brazilian Amazon basin.ResultsResults for both markers were congruent, revealing a homogeneous genetic diversity in all the sampled locations, in addition to the absence of spatial and temporal genetic structure, indicating that the species forms a large panmictic population in the Brazilian Amazon.DiscussionAlthough overfishing does not yet appear to have affected the levels of genetic variability of S. insignis, signals of reduction of the effective population size and a bottleneck provide an early alert to the effects of overfishing. Thus, the ever-decreasing populations may threaten S. insignis in the future. Therefore, it is hoped that the results of this study may contribute to the elaboration of management plans or any other measures that aim at the management and conservation of this species of great importance for the Amazon basin. creator: Ingrid Nunes creator: Kelmer Passos creator: Aline Mourão Ximenes creator: Tomas Hrbek creator: Izeni Pires Farias uri: https://doi.org/10.7717/peerj.15503 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Nunes et al. title: The reliability and validity of repeat power ability assessments and measurement indices in loaded vertical jumps link: https://peerj.com/articles/15553 last-modified: 2023-06-20 description: BackgroundRepeat power ability (RPA) assessments are a valuable evaluation of an athlete’s ability to repeatedly perform high intensity movements. Establishing the most reliable and valid loaded jump RPA assessment and method to quantify RPA has yet to be determined. This study aimed to compare the reliability and validity of an RPA assessment performed with loaded squat jumps (SJ) or countermovement jumps (CMJ) using force-time derived mean and peak power output.Materials and MethodsRPA was quantified using calculations of average power output, a fatigue index and a percent decrement score for all repetitions and with the first and last repetitions removed. Validity was established by comparing to a 30 second Bosco repeated jump test (30BJT). Eleven well-trained male field hockey players performed one set of 20 repetitions of both SJs (20SJ) and CMJs (20CMJ) on separate occasions using a 30% one repetition maximum half squat load. These assessments were repeated 7 days apart to establish inter-test reliability. On a separate occasion, each participant performed the 30BJT.ResultsThe reliability of average peak power for 20SJ and 20CMJ was acceptable (CV < 5%; ICC > 0.9), while average mean power reliability for 20CMJ (CV < 5%; ICC > 0.9) was better than 20SJ (CV > 5%; ICC > 0.8). Percent decrement of 20CMJ peak power, with the first and final jump removed from the percent decrement calculation (PD%CMJpeak18), was the most reliable measurement of power output decline (CV < 5 %; ICC > 0.8). Average mean and peak power for both RPA protocols had moderate to strong correlations with 30BJT average mean and peak power (r = 0.5–0.8; p< 0.05–0.01). No RPA measurements of power decline were significantly related to BJT measurements of power decline.ConclusionsThese findings indicate that PD%CMJpeak18 is the most reliable measure of RPA power decline. The lack of relationship between power decline in the loaded RPA and the 30BJT assessment suggest that each assessment may be measuring a different physical quality. These results provide sport science practitioners with additional methods to assess RPA and provide useful information on the reliability and validity of these outcome measures. Additional research needs to be performed to examine the reliability and validity of the novel RPA assessments in other athletic populations and to determine the sensitivity of these measurements to training and injury. creator: Alex O. Natera creator: Dale W. Chapman creator: Neil D. Chapman creator: Justin W.L. Keogh uri: https://doi.org/10.7717/peerj.15553 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Natera et al. title: Exploring the molecular basis of resistance to Botrytis cinerea in chickpea genotypes through biochemical and morphological markers link: https://peerj.com/articles/15560 last-modified: 2023-06-20 description: Chickpea (Cicer arietinum L.) is an important pulse crop around the globe and a valuable source of protein in the human diet. However, it is highly susceptible to various plant pathogens such as fungi, bacteria, and viruses, which can cause significant damage from the seedling phase until harvest, leading to reduced yields and affecting its production. Botrytis cinerea can cause significant damage to chickpea crops, especially under high humidity and moisture conditions. This fungus can cause grey mould disease, which can lead to wilting, stem and pod rot, and reduced yields. Chickpea plants have developed specific barriers to counteract the harmful effects of this fungus. These barriers include biochemical and structural defences. In this study, the defence responses against B. cinerea were measured by the quantification of biochemical metabolites such as antioxidant enzymes, malondialdehyde (MDA), proline, glutathione (GSH), H2O2, ascorbic acid (AA) and total phenol in the leaf samples of chickpea genotypes (one accession of wild Cicer species, viz. Cicer pinnatifidum188 identified with high level of resistance to Botrytis grey mould (BGM) and a cultivar, Cicer arietinumPBG5 susceptible to BGM grown in the greenhouse). Seedlings of both the genotypes were inoculated with (1 × 104 spore mL−1) inoculum of isolate 24, race 510 of B. cinerea and samples were collected after 1, 3, 5, and 7 days post-inoculation (dpi). The enhanced enzymatic activity was observed in the pathogen-inoculated leaf samples as compared to uninoculated (healthy control). Among inoculated genotypes, the resistant one exhibited a significant change in enzymatic activity, total phenolic content, MDA, proline, GSH, H2O2, and AA, compared to the susceptible genotype. The study also examined the isozyme pattern of antioxidant enzymes at various stages of B. cinerea inoculation. Results from scanning electron microscopy (SEM) and Fourier transform infrared (FTIR) spectroscopy revealed that BGM had a more significant impact on susceptible genotypes compared to resistant ones when compared to the control (un-inoculated). In addition, SEM and FTIR spectroscopy analyses confirmed the greater severity of BGM on susceptible genotypes compared to their resistant counterparts. Our results suggest the role of antioxidant enzymes and other metabolites as defence tools and biochemical markers to understand compatible and non-compatible plant-pathogen interactions better. The present investigation will assist future plant breeding programs aimed at developing resistant varieties. creator: Richa Thakur creator: Sucheta Sharma creator: Rajni Devi creator: Asmita Sirari creator: Rahul Kumar Tiwari creator: Milan Kumar Lal creator: Ravinder Kumar uri: https://doi.org/10.7717/peerj.15560 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Thakur et al. title: Revisiting the evolutionary trend toward the mammalian lower jaw in non-mammalian synapsids in a phylogenetic context link: https://peerj.com/articles/15575 last-modified: 2023-06-20 description: The mammalian lower jaw comprises a single bone, the dentary, which is a unique feature among vertebrates. The lower jaws of extinct non-mammalian synapsids were composed of the dentary and several postdentary bones. Synapsid fossils exhibit variation in the dentary size relative to the overall lower jaw. An evolutionary trend toward dentary enlargement and postdentary reduction in non-mammalian synapsids has long been documented but has not been established using modern phylogenetic comparative methods. In this study, we examine the evolutionary pattern of dentary size relative to the lower jaw through phylogenetic analyses of measurements in a broad range of non-mammalian synapsid taxa. Our analyses revealed an evolutionary trend toward dentary area enlargement relative to the overall lower jaw in the lateral view across all non-mammalian synapsids. This trend is likely due to vertical expansion of the dentary given that the same trend is not evident when looking at anterior to posterior measurements of the dentary relative to the lower jaw as a whole in lateral view. Ancestral character reconstructions revealed that the evolution of the measurements was not unidirectional in non-mammalian synapsids. Our results provide no evidence of an evolutionary trend toward the dentary enlargement at the expense of postdentary bones across non-mammalian synapsids. This implies that the evolutionary origin of the mammalian lower jaw is not adequately explained by the evolutionary trend of dentary enlargement throughout non-mammalian synapsids. Instead, selection that occurred during the transition from non-mammalian cynodonts to early mammals may have produced the mammalian lower jaw. creator: Tomohiro Harano creator: Masakazu Asahara uri: https://doi.org/10.7717/peerj.15575 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Harano and Asahara title: Self-reported depression and anxiety rates among females with cutaneous leishmaniasis in Hubuna, Saudi Arabia link: https://peerj.com/articles/15582 last-modified: 2023-06-20 description: BackgroundCutaneous leishmaniasis (CL) is a parasitic disease transmitted through the bite of infected sandflies, causing disfiguring skin lesions and a range of physical symptoms. However, the psychological impact of CL is often overlooked despite the significant burden it imposes on the affected individuals and communities. This is especially true in Saudi Arabia, where limited research exists on the psychological consequences of CL, particularly among females. This study aimed to address this knowledge gap by investigating the perceived psychological problems associated with CL among females living in the Hubuna area of Saudi Arabia.MethodsThis cross-sectional study recruited 213 females with CL in the Hubuna area of Saudi Arabia using purposive sampling. Data was collected using a self-administered electronic questionnaire that included socio-demographic characteristics and measures of depression and anxiety using the BDI and GAD-7 tools. Descriptive analysis was used to determine the psychological impact of CL, including means and standard deviations for the BDI and GAD-7 scores, as well as frequencies and percentages for other variables of interest. Logistic regression was performed to identify independent predictors of anxiety and depression, including variables such as age, marital status, education, occupation, number and location of lesions. The significance level for all statistical tests was set at p < 0.05. The study was carried out between September and December of 2022.ResultsThe study found that the mean Beck Depression Inventory (BDI) and Generalized Anxiety Disorder-7 (GAD-7) scores among the participants were 8.67 ± 4.82 out of 63 and 8.20 ± 7.08 out of 21, respectively. Furthermore, the prevalence of depression and anxiety was 55.9% and 68.1%, respectively, indicating a significant psychological burden associated with CL in the study population. The results of the logistic regression analysis showed that anxiety and depression were significantly associated with age, marital status, number of lesions, and location of the lesions on the body, highlighting the importance of considering these factors when designing interventions aimed at improving the mental health of CL patients.ConclusionsIn conclusion, this study highlights the significant psychological impact of CL among females in the Hubuna area of Saudi Arabia, calling for urgent action to address this neglected aspect of the disease. By integrating mental health considerations into CL prevention and management efforts, healthcare providers can improve the overall well-being of affected individuals and contribute to the broader goal of eliminating CL as a public health concern. creator: Nahid Elfaki creator: Mohammed Alzahrani creator: Yahya Hussein Ahmed Abdalla creator: Mugahed Ali Alkhadher creator: Abdalla MohamedAhmed Osman creator: Wargaa Taha creator: Wael Alghamdi creator: Faroq Abdulghani Alshameri creator: Waled A. M. Ahmed uri: https://doi.org/10.7717/peerj.15582 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Elfaki et al. title: The cytotoxicity effect of 7-hydroxy-3,4-dihydrocadalene from Heterotheca inuloides and semisynthetic cadalenes derivates towards breast cancer cells: involvement of oxidative stress-mediated apoptosis link: https://peerj.com/articles/15586 last-modified: 2023-06-20 description: BackgroundHeterotheca inuloides, traditionally employed in Mexico, has demonstrated anticancer activities. Although it has been proven that the cytotoxic effect is attributed to cadinane-type sesquiterpenes such as 7-hydroxy-3,4-dihydrocadalene, the mechanism of action by which these agents act in tumor lines and their regulation remain unknown. This study was undertaken to investigate for first time the cytotoxic activity and mechanism of action of 7-hydroxy-3,4-dihydrocadalene and two semi-synthetic cadinanes derivatives towards breast cancer cells.MethodsCell viability and proliferation were assayed by thiazolyl blue tetrazolium bromide (MTT) assay and Trypan blue dye exclusion assay. Cell migration measure was tested by wound-healing assay. Moreover, the reactive oxygen species (ROS) and lipid peroxidation generation were measured by 2′,7′-dichlorofluorescein diacetate (DCFH-DA) assay and thiobarbituric acid reactive substance (TBARS) assay, respectively. Furthermore, expression of caspase-3, Bcl-2 and GAPDH were analyzed by western blot.ResultsThe results showed that 7-hydroxy-3,4-dihydrocadalene inhibited MCF7 cell viability in a concentration and time dependent manner. The cytotoxic potency of semisynthetic derivatives 7-(phenylcarbamate)-3,4-dihydrocadalene and 7-(phenylcarbamate)-cadalene was remarkably lower. Moreover, in silico studies showed that 7-hydroxy-3,4-dihydrocadalene, and not so the semi-synthetic derivatives, has optimal physical-chemical properties to lead a promising cytotoxic agent. Further examination on the action mechanism of 7-hydroxy-3,4-dihydrocadalene suggested that this natural product exerted cytotoxicity via oxidative stress as evidenced in a significantly increase of intracellular ROS levels and in an induction of lipid peroxidation. Furthermore, the compound increased caspase-3 and caspase-9 activities and slightly inhibited Bcl-2 levels. Interestingly, it also reduced mitochondrial ATP synthesis and induced mitochondrial uncoupling.ConclusionTaken together, 7-hydroxy-3,4-dihydrocadalene is a promising cytotoxic compound against breast cancer via oxidative stress-induction. creator: Alan Mendoza-Fuentes creator: Elena González-Burgos creator: Omar Emiliano Aparicio Trejo creator: Guillermo Delgado-Lamas creator: José Luis Rodríguez-Chávez creator: José Pedraza-Chaverri creator: M. Pilar Gómez-Serranillos creator: Daniela Araiza-Olivera uri: https://doi.org/10.7717/peerj.15586 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Mendoza-Fuentes et al. title: C/EBPα involvement in microglial polarization via HDAC1/STAT3 pathway aggravated sevoflurane-induced cognitive impairment in aged rats link: https://peerj.com/articles/15466 last-modified: 2023-06-19 description: BackgroundPostoperative cognitive dysfunction (POCD) is a clinically frequent postoperative complication in the elderly, which is mainly manifested by the occurrence of cognitive dysfunction after anesthetized surgery in patients. To explore the involvement of C/EBPα in microglial polarization in sevoflurane anesthesia induced cognitive impairment in aged rats.MethodsSprague-Dawley (SD) rats were anesthetized by inhalation of 3% sevoflurane for 6 h to establish the POCD model. The histopathological structure of hippocampus was observed by hematoxylin and eosin (HE) staining. Associative learning and memory function and spatial learning and memory function were assessed by conditioned fear test and water maze test. The concentrations of inflammatory factors in the hippocampus were measured by ELISA. The levels of microglial activation marker (Iba1) and microglial M1 (CD86) and M2 (CD206) polarization markers were determined by immunofluorescence staining and RT-qPCR, respectively. The transcriptional regulation of HDAC1 by C/EBPα was confirmed by dual luciferase reporter assay and ChIP assay.ResultsSevoflurane-induced pathomorphological damage in the hippocampal tissue of aged rats, accompanied by elevated expression of C/EBPα. Silencing of C/EBPα alleviated hippocampal histopathological injury, inhibited M1 microglial activation and the expression of M1 marker CD86, enhanced the expression of M2 marker CD206. C/EBPα transcriptionally activated HDAC1. Knockdown of C/EBPα downregulated the expression of HDAC1 and STAT3 phosphorylated proteins, which inhibited the pro-inflammatory factors (IL-6 and TNF-α) and accelerated anti-inflammatory factors (IL-10 and TGF-β) secretion. In addition, silencing of C/EBPα caused rats to have a delayed freezing time in contextual conditioned fear, a shorter escape latency, and an increased number of platform crossings.ConclusionInhibition of C/EBPα promotes the M2 polarization of microglia and reduces the production of pro-inflammatory cytokines to alleviate the cognitive dysfunction of sevoflurane-induced elderly rats by HDAC1/STAT3 pathway. creator: Zhao Xu creator: Xi Yao creator: Yikang Zhao creator: Bo Yao uri: https://doi.org/10.7717/peerj.15466 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Xu et al. title: Phylogenetic diversity and the structure of host-epiphyte interactions across the Neotropics link: https://peerj.com/articles/15500 last-modified: 2023-06-19 description: Understanding the mechanisms driving community assembly has been a major focus of ecological research for nearly a century, yet little is known about these mechanisms in commensal communities, particularly with respect to their historical/evolutionary components. Here, we use a large-scale dataset of 4,440 vascular plant species to explore the relationship between the evolutionary distinctiveness (ED) (as measured by the ’species evolutionary history’ (SEH)) of host species and the phylogenetic diversity (PD) of their associated epiphyte species. Although there was considerable variation across hosts and their associated epiphyte species, they were largely unrelated to host SEH. Our results mostly support the idea that the determinants of epiphyte colonization success might involve host characteristics that are unrelated to host SEH (e.g., architectural differences between hosts). While determinants of PD of epiphyte assemblages are poorly known, they do not appear to be related to the evolutionary history of host species. Instead, they might be better explained by neutral processes of colonization and extinction. However, the high level of phylogenetic signal in epiphyte PD (independent of SEH) suggests it might still be influenced by yet unrecognized evolutionary determinants. This study highlights how little is still known about the phylogenetic determinants of epiphyte communities. creator: Marcio R. Pie creator: Fernanda S. Caron creator: Thom Dallimore creator: Helena Einzmann creator: Peter Hietz creator: Michael Kessler creator: Flavio Nunes Ramos creator: João Pedro Costa Elias creator: Holger Kreft creator: Thorsten Krömer creator: Maria Judith Carmona Higuita creator: Daniel Zuleta creator: Giesta Machado creator: André Luís de Gasper creator: Gerhard Zotz creator: Glenda Mendieta Leiva creator: Derio Antonio Jimenez-Lopez creator: Alex Fernando Mendes creator: Pedro Brancalion creator: Sara Mortara creator: Christopher Thomas Blum creator: Mariana Victória Irume creator: Nayely Martínez-Meléndez Nayely creator: Ana Maria Benavides creator: Carlos Renato Boelter creator: Sven Batke uri: https://doi.org/10.7717/peerj.15500 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Pie et al.